Human Gene TRIM4 (uc003usd.3)
  Description: Homo sapiens tripartite motif containing 4 (TRIM4), transcript variant alpha, mRNA.
RefSeq Summary (NM_033017): 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 protein localizes to cytoplasmic bodies. Its function has not been identified. Alternatively spliced transcript variants that encode different isoforms have been described.[provided by RefSeq, Jul 2010].
Transcript (Including UTRs)
   Position: hg19 chr7:99,488,030-99,517,223 Size: 29,194 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr7:99,489,786-99,517,024 Size: 27,239 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:99,488,030-99,517,223)mRNA (may differ from genome)Protein (500 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedReactomeTreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TRIM4_HUMAN
DESCRIPTION: RecName: Full=Tripartite motif-containing protein 4; AltName: Full=RING finger protein 87;
SIMILARITY: Belongs to the TRIM/RBCC family.
SIMILARITY: Contains 1 B box-type zinc finger.
SIMILARITY: Contains 1 B30.2/SPRY domain.
SIMILARITY: Contains 1 RING-type zinc finger.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRIM4
CDC HuGE Published Literature: TRIM4
Positive Disease Associations: Creatinine , Dehydroepiandrosterone Sulfate , Glomerular Filtration Rate , Metabolism
Related Studies:
  1. Creatinine
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. Dehydroepiandrosterone Sulfate
    Guangju Zhai et al. PLoS genetics 2011, Eight common genetic variants associated with serum DHEAS levels suggest a key role in ageing mechanisms., PLoS genetics. [PubMed 21533175]
  3. Glomerular Filtration Rate
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.04 RPKM in Ovary
Total median expression: 425.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -80.10199-0.403 Picture PostScript Text
3' UTR -493.161756-0.281 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001870 - B30.2/SPRY
IPR003879 - Butyrophylin
IPR008985 - ConA-like_lec_gl_sf
IPR003877 - SPRY_rcpt
IPR000315 - Znf_B-box
IPR018957 - Znf_C3HC4_RING-type
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF00622 - SPRY domain
PF00643 - B-box zinc finger
PF13445 - RING-type zinc-finger
PF13639 - Ring finger domain
PF13920 - Zinc finger, C3HC4 type (RING finger)
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF14560 - Ubiquitin-like domain
PF15227 - zinc finger of C3HC4-type, RING

SCOP Domains:
57845 - B-box zinc-binding domain
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q9C037
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0002376 immune system process
GO:0016567 protein ubiquitination
GO:0045087 innate immune response
GO:0070206 protein trimerization

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AF220023 - Homo sapiens tripartite motif protein TRIM4 isoform alpha (TRIM4) mRNA, complete cds; alternatively spliced.
AF220024 - Homo sapiens tripartite motif protein TRIM4 isoform beta (TRIM4) mRNA, complete cds; alternatively spliced.
JD119893 - Sequence 100917 from Patent EP1572962.
JD055568 - Sequence 36592 from Patent EP1572962.
JD054329 - Sequence 35353 from Patent EP1572962.
JD267151 - Sequence 248175 from Patent EP1572962.
JD121811 - Sequence 102835 from Patent EP1572962.
JD223460 - Sequence 204484 from Patent EP1572962.
AK092892 - Homo sapiens cDNA FLJ35573 fis, clone SPLEN2005927, highly similar to Tripartite motif-containing protein 4.
AX747794 - Sequence 1319 from Patent EP1308459.
JD509056 - Sequence 490080 from Patent EP1572962.
JD085677 - Sequence 66701 from Patent EP1572962.
JD248898 - Sequence 229922 from Patent EP1572962.
JD565195 - Sequence 546219 from Patent EP1572962.
JD192305 - Sequence 173329 from Patent EP1572962.
JD259402 - Sequence 240426 from Patent EP1572962.
JD259824 - Sequence 240848 from Patent EP1572962.
AK293565 - Homo sapiens cDNA FLJ60086 complete cds, highly similar to Tripartite motif-containing protein 4.
JD279474 - Sequence 260498 from Patent EP1572962.
JD355842 - Sequence 336866 from Patent EP1572962.
JD223260 - Sequence 204284 from Patent EP1572962.
JD252806 - Sequence 233830 from Patent EP1572962.
JD122793 - Sequence 103817 from Patent EP1572962.
JD136073 - Sequence 117097 from Patent EP1572962.
JD253623 - Sequence 234647 from Patent EP1572962.
BC011763 - Homo sapiens tripartite motif-containing 4, mRNA (cDNA clone MGC:19745 IMAGE:3617674), complete cds.
BC025949 - Homo sapiens tripartite motif-containing 4, mRNA (cDNA clone MGC:39082 IMAGE:4620469), complete cds.
KJ903526 - Synthetic construct Homo sapiens clone ccsbBroadEn_12920 TRIM4 gene, encodes complete protein.
JD058196 - Sequence 39220 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9C037 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A4D298, NM_033017, NP_148977, Q75MK1, Q96F06, Q9C036, Q9C037, RNF87, TRIM4_HUMAN
UCSC ID: uc003usd.3
RefSeq Accession: NM_033017
Protein: Q9C037 (aka TRIM4_HUMAN or TRM4_HUMAN)
CCDS: CCDS5679.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_033017.3
exon count: 7CDS single in 3' UTR: no RNA size: 3458
ORF size: 1503CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2696.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.