Human Gene TRIM38 (ENST00000357085.5) Description and Page Index
  Description: Homo sapiens tripartite motif containing 38 (TRIM38), mRNA. (from RefSeq NM_006355)
RefSeq Summary (NM_006355): This gene encodes a member of the tripartite motif (TRIM) family. The encoded protein contains a RING-type zinc finger, B box-type zinc finger and SPRY domain. The function of this protein has not been identified. A pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Jul 2012]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000357085.5
Gencode Gene: ENSG00000112343.11
Transcript (Including UTRs)
   Position: hg38 chr6:25,962,802-25,991,231 Size: 28,430 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr6:25,966,523-25,983,687 Size: 17,165 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:25,962,802-25,991,231)mRNA (may differ from genome)Protein (465 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtPubMedReactome
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TRI38_HUMAN
DESCRIPTION: RecName: Full=Tripartite motif-containing protein 38; AltName: Full=RING finger protein 15; AltName: Full=Zinc finger protein RoRet;
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Contains 1 B box-type zinc finger.
SIMILARITY: Contains 1 B30.2/SPRY domain.
SIMILARITY: Contains 1 RING-type zinc finger.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.09 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 290.79 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.50476-0.331 Picture PostScript Text
3' UTR -2228.207544-0.295 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
IPR006574 - PRY
IPR018355 - SPla/RYanodine_receptor_subgr
IPR003877 - SPRY_rcpt
IPR000315 - Znf_B-box
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00622 - SPRY domain
PF00643 - B-box zinc finger

ModBase Predicted Comparative 3D Structure on O00635
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
Genome BrowserNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein Sequence     
Alignment     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
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:0032648 regulation of interferon-beta production
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045070 positive regulation of viral genome replication
GO:0045087 innate immune response
GO:0046598 positive regulation of viral entry into host cell
GO:0050687 negative regulation of defense response to virus
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0060333 interferon-gamma-mediated signaling pathway
GO:0070936 protein K48-linked ubiquitination

Cellular Component:
GO:0005575 cellular_component
GO:0005622 intracellular
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BX640949 - Homo sapiens mRNA; cDNA DKFZp686F23130 (from clone DKFZp686F23130).
AK313248 - Homo sapiens cDNA, FLJ93754, highly similar to Homo sapiens tripartite motif-containing 38 (TRIM38), mRNA.
BC026930 - Homo sapiens tripartite motif-containing 38, mRNA (cDNA clone MGC:8946 IMAGE:3879491), complete cds.
AB209906 - Homo sapiens mRNA for tripartite motif-containing 38 variant protein.
JD170220 - Sequence 151244 from Patent EP1572962.
JD445853 - Sequence 426877 from Patent EP1572962.
JD062259 - Sequence 43283 from Patent EP1572962.
JD436323 - Sequence 417347 from Patent EP1572962.
JD383064 - Sequence 364088 from Patent EP1572962.
JD103763 - Sequence 84787 from Patent EP1572962.
JD064295 - Sequence 45319 from Patent EP1572962.
JD064296 - Sequence 45320 from Patent EP1572962.
CR936707 - Homo sapiens mRNA; cDNA DKFZp686D03106 (from clone DKFZp686D03106).
JD349360 - Sequence 330384 from Patent EP1572962.
JD299879 - Sequence 280903 from Patent EP1572962.
JD305889 - Sequence 286913 from Patent EP1572962.
JD305890 - Sequence 286914 from Patent EP1572962.
U90547 - Human Ro/SSA ribonucleoprotein homolog (RoRet) mRNA, complete cds.
JD038638 - Sequence 19662 from Patent EP1572962.
JD147063 - Sequence 128087 from Patent EP1572962.
AB527948 - Synthetic construct DNA, clone: pF1KB0996, Homo sapiens TRIM38 gene for tripartite motif-containing 38, without stop codon, in Flexi system.
DQ894918 - Synthetic construct Homo sapiens clone IMAGE:100009378; FLH179940.01L; RZPDo839E03131D tripartite motif-containing 38 (TRIM38) gene, encodes complete protein.
EU831816 - Synthetic construct Homo sapiens clone HAIB:100066845; DKFZo008F1221 tripartite motif-containing 38 protein (TRIM38) gene, encodes complete protein.
EU831893 - Synthetic construct Homo sapiens clone HAIB:100066922; DKFZo004F1222 tripartite motif-containing 38 protein (TRIM38) gene, encodes complete protein.
EU176297 - Synthetic construct Homo sapiens clone IMAGE:100006407; FLH179947.01X; RZPDo839B03251D tripartite motif-containing 38 (TRIM38) gene, encodes complete protein.
AK310777 - Homo sapiens cDNA, FLJ17819.
JD102707 - Sequence 83731 from Patent EP1572962.
JD494320 - Sequence 475344 from Patent EP1572962.
JD237849 - Sequence 218873 from Patent EP1572962.
JD405033 - Sequence 386057 from Patent EP1572962.
JD184886 - Sequence 165910 from Patent EP1572962.
JD268080 - Sequence 249104 from Patent EP1572962.
JD241530 - Sequence 222554 from Patent EP1572962.
JD331356 - Sequence 312380 from Patent EP1572962.
JD198060 - Sequence 179084 from Patent EP1572962.
JD246863 - Sequence 227887 from Patent EP1572962.
JD238039 - Sequence 219063 from Patent EP1572962.
JD291738 - Sequence 272762 from Patent EP1572962.
JD533697 - Sequence 514721 from Patent EP1572962.
JD373405 - Sequence 354429 from Patent EP1572962.
JD340651 - Sequence 321675 from Patent EP1572962.
JD242205 - Sequence 223229 from Patent EP1572962.
JD077347 - Sequence 58371 from Patent EP1572962.
JD503610 - Sequence 484634 from Patent EP1572962.
JD558921 - Sequence 539945 from Patent EP1572962.
JD443699 - Sequence 424723 from Patent EP1572962.
JD070889 - Sequence 51913 from Patent EP1572962.
JD535300 - Sequence 516324 from Patent EP1572962.
JD453741 - Sequence 434765 from Patent EP1572962.
JD132966 - Sequence 113990 from Patent EP1572962.
JD507808 - Sequence 488832 from Patent EP1572962.
JD065760 - Sequence 46784 from Patent EP1572962.
JD553911 - Sequence 534935 from Patent EP1572962.

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

Protein O00635 (Reactome details) participates in the following event(s):

R-HSA-877300 Interferon gamma signaling
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006355, O00635, RNF15, RORET, TRI38_HUMAN, uc003nfm.1, uc003nfm.2, uc003nfm.3, uc003nfm.4, uc003nfm.5, uc003nfm.6
UCSC ID: uc003nfm.6
RefSeq Accession: NM_006355
Protein: O00635 (aka TRI38_HUMAN or RN15_HUMAN)
CCDS: CCDS4568.1

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