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TRIM13 tripartite motif containing 13 [ Homo sapiens (human) ]

Gene ID: 10206, updated on 11-Sep-2019

Summary

Official Symbol
TRIM13provided by HGNC
Official Full Name
tripartite motif containing 13provided by HGNC
Primary source
HGNC:HGNC:9976
See related
Ensembl:ENSG00000204977 MIM:605661
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CAR; LEU5; RFP2; DLEU5; RNF77
Summary
This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This gene is located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 17.7), bone marrow (RPKM 8.8) and 25 other tissues See more
Orthologs

Genomic context

See TRIM13 in Genome Data Viewer
Location:
13q14.2
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (49997042..50018467)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50571143..50592603)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 Neighboring gene deleted in lymphocytic leukemia 2 Neighboring gene microRNA 3613 Neighboring gene potassium channel regulator Neighboring gene microRNA 16-1 Neighboring gene microRNA 15a

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • Calnexin/calreticulin cycle, organism-specific biosystem (from REACTOME)
    Calnexin/calreticulin cycle, organism-specific biosystemThe unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and P...
  • ER Quality Control Compartment (ERQC), organism-specific biosystem (from REACTOME)
    ER Quality Control Compartment (ERQC), organism-specific biosystemProteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to ...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
    N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum quality control compartment IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
perinuclear endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase TRIM13
Names
B-cell chronic lymphocytic leukemia tumor suppressor Leu5
CLL-associated RING finger
RING finger protein 77
RING-type E3 ubiquitin transferase TRIM13
leukemia-associated protein 5
putative tumor suppressor RFP2
ret finger protein 2
tripartite motif protein 13
tripartite motif-containing protein 13
NP_001007279.1
NP_005789.2
NP_434698.1
NP_998755.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001007278.3NP_001007279.1  E3 ubiquitin-protein ligase TRIM13 isoform 2

    See identical proteins and their annotated locations for NP_001007279.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional internal exon, which contains an upstream in-frame AUG start codon compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL832695, AY455758, AY764035, KF455768
    Consensus CDS
    CCDS41888.1
    UniProtKB/Swiss-Prot
    O60858
    UniProtKB/TrEMBL
    L7MTJ6
    Related
    ENSP00000348299.4, ENST00000356017.8
    Conserved Domains (2) summary
    smart00336
    Location:93134
    BBOX; B-Box-type zinc finger
    cd00162
    Location:1264
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
  2. NM_005798.5NP_005789.2  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_005789.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the same protein (isoform 1) as variants 2 and 3.
    Source sequence(s)
    AF241850, AL832695, AY455758, BI668033, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    O60858
    UniProtKB/TrEMBL
    A0A024RDU3, L7MTJ6
    Related
    ENSP00000412943.2, ENST00000420995.6
    Conserved Domains (3) summary
    smart00336
    Location:90131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:561
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins
  3. NM_052811.4NP_434698.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_434698.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AL832695, AY191002, AY455758, BI668033, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    O60858
    UniProtKB/TrEMBL
    A0A024RDU3, L7MTJ6
    Related
    ENSP00000399206.2, ENST00000457662.2
    Conserved Domains (3) summary
    smart00336
    Location:90131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:561
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins
  4. NM_213590.3NP_998755.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

    See identical proteins and their annotated locations for NP_998755.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AL832695, AY455758, KF455768
    Consensus CDS
    CCDS9423.1
    UniProtKB/Swiss-Prot
    O60858
    UniProtKB/TrEMBL
    A0A024RDU3, L7MTJ6
    Related
    ENSP00000367424.3, ENST00000378182.4
    Conserved Domains (3) summary
    smart00336
    Location:90131
    BBOX; B-Box-type zinc finger
    pfam12252
    Location:163234
    SidE; Dot/Icm substrate protein
    cd16762
    Location:561
    RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    49997042..50018467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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