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UniProtKB - D3ZMU8 (D3ZMU8_RAT)

Entry version 91 (26 Feb 2020)
Sequence version 1 (20 Apr 2010)
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Protein
Submitted name:

SIM bHLH transcription factor 1

Gene

Sim1

Organism
Rattus norvegicus (Rat)
Status
Unreviewed-Annotation score:

Annotation score:2 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>-Protein predictedi <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

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionDNA-bindingSAAS annotation
Biological processTranscription, Transcription regulationSAAS annotation

<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
Submitted name:
SIM bHLH transcription factor 1Imported
Submitted name:
Single-minded 1 (Predicted)Imported
<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:Sim1Imported
Synonyms:Sim1_predictedImported
ORF Names:rCG_58489Imported
<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>OrganismiRattus norvegicus (Rat)Imported
<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 identifieri10116 [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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
<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
  • UP000002494 <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: Chromosome 20

Organism-specific databases

Rat genome database

More...RGDi		1309949 Sim1

<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

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

NucleusSAAS annotation

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSRNOG00000037600 Expressed in adult mammalian kidney and 2 other tissues

<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

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		10116.ENSRNOP00000053843

<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>Domaini1 – 53BHLHInterPro annotationAdd BLAST53
Domaini77 – 140PASInterPro annotationAdd BLAST64
Domaini233 – 270PASInterPro annotationAdd BLAST38
Domaini336 – 765Single-minded C-terminalInterPro annotationAdd BLAST430

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni350 – 428DisorderedSequence analysisAdd BLAST79
Regioni527 – 563DisorderedSequence analysisAdd BLAST37
Regioni642 – 661DisorderedSequence analysisAdd BLAST20

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 biasi350 – 394PolarSequence analysisAdd BLAST45
Compositional biasi535 – 563PolarSequence analysisAdd BLAST29
Compositional biasi645 – 661PolarSequence analysisAdd BLAST17

Keywords - Domaini

RepeatSAAS annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG3559 Eukaryota
ENOG410XY57 LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000156143

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_010044_4_0_1

KEGG Orthology (KO)

More...KOi		K09100

Identification of Orthologs from Complete Genome Data

More...OMAi		ISPNCFG

Database of Orthologous Groups

More...OrthoDBi		231698at2759

TreeFam database of animal gene trees

More...TreeFami		TF317772

Family and domain databases

Conserved Domains Database

More...CDDi		cd00083 HLH, 1 hit
cd00130 PAS, 2 hits

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		4.10.280.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR011598 bHLH_dom
IPR036638 HLH_DNA-bd_sf
IPR001610 PAC
IPR000014 PAS
IPR035965 PAS-like_dom_sf
IPR013767 PAS_fold
IPR013655 PAS_fold_3
IPR010578 SIM_C

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00010 HLH, 1 hit
PF00989 PAS, 1 hit
PF08447 PAS_3, 1 hit
PF06621 SIM_C, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00353 HLH, 1 hit
SM00086 PAC, 1 hit
SM00091 PAS, 2 hits

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47459 SSF47459, 1 hit
SSF55785 SSF55785, 2 hits

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50888 BHLH, 1 hit
PS50112 PAS, 2 hits
PS51302 SIM_C, 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>Sequencei

<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.

D3ZMU8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKEKSKNAAR TRREKENSEF YELAKLLPLP SAITSQLDKA SIIRLTTSYL 
        60         70         80         90        100
KMRVVFPEGL GEAWGHTSRT SPLDNVGREL GSHLLQTLDG FIFVVAPDGK 
       110        120        130        140        150
IMYISETASV HLGLSQVELT GNSIYEYIHP ADHDEMTAVL TAHQPYHSHF 
       160        170        180        190        200
VQEYEIERSF FLRMKCVLAK RNAGLTCGGY KVIHCSGYLK IRQYSLDMSP 
       210        220        230        240        250
FDGCYQNVGL VAVGHSLPPS AVTEIKLHSN MFMFRASLDM KLIFLDSRVA 
       260        270        280        290        300
ELTGYEPQDL IEKTLYHHVH GCDTFHLRCA HHLLLVKGQV TTKYYRFLAK 
       310        320        330        340        350
HGGWVWVQSY ATIVHNSRSS RPHCIVSVNY VLTDTEYKGL QLSLDQISPS 
       360        370        380        390        400
KPTFSYTSSS TPTITDNRKG AKSRLSSSKS KSRTSPYPQY SGFHTERSES 
       410        420        430        440        450
DHDSQWGGSP LTDTASPQLL DPERPGSQHE LSCAYRQFPD RGSLCYGFAL 
       460        470        480        490        500
DHSRLVEDRH FHTQACEGGR CEAGRYFLGA PPAGRDPWWG SRAALPLTKA 
       510        520        530        540        550
SPESRETYEN SMPHITSVHR LHGRGHWDED SVVSSPDPGS ASESGDRYRS 
       560        570        580        590        600
EQYQNSPHEP SKIETLIRAT QQMIKEEENR LQLRKAPPDQ LASINGAGKK 
       610        620        630        640        650
HSLCFANYQQ PPPAGEVCHS SALTSTSPCD HIQQREGKML SPHENDYDNS 
       660        670        680        690        700
PTALSRISSP SSDRITKSSL ILAKDYLHSD MSPHQTAGDH PAISPNCFGS 
       710        720        730        740        750
HRQYFDKHAY TLTGYALEHL YDSETIRNYS LGCNGSHFDV TSHLRMQPDP 
       760 
AQGHKGTSVI ITNGS
Length:765
Mass (Da):85,532
Last modified:April 20, 2010 - v1
<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:iF49BC0AA9EE52F80
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
AABR07045656 Genomic DNA No translation available.
AABR07045657 Genomic DNA No translation available.
AABR07045658 Genomic DNA No translation available.
CH474025 Genomic DNA Translation: EDL99652.1

NCBI Reference Sequences

More...RefSeqi		NP_001101111.1, NM_001107641.1
XP_006256666.1, XM_006256604.2
XP_008771216.1, XM_008772994.2
XP_008771217.1, XM_008772995.2
XP_008771218.1, XM_008772996.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSRNOT00000057010; ENSRNOP00000053843; ENSRNOG00000037600

Database of genes from NCBI RefSeq genomes

More...GeneIDi		309888

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		rno:309888

UCSC genome browser

More...UCSCi		RGD:1309949 rat

<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
AABR07045656 Genomic DNA No translation available.
AABR07045657 Genomic DNA No translation available.
AABR07045658 Genomic DNA No translation available.
CH474025 Genomic DNA Translation: EDL99652.1
RefSeqiNP_001101111.1, NM_001107641.1
XP_006256666.1, XM_006256604.2
XP_008771216.1, XM_008772994.2
XP_008771217.1, XM_008772995.2
XP_008771218.1, XM_008772996.1

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000053843

Genome annotation databases

EnsembliENSRNOT00000057010; ENSRNOP00000053843; ENSRNOG00000037600
GeneIDi309888
KEGGirno:309888
UCSCiRGD:1309949 rat

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		6492
RGDi1309949 Sim1

Phylogenomic databases

eggNOGiKOG3559 Eukaryota
ENOG410XY57 LUCA
GeneTreeiENSGT00940000156143
HOGENOMiCLU_010044_4_0_1
KOiK09100
OMAiISPNCFG
OrthoDBi231698at2759
TreeFamiTF317772

Gene expression databases

BgeeiENSRNOG00000037600 Expressed in adult mammalian kidney and 2 other tissues

Family and domain databases

CDDicd00083 HLH, 1 hit
cd00130 PAS, 2 hits
Gene3Di4.10.280.10, 1 hit
InterProiView protein in InterPro
IPR011598 bHLH_dom
IPR036638 HLH_DNA-bd_sf
IPR001610 PAC
IPR000014 PAS
IPR035965 PAS-like_dom_sf
IPR013767 PAS_fold
IPR013655 PAS_fold_3
IPR010578 SIM_C
PfamiView protein in Pfam
PF00010 HLH, 1 hit
PF00989 PAS, 1 hit
PF08447 PAS_3, 1 hit
PF06621 SIM_C, 1 hit
SMARTiView protein in SMART
SM00353 HLH, 1 hit
SM00086 PAC, 1 hit
SM00091 PAS, 2 hits
SUPFAMiSSF47459 SSF47459, 1 hit
SSF55785 SSF55785, 2 hits
PROSITEiView protein in PROSITE
PS50888 BHLH, 1 hit
PS50112 PAS, 2 hits
PS51302 SIM_C, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...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 nameiD3ZMU8_RAT
<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: D3ZMU8
<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/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: February 26, 2020
This is version 91 of the entry and version 1 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

Reference proteomeImported
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