Human Gene SKIC3 (ENST00000358746.7_11) from GENCODE V47lift37
  Description: tetratricopeptide repeat domain 37 (from RefSeq NM_014639.4)
Gencode Transcript: ENST00000358746.7_11
Gencode Gene: ENSG00000198677.13_16
Transcript (Including UTRs)
   Position: hg19 chr5:94,799,598-94,890,681 Size: 91,084 Total Exon Count: 43 Strand: -
Coding Region
   Position: hg19 chr5:94,800,311-94,882,854 Size: 82,544 Coding Exon Count: 40 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:94,799,598-94,890,681)mRNA (may differ from genome)Protein (1564 aa)
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-  Comments and Description Text from UniProtKB
  ID: TTC37_HUMAN
DESCRIPTION: RecName: Full=Tetratricopeptide repeat protein 37; Short=TPR repeat protein 37; AltName: Full=SKI3 homolog; Short=Ski3; AltName: Full=Tricho-hepatic-enteric syndrome protein; Short=Thespin;
FUNCTION: Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).
SUBUNIT: Component of the SKI complex which consists of WDR61, SKIV2L and TTC37. Interacts with PAF1.
INTERACTION: Q8N7H5:PAF1; NbExp=2; IntAct=EBI-6083436, EBI-2607770;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Widely expressed with the highest levels observed in vascular tissues, lymph node, pituitary, lung and intestine. Not expressed in the liver.
DISEASE: Defects in TTC37 are the cause of trichohepatoenteric syndrome type 1 (THES1) [MIM:222470]. A syndrome characterized by intrauterine growth retardation, severe diarrhea in infancy requiring total parenteral nutrition, facial dysmorphism, immunodeficiency, and hair abnormalities, mostly trichorrhexis nodosa. Hepatic involvement contributes to the poor prognosis of affected patients.
SIMILARITY: Contains 20 TPR repeats.
SEQUENCE CAUTION: Sequence=BAA20827.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.74 RPKM in Brain - Cerebellum
Total median expression: 717.77 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 -53.40269-0.199 Picture PostScript Text
3' UTR -121.50713-0.170 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
IPR006597 - Sel1-like
IPR001440 - TPR-1
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF08238 - Sel1 repeat
PF12862 - Anaphase-promoting complex subunit 5
PF13174 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat
PF13432 - Tetratricopeptide repeat

SCOP Domains:
48371 - ARM repeat
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
48613 - Heme oxygenase-like
101148 - Plant invertase/pectin methylesterase inhibitor
47986 - DEATH domain
144059 - ImpE-like

ModBase Predicted Comparative 3D Structure on Q6PGP7
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-  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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035327 transcriptionally active chromatin
GO:0055087 Ski complex


-  Descriptions from all associated GenBank mRNAs
  BC015163 - Homo sapiens tetratricopeptide repeat domain 37, mRNA (cDNA clone IMAGE:3889120), partial cds.
AB002370 - Homo sapiens mRNA for KIAA0372 gene.
JD454359 - Sequence 435383 from Patent EP1572962.
JD302449 - Sequence 283473 from Patent EP1572962.
BC056893 - Homo sapiens tetratricopeptide repeat domain 37, mRNA (cDNA clone MGC:65037 IMAGE:6164578), complete cds.
JD327950 - Sequence 308974 from Patent EP1572962.
JD096984 - Sequence 78008 from Patent EP1572962.
AB383863 - Synthetic construct DNA, clone: pF1KSDA0372, Homo sapiens KIAA0372 gene for KIAA0372 protein, complete cds, without stop codon, in Flexi system.
AK307531 - Homo sapiens cDNA, FLJ97479.
BC030966 - Homo sapiens tetratricopeptide repeat domain 37, mRNA (cDNA clone IMAGE:4108519), **** WARNING: chimeric clone ****.
BC009767 - Homo sapiens KIAA0372, mRNA (cDNA clone IMAGE:4274942), with apparent retained intron.
JD297057 - Sequence 278081 from Patent EP1572962.
JD503542 - Sequence 484566 from Patent EP1572962.
JD314077 - Sequence 295101 from Patent EP1572962.
JD418268 - Sequence 399292 from Patent EP1572962.
JD045019 - Sequence 26043 from Patent EP1572962.

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

Protein Q6PGP7 (Reactome details) participates in the following event(s):

R-HSA-430028 Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion
R-HSA-429958 mRNA decay by 3' to 5' exoribonuclease
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000358746.1, ENST00000358746.2, ENST00000358746.3, ENST00000358746.4, ENST00000358746.5, ENST00000358746.6, KIAA0372 , NM_014639, O15077, Q6PGP7, Q6PJI3, SKI3_HUMAN, SKIC3 , TTC37 , uc318asi.1, uc318asi.2
UCSC ID: ENST00000358746.7_11
RefSeq Accession: NM_014639.4
Protein: Q6PGP7 (aka TTC37_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SKIC3:
sd-thes (Trichohepatoenteric Syndrome)

-  Gene Model Information
  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.