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TRIM39 tripartite motif containing 39 [ Homo sapiens (human) ]

Gene ID: 56658, updated on 21-Dec-2019

Summary

Official Symbol
TRIM39provided by HGNC
Official Full Name
tripartite motif containing 39provided by HGNC
Primary source
HGNC:HGNC:10065
See related
Ensembl:ENSG00000204599 MIM:605700
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
TFP; RNF23; TRIM39B
Summary
The protein encoded by this gene is 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. The function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 12.0), thyroid (RPKM 6.0) and 25 other tissues See more
Orthologs

Genomic context

See TRIM39 in Genome Data Viewer
Location:
6p22.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (30326469..30343729)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30294227..30311506)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 26B, pseudogene Neighboring gene HLA complex group 17 Neighboring gene major histocompatibility complex, class I, L (pseudogene) Neighboring gene HLA complex group 18 Neighboring gene TRIM39-RPP21 readthrough Neighboring gene ribonuclease P/MRP subunit p21 Neighboring gene major histocompatibility complex, class I, N (pseudogene)

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC32984

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transferase activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase TRIM39
Names
RING-type E3 ubiquitin transferase TRIM39
ring finger protein 23
testis-abundant finger protein
tripartite motif-containing protein 39
NP_001356450.1
NP_001356451.1
NP_001356452.1
NP_067076.2
NP_742013.1

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_001369521.1NP_001356450.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL662795
    Related
    ENSP00000379800.3, ENST00000396551.7
    Conserved Domains (4) summary
    COG5432
    Location:20179
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    TIGR02169
    Location:148295
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd13745
    Location:305483
    SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
    cd16601
    Location:2669
    RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
  2. NM_001369522.1NP_001356451.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL662795
    Conserved Domains (4) summary
    COG5432
    Location:20179
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    TIGR02169
    Location:148295
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd13745
    Location:305483
    SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
    cd16601
    Location:2669
    RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
  3. NM_001369523.1NP_001356452.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL662795
    Related
    ENSP00000379797.1, ENST00000396548.5
    Conserved Domains (4) summary
    COG5432
    Location:20179
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    TIGR02169
    Location:148295
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd13745
    Location:305483
    SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
    cd16601
    Location:2669
    RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
  4. NM_021253.4NP_067076.2  E3 ubiquitin-protein ligase TRIM39 isoform 1

    See identical proteins and their annotated locations for NP_067076.2

    Status: REVIEWED

    Source sequence(s)
    AL662795
    Consensus CDS
    CCDS34377.1
    UniProtKB/Swiss-Prot
    Q9HCM9
    UniProtKB/TrEMBL
    A0A024RCP5
    Related
    ENSP00000365844.4, ENST00000376656.8
    Conserved Domains (4) summary
    cd13745
    Location:335513
    SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
    cd16601
    Location:2669
    RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
    cl28410
    Location:20179
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    cl28522
    Location:175352
    AtpF; FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]
  5. NM_172016.2NP_742013.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

    See identical proteins and their annotated locations for NP_742013.1

    Status: REVIEWED

    Source sequence(s)
    AL662795, BC034985, DB071507
    Consensus CDS
    CCDS34378.1
    UniProtKB/Swiss-Prot
    Q9HCM9
    UniProtKB/TrEMBL
    A0A024RCR1
    Related
    ENSP00000365847.5, ENST00000376659.9
    Conserved Domains (4) summary
    COG5432
    Location:20179
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    TIGR02169
    Location:148295
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    cd13745
    Location:305483
    SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
    cd16601
    Location:2669
    RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    30326469..30343729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    1655959..1673225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    1806146..1823410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    1582309..1599575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    1636694..1653960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    1581544..1598811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    1624923..1642186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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