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Entry version 60 (12 Aug 2020)
Sequence version 1 (20 Apr 2010)
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Protein

Tetratricopeptide repeat protein 39B

Gene

Ttc39b

Organism
Rattus norvegicus (Rat)
Status
Reviewed-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 inferred from homologyi <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

Regulates high density lipoprotein (HDL) cholesterol metabolism by promoting the ubiquitination and degradation of the oxysterols receptors LXR (NR1H2 and NR1H3).By similarity

<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 - 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

Biological processLipid metabolism

<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:
Tetratricopeptide repeat protein 39B
Short name:
TPR repeat protein 39B
<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:Ttc39b
<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)
<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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<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 5
  • UP000234681 Componentsi: Chromosome 5, Unassembled WGS sequence

Organism-specific databases

Rat genome database

More...
RGDi
1305797, Ttc39b

<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 '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_00004167701 – 617Tetratricopeptide repeat protein 39BAdd BLAST617

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
D3ZC96

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
D3ZC96

PeptideAtlas

More...
PeptideAtlasi
D3ZC96

PRoteomics IDEntifications database

More...
PRIDEi
D3ZC96

<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
ENSRNOG00000042603, Expressed in duodenum and 20 other tissues

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
D3ZC96, RN

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
10116.ENSRNOP00000055409

<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 'Family and Domains' section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati328 – 361TPR 1Add BLAST34
Repeati561 – 594TPR 2Add BLAST34

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the TTC39 family.Curated

Keywords - Domaini

Repeat, TPR repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
KOG3783, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00950000182917

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_010086_3_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
D3ZC96

Identification of Orthologs from Complete Genome Data

More...
OMAi
ELMYVWN

Database of Orthologous Groups

More...
OrthoDBi
754120at2759

TreeFam database of animal gene trees

More...
TreeFami
TF313761

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR019412, Iml2/TPR_39
IPR011990, TPR-like_helical_dom_sf
IPR034305, TTC39B

The PANTHER Classification System

More...
PANTHERi
PTHR31859, PTHR31859, 1 hit
PTHR31859:SF4, PTHR31859:SF4, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF10300, DUF3808, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF48452, SSF48452, 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.

D3ZC96-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MALVGSRVEL DADEDIFEDA LETISRSPSD MATSGFHFVP CDTKRTSRQL
60 70 80 90 100
GAPAVGRAEG SSAKVDLKSG LEECAAALNL FLSNRFKDAL ELLRPWAKES
110 120 130 140 150
MYHALGYSTI VVLQAVMTFE QQDIQNGISA MKDALQTCQK YRKKCTVVES
160 170 180 190 200
FSSLLSRGSL EQLSEEEMHA EICYAECLLQ KAALTFVQDE NMINFIKGGL
210 220 230 240 250
KIRTSYQIYK ECLSILHVIQ KNKEEQHFFY EFEGGVKLGT GAFNLMLSLL
260 270 280 290 300
PARIIRLLEF IGFSGNRDLG LLQLREGASG SSMRSPLCCL TILAFHTYIS
310 320 330 340 350
LILGTGEVNV AEAESLLAPF LQQFPNGSLI LFYHARIELL KGNAEKAQET
360 370 380 390 400
FRKCISVQEE WKQFHHLCYW ELMWIYIYQQ NWMQAYYYSD LLCKESKWSK
410 420 430 440 450
ATYVFLKAAI LSMLPEEEVA VTKENVVSLF RQVDGLKQRI AGKSLPTEKF
460 470 480 490 500
AVRKARRYSP SSGVPGKLVL PALEMMYVWN GFSIVGKRKD LSENLLVTVE
510 520 530 540 550
KAEEALQNQN FTDYSVDDEC LVKLLKGCCL KNLQRPLQAE LCFNHVLESE
560 570 580 590 600
KLLKYDHYLV PFTLFELAFL YKSQGEIDKA IKVLETARNN YKDYSLESRL
610
HFRIQAALHL WKKPSSD
Length:617
Mass (Da):70,168
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:i3599652EB341ACF7
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AABR03040249 Genomic DNA No translation available.
CH473978 Genomic DNA Translation: EDM10461.1

NCBI Reference Sequences

More...
RefSeqi
NP_001100135.1, NM_001106665.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSRNOT00000058611; ENSRNOP00000055409; ENSRNOG00000042603

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
298186

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:298186

<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
AABR03040249 Genomic DNA No translation available.
CH473978 Genomic DNA Translation: EDM10461.1
RefSeqiNP_001100135.1, NM_001106665.1

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.ENSRNOP00000055409

Proteomic databases

jPOSTiD3ZC96
PaxDbiD3ZC96
PeptideAtlasiD3ZC96
PRIDEiD3ZC96

Genome annotation databases

EnsembliENSRNOT00000058611; ENSRNOP00000055409; ENSRNOG00000042603
GeneIDi298186
KEGGirno:298186

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
158219
RGDi1305797, Ttc39b

Phylogenomic databases

eggNOGiKOG3783, Eukaryota
GeneTreeiENSGT00950000182917
HOGENOMiCLU_010086_3_0_1
InParanoidiD3ZC96
OMAiELMYVWN
OrthoDBi754120at2759
TreeFamiTF313761

Miscellaneous databases

Protein Ontology

More...
PROi
PR:D3ZC96

Gene expression databases

BgeeiENSRNOG00000042603, Expressed in duodenum and 20 other tissues
GenevisibleiD3ZC96, RN

Family and domain databases

InterProiView protein in InterPro
IPR019412, Iml2/TPR_39
IPR011990, TPR-like_helical_dom_sf
IPR034305, TTC39B
PANTHERiPTHR31859, PTHR31859, 1 hit
PTHR31859:SF4, PTHR31859:SF4, 1 hit
PfamiView protein in Pfam
PF10300, DUF3808, 1 hit
SUPFAMiSSF48452, SSF48452, 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 nameiTT39B_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: D3ZC96
<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: April 18, 2012
Last sequence update: April 20, 2010
Last modified: August 12, 2020
This is version 60 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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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