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Entry version 124 (07 Oct 2020)
Sequence version 3 (28 Feb 2018)
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Protein

Gag-Pro-Pol polyprotein

Gene

pol

Organism
Squirrel monkey retrovirus (SMRV-H) (SMRV-HLB)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Matrix protein.By similarity
Capsid protein.By similarity
Matrix protein p10: Matrix protein.By similarity
Nucleocapsid protein p14: Nucleocapsid protein.By similarity
Capsid protein p27: capsid protein.By similarity
The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.PROSITE-ProRule annotationBy similarity
The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.PROSITE-ProRule annotationBy similarity
Enhances the activity of the reverse transcriptase. May be part of the mature RT.By similarity
RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perfom a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends.PROSITE-ProRule annotation
Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.1 Publication

Miscellaneous

The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template swiching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs.PROSITE-ProRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei868Protease; shared with dimeric partnerPROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi1109Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1184Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1185Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1464Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1493Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1514Magnesium; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1578MagnesiumPROSITE-ProRule annotation1
Metal bindingi1654Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1711Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1747Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri1589 – 1630Integrase-typePROSITE-ProRule annotationAdd BLAST42
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi1809 – 1858Integrase-typePROSITE-ProRule annotationAdd BLAST50

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAspartyl protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein
Biological processDNA integration, DNA recombination, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Gag-Pro-Pol polyprotein
Cleaved into the following 9 chains:
Alternative name(s):
Capsid protein p34
Probable nucleocapsid protein-dUTPase (EC:3.6.1.23By similarity)
Short name:
NC-dUTPase
Protease 17 kDaBy similarity (EC:3.4.23.-PROSITE-ProRule annotation)
Protease 13 kDaBy similarity (EC:3.4.23.-PROSITE-ProRule annotation)
G-patch peptideBy similarity
Reverse transcriptase/ribonuclease H (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
RT
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:pol
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSquirrel monkey retrovirus (SMRV-H) (SMRV-HLB)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri11856 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesRiboviriaPararnaviraeArtverviricotaRevtraviricetesOrterviralesRetroviridaeOrthoretrovirinaeBetaretrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiMammalia [TaxID: 40674]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000007223 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Viral matrix protein, Virion

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved; by hostSequence analysis
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001254962 – 1880Gag-Pro-Pol polyproteinAdd BLAST1879
ChainiPRO_00004431482 – 163Matrix protein p19Add BLAST162
ChainiPRO_0000443149164 – 318Core protein p16Add BLAST155
ChainiPRO_0000443150319 – 585Capsid protein p35Add BLAST267
ChainiPRO_0000443151586 – 842Probable nucleocapsid protein-dUTPaseAdd BLAST257
ChainiPRO_0000443152843 – 996Protease 17 kDaAdd BLAST154
ChainiPRO_0000443153843 – 960Protease 13 kDaAdd BLAST118
<p>This subsection of the 'PTM / Processing' section describes the position and length of an active peptide in the mature protein.<p><a href='/help/peptide' target='_top'>More...</a></p>PeptideiPRO_0000443154961 – 997G-patch peptideAdd BLAST37
ChainiPRO_0000443155998 – ?1589Reverse transcriptase/ribonuclease HAdd BLAST592
ChainiPRO_0000443156?1590 – 1880IntegraseAdd BLAST291

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position(s) and the type of covalently attached lipid group(s).<p><a href='/help/lipid' target='_top'>More...</a></p>Lipidationi2N-myristoyl glycine; by hostSequence analysis1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Myristoylated. Myristoylation of the matrix (MA) domain mediates the transport and binding of Gag polyproteins to the host plasma membrane and is required for the assembly of viral particles.By similarity
Specific enzymatic cleavages in vivo yield mature proteins.1 Publication
Released by autocatalytic processing. The protease can undergo further autoprocessing to yield 2 shorter but enzymatically active forms of 12 kDa and 13 kDa.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei163 – 164Cleavage; by viral protease1 Publication2
Sitei318 – 319Cleavage; by viral protease1 Publication2
Sitei585 – 586Cleavage; by viral protease1 Publication2
Sitei648 – 649Cleavage; by viral protease1 Publication2
Sitei842 – 843Cleavage; by viral proteaseBy similarity2
Sitei960 – 961Cleavage; by viral proteaseBy similarity2
Sitei997 – 998Cleavage; by viral proteaseBy similarity2
Sitei1589 – 1590Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
P03364

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

Curated

Interacts with the G-patch peptide.

By similarity

Interacts with the reverse transcriptase/ribonuclease H.

By similarity

Homotrimer.

By similarity

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P03364

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini863 – 939Peptidase A2PROSITE-ProRule annotationAdd BLAST77
Domaini950 – 996G-patchPROSITE-ProRule annotationAdd BLAST47
Domaini1044 – 1232Reverse transcriptasePROSITE-ProRule annotationAdd BLAST189
Domaini1455 – 1586RNase HPROSITE-ProRule annotationAdd BLAST132
Domaini1643 – 1804Integrase catalyticPROSITE-ProRule annotationAdd BLAST162

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi346 – 349Poly-GluSequence analysis4
Compositional biasi1322 – 1329Poly-LeuSequence analysis8

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Gag polyprotein: Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. Gag-p35 contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 (Potential).Curated
The glycine-rich G-patch domain (GPD) is present at the C-terminus of the protease from which it is then detached by the protease itself.By similarity

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1589 – 1630Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05482, HIV_retropepsin_like, 1 hit
cd07557, trimeric_dUTPase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.490, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
2.70.40.10, 1 hit
3.30.420.10, 2 hits
3.30.70.270, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001969, Aspartic_peptidase_AS
IPR003322, B_retro_matrix
IPR038124, B_retro_matrix_sf
IPR043502, DNA/RNA_pol_sf
IPR029054, dUTPase-like
IPR036157, dUTPase-like_sf
IPR033704, dUTPase_trimeric
IPR000467, G_patch_dom
IPR000721, Gag_p24
IPR017856, Integrase-like_N
IPR036862, Integrase_C_dom_sf_retrovir
IPR001037, Integrase_C_retrovir
IPR001584, Integrase_cat-core
IPR003308, Integrase_Zn-bd_dom_N
IPR001995, Peptidase_A2_cat
IPR021109, Peptidase_aspartic_dom_sf
IPR034170, Retropepsin-like_cat_dom
IPR018061, Retropepsins
IPR008916, Retrov_capsid_C
IPR008919, Retrov_capsid_N
IPR010999, Retrovr_matrix
IPR043128, Rev_trsase/Diguanyl_cyclase
IPR012337, RNaseH-like_sf
IPR002156, RNaseH_domain
IPR036397, RNaseH_sf
IPR000477, RT_dom
IPR010661, RVT_thumb
IPR036875, Znf_CCHC_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00692, dUTPase, 1 hit
PF01585, G-patch, 1 hit
PF02337, Gag_p10, 1 hit
PF00607, Gag_p24, 1 hit
PF00552, IN_DBD_C, 1 hit
PF02022, Integrase_Zn, 1 hit
PF00075, RNase_H, 1 hit
PF00665, rve, 1 hit
PF00077, RVP, 1 hit
PF00078, RVT_1, 1 hit
PF06817, RVT_thumb, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00443, G_patch, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46919, SSF46919, 1 hit
SSF47836, SSF47836, 1 hit
SSF47943, SSF47943, 1 hit
SSF50122, SSF50122, 1 hit
SSF50630, SSF50630, 1 hit
SSF51283, SSF51283, 1 hit
SSF53098, SSF53098, 2 hits
SSF56672, SSF56672, 1 hit
SSF57756, SSF57756, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50175, ASP_PROT_RETROV, 1 hit
PS00141, ASP_PROTEASE, 1 hit
PS50174, G_PATCH, 1 hit
PS50994, INTEGRASE, 1 hit
PS51027, INTEGRASE_DBD, 1 hit
PS50879, RNASE_H, 1 hit
PS50878, RT_POL, 1 hit
PS50876, ZF_INTEGRASE, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (3)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform. This section is only present in reviewed entries, i.e. in UniProtKB/Swiss-Prot.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Isoform Gag-Pro-Pol polyprotein (identifier: P03364-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MGQASSHSEN DLFISHLKES LKVRRIRVRK KDLVSFFSFI FKTCPWFPQE
60 70 80 90 100
GSIDSRVWGR VGDCLNDYYR VFGPETIPIT TFNYYNLIRD VLTNQSDSPD
110 120 130 140 150
IQRLCKEGHK ILISHSRPPS RQAPVTITTS EKASSRPPSR APSTCPSVAI
160 170 180 190 200
DIGSHDTGQS SLYPNLATLT DPPIQSPHSR AHTPPQHLPL LANSKTLHNS
210 220 230 240 250
GSQDDQLNPA DQADLEEAAA QYNNPDWPQL TNTPALPPFR PPSYVSTAVP
260 270 280 290 300
PVAVAAPVLH APTSGVPGSP TAPNLPGVAL AKPSGPIDET VSLLDGVKTL
310 320 330 340 350
VTKLSDLALL PPAGVMAFPV TRSQGQVSSN TTGRASPHPD THTIPEEEEA
360 370 380 390 400
DSGESDSEDD EEESSEPTEP TYTHSYKRLN LKTIEKIKTA VANYGPTAPF
410 420 430 440 450
TVALVESLSE RWLTPSDWFF LSRAALSGGD NILWKSEYED ISKQFAERTR
460 470 480 490 500
VRPPPKDGPL KIPGASPYQN NDKQAQFPPG LLTQIQSAGL KAWKRLPQKG
510 520 530 540 550
AATTSLAKIR QGPDESYSDF VSRLQETADR LFGSGESESS FVKHLAYENA
560 570 580 590 600
NPACQSAIRP FRQKELSTMS PLLWYCSAHA VGLAIGAALQ NLAPAQLLEP
610 620 630 640 650
RPAFAIIVTN PAIFQETAPK KIQPPTQLPT QPNAPQASLI KNLGPTTKCP
660 670 680 690 700
RCKKGFHWAS ECRSRLDING QPIIKQGNLE QGPAPGPHYR DELRGFTVHP
710 720 730 740 750
PIPPANPCPP SNQPRRYVTD LWRATAGSAG LDLCTTTDTI LTTQNSPLTL
760 770 780 790 800
PVGIYGPLPP QTFGLILAEP ALPSKGIQVL PGILDNDFEG EIHIILSTTK
810 820 830 840 850
DLVTIPKGTR LAQIVILPLQ QINSNFHKPY RGASAPGSSD VYWVQQISQQ
860 870 880 890 900
RPTLKLKLNG KLFSGILDTG ADATVISYTH WPRNWPLTTV ATHLRGIGQA
910 920 930 940 950
TNPQQSAQML KWEDSEGNNG HITPYVLPNL PVNLWGRDIL SQMKLVMCSP
960 970 980 990 1000
NDTVMTQMLS QGYLPGQGLG KNNQGITQPI TITPKKDKTG LGFHQNLPRS
1010 1020 1030 1040 1050
RAIDIPVPHA DKISWKITDP VWVDQWPLTY EKTLAAIALV QEQLAAGHIE
1060 1070 1080 1090 1100
PTNSPWNTPI FIIKKKSGSW RLLQDLRAVN KVMVPMGALQ PGLPSPVAIP
1110 1120 1130 1140 1150
LNYHKIVIDL KDCFFTIPLH PEDRPYFAFS VPQINFQSPM PRYQWKVLPQ
1160 1170 1180 1190 1200
GMANSPTLCQ KFVAAAIAPV RSQWPEAYIL HYMDDILLAC DSAEAAKACY
1210 1220 1230 1240 1250
AHIISCLTSY GLKIAPDKVQ VSEPFSYLGF ELHHQQVFTP RVCLKTDHLK
1260 1270 1280 1290 1300
TLNDFQKLLG DIQWLRPYLK LPTSALVPLN NILKGDPNPL SVRALTPEAK
1310 1320 1330 1340 1350
QSLALINKAI QNQSVQQISY NLPLVLLLLP TPHTPTAVFW QPNGTDPTKN
1360 1370 1380 1390 1400
GSPLLWLHLP ASPSKVLLTY PSLLAMLIIK GRYTGRQLFG RDPHSIIIPY
1410 1420 1430 1440 1450
TQDQLTWLLQ TSDEWAIALS SFTGDIDNHY PSDPVIQFAK LHQFIFPKIT
1460 1470 1480 1490 1500
KCAPIPQATL VFTDGSSNGI AAYVIDNQPI SIKSPYLSAQ LVELYAILQV
1510 1520 1530 1540 1550
FTVLAHQPFN LYTDSAYIAQ SVPLLETVPF IKSSTNATPL FSKLQQLILN
1560 1570 1580 1590 1600
RQHPFFIGHL RAHLNLPGPL AEGNALADAA TQIFPIISDP IHEATQAHTL
1610 1620 1630 1640 1650
HHLNAHTLRL LYKITREQAR DIVKACKQCV VATPVPHLGV NPRGLVPNAI
1660 1670 1680 1690 1700
WQMDVTHFTP FGKQRFVHVT VDTFSGFILA TPQTGEASKN VISHVIHCLA
1710 1720 1730 1740 1750
TIGKPHTIKT DNGPGYTGKN FQDFCQKLQI KHVTGIPYNP QGQGVVERAH
1760 1770 1780 1790 1800
QTLKNALNRL ARSPLGFSMQ QPRNLLSHAL FQLNFLQLDS QGRSAADRLW
1810 1820 1830 1840 1850
HPQTSQQHAT VMWRDPLTSV WKGPDPVLIW GRGSACIYDQ KEDGPRWLPE
1860 1870 1880
RLIRHINNQT APLCDRPSNP NTAPGPKGSP
Note: Produced by -1 ribosomal frameshiftings between gag-pro and pro-pol.1 Publication
Length:1,880
Mass (Da):207,175
Last modified:February 28, 2018 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4BB9A4268FF31A88
GO
Isoform Gag-Pro polyprotein (identifier: P21407-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P21407.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:998
Mass (Da):108,735
GO
Isoform Gag polyprotein (identifier: P21411-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P21411.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:740
Mass (Da):80,543
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA66453 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
K01706 Genomic RNA Translation: AAA46815.1
M23385 Genomic RNA Translation: AAA66453.1 Different initiation.

Protein sequence database of the Protein Information Resource

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PIRi
A05072
C31827, GNLJHD

NCBI Reference Sequences

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RefSeqi
NP_041261.1, NC_001514.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

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GeneIDi
1491962

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:1491962

Keywords - Coding sequence diversityi

Ribosomal frameshifting

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K01706 Genomic RNA Translation: AAA46815.1
M23385 Genomic RNA Translation: AAA66453.1 Different initiation.
PIRiA05072
C31827, GNLJHD
RefSeqiNP_041261.1, NC_001514.1

3D structure databases

SMRiP03364
ModBaseiSearch...

Proteomic databases

PRIDEiP03364

Genome annotation databases

GeneIDi1491962
KEGGivg:1491962

Family and domain databases

CDDicd05482, HIV_retropepsin_like, 1 hit
cd07557, trimeric_dUTPase, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.490, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
2.70.40.10, 1 hit
3.30.420.10, 2 hits
3.30.70.270, 2 hits
InterProiView protein in InterPro
IPR001969, Aspartic_peptidase_AS
IPR003322, B_retro_matrix
IPR038124, B_retro_matrix_sf
IPR043502, DNA/RNA_pol_sf
IPR029054, dUTPase-like
IPR036157, dUTPase-like_sf
IPR033704, dUTPase_trimeric
IPR000467, G_patch_dom
IPR000721, Gag_p24
IPR017856, Integrase-like_N
IPR036862, Integrase_C_dom_sf_retrovir
IPR001037, Integrase_C_retrovir
IPR001584, Integrase_cat-core
IPR003308, Integrase_Zn-bd_dom_N
IPR001995, Peptidase_A2_cat
IPR021109, Peptidase_aspartic_dom_sf
IPR034170, Retropepsin-like_cat_dom
IPR018061, Retropepsins
IPR008916, Retrov_capsid_C
IPR008919, Retrov_capsid_N
IPR010999, Retrovr_matrix
IPR043128, Rev_trsase/Diguanyl_cyclase
IPR012337, RNaseH-like_sf
IPR002156, RNaseH_domain
IPR036397, RNaseH_sf
IPR000477, RT_dom
IPR010661, RVT_thumb
IPR036875, Znf_CCHC_sf
PfamiView protein in Pfam
PF00692, dUTPase, 1 hit
PF01585, G-patch, 1 hit
PF02337, Gag_p10, 1 hit
PF00607, Gag_p24, 1 hit
PF00552, IN_DBD_C, 1 hit
PF02022, Integrase_Zn, 1 hit
PF00075, RNase_H, 1 hit
PF00665, rve, 1 hit
PF00077, RVP, 1 hit
PF00078, RVT_1, 1 hit
PF06817, RVT_thumb, 1 hit
SMARTiView protein in SMART
SM00443, G_patch, 1 hit
SUPFAMiSSF46919, SSF46919, 1 hit
SSF47836, SSF47836, 1 hit
SSF47943, SSF47943, 1 hit
SSF50122, SSF50122, 1 hit
SSF50630, SSF50630, 1 hit
SSF51283, SSF51283, 1 hit
SSF53098, SSF53098, 2 hits
SSF56672, SSF56672, 1 hit
SSF57756, SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175, ASP_PROT_RETROV, 1 hit
PS00141, ASP_PROTEASE, 1 hit
PS50174, G_PATCH, 1 hit
PS50994, INTEGRASE, 1 hit
PS51027, INTEGRASE_DBD, 1 hit
PS50879, RNASE_H, 1 hit
PS50878, RT_POL, 1 hit
PS50876, ZF_INTEGRASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPOL_SMRVH
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P03364
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: February 28, 2018
Last modified: October 7, 2020
This is version 124 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Direct protein sequencing
UniProt is an ELIXIR core data resource
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