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TRIM40 tripartite motif containing 40 [ Homo sapiens (human) ]

Gene ID: 135644, updated on 22-Aug-2020

Summary

Official Symbol
TRIM40provided by HGNC
Official Full Name
tripartite motif containing 40provided by HGNC
Primary source
HGNC:HGNC:18736
See related
Ensembl:ENSG00000204614 MIM:616976
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
RNF35
Summary
This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
Expression
Biased expression in small intestine (RPKM 3.6), duodenum (RPKM 3.4) and 4 other tissues See more
Orthologs

Genomic context

See TRIM40 in Genome Data Viewer
Location:
6p22.1
Exon count:
6
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (30135998..30148773)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30103885..30116512)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 11 Neighboring gene ring finger protein 39 Neighboring gene TRIM31 antisense RNA 1 Neighboring gene tripartite motif containing 31 Neighboring gene tripartite motif containing 10 Neighboring gene tripartite motif containing 15

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

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NIK/NF-kappaB signaling NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of cell growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein localization to nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein neddylation IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
IkappaB kinase complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
tripartite motif-containing protein 40
Names
RING finger protein 35
probable E3 NEDD8-protein ligase
ring finger RNF35

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.

Genomic

  1. NG_033972.1 RefSeqGene

    Range
    5033..17621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001286633.2NP_001273562.1  tripartite motif-containing protein 40 isoform a

    See identical proteins and their annotated locations for NP_001273562.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL669914, BC060785
    Consensus CDS
    CCDS69069.1
    UniProtKB/Swiss-Prot
    Q6P9F5
    UniProtKB/TrEMBL
    A0A1U9X8U1
    Related
    ENSP00000379826.1, ENST00000396581.6
    Conserved Domains (1) summary
    cd16583
    Location:1358
    RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins
  2. NM_138700.4NP_619645.1  tripartite motif-containing protein 40 isoform b

    See identical proteins and their annotated locations for NP_619645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF489517, AL669914, BC060785
    Consensus CDS
    CCDS4675.1
    UniProtKB/Swiss-Prot
    Q6P9F5
    Related
    ENSP00000308310.4, ENST00000307859.4
    Conserved Domains (1) summary
    cd00162
    Location:1460
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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
    30135998..30148773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514305.1XP_011512607.1  tripartite motif-containing protein 40 isoform X1

    See identical proteins and their annotated locations for XP_011512607.1

    UniProtKB/Swiss-Prot
    Q6P9F5
    UniProtKB/TrEMBL
    A0A1U9X8U1
    Conserved Domains (1) summary
    cd16583
    Location:1358
    RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins
  2. XM_011514309.1XP_011512611.1  tripartite motif-containing protein 40 isoform X3

    See identical proteins and their annotated locations for XP_011512611.1

    Conserved Domains (1) summary
    cd00162
    Location:1460
    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 ...
  3. XM_011514306.1XP_011512608.1  tripartite motif-containing protein 40 isoform X1

    See identical proteins and their annotated locations for XP_011512608.1

    UniProtKB/Swiss-Prot
    Q6P9F5
    UniProtKB/TrEMBL
    A0A1U9X8U1
    Conserved Domains (1) summary
    cd16583
    Location:1358
    RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins
  4. XM_011514308.1XP_011512610.1  tripartite motif-containing protein 40 isoform X2

    Conserved Domains (1) summary
    cd00162
    Location:1460
    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 ...

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    1394236..1406831
    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
    1615945..1628543
    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
    1392058..1404652
    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
    1446862..1459457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    1480229..1492817
    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
    1391268..1403864
    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
    1435079..1447667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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