Human Gene SART1 (uc001ogl.3) Description and Page Index
  Description: Homo sapiens squamous cell carcinoma antigen recognized by T cells (SART1), mRNA.
RefSeq Summary (NM_005146): This gene encodes two proteins, the SART1(800) protein expressed in the nucleus of the majority of proliferating cells, and the SART1(259) protein expressed in the cytosol of epithelial cancers. The SART1(259) protein is translated by the mechanism of -1 frameshifting during posttranscriptional regulation; its full-length sequence is not published yet. The two encoded proteins are thought to be involved in the regulation of proliferation. Both proteins have tumor-rejection antigens. The SART1(259) protein possesses tumor epitopes capable of inducing HLA-A2402-restricted cytotoxic T lymphocytes in cancer patients. This SART1(259) antigen may be useful in specific immunotherapy for cancer patients and may serve as a paradigmatic tool for the diagnosis and treatment of patients with atopy. The SART1(259) protein is found to be essential for the recruitment of the tri-snRNP to the pre-spliceosome in the spliceosome assembly pathway. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803614.130432.1, SRR1660807.226377.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000312397.10/ ENSP00000310448.5 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:65,729,160-65,747,607 Size: 18,448 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr11:65,729,252-65,746,501 Size: 17,250 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:65,729,160-65,747,607)mRNA (may differ from genome)Protein (800 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SNUT1_HUMAN
DESCRIPTION: RecName: Full=U4/U6.U5 tri-snRNP-associated protein 1; AltName: Full=SNU66 homolog; Short=hSnu66; AltName: Full=Squamous cell carcinoma antigen recognized by T-cells 1; Short=SART-1; Short=hSART-1; AltName: Full=U4/U6.U5 tri-snRNP-associated 110 kDa protein; AltName: Allergen=Hom s 1;
FUNCTION: May play a role in mRNA splicing. May also bind to DNA.
SUBUNIT: Identified in the spliceosome C complex. Part of a tri- snRNP complex.
INTERACTION: P63165:SUMO1; NbExp=2; IntAct=EBI-607761, EBI-80140; P55854:SUMO3; NbExp=2; IntAct=EBI-607761, EBI-474067;
SUBCELLULAR LOCATION: Nucleus. Note=Found in the nucleus of mitogen-activated peripheral blood mononuclear cells (PBMCs), tumor cells, or normal cell lines, but not in normal tissues except testis and fetal liver or in unstimulated PBMCs, suggesting preferential expression in proliferating cells.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Sumoylated with SUMO2.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
ALLERGEN: Causes an allergic reaction in human. Binds to IgE from atopic dermatitis (AD) patients. Identified as an IgE autoantigen in atopic dermatitis (AD) patients with severe skin manifestations.
SIMILARITY: Belongs to the SNU66/SART1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SART1
CDC HuGE Published Literature: SART1

-  MalaCards Disease Associations
  MalaCards Gene Search: SART1
Diseases sorted by gene-association score: squamous cell carcinoma (14), atopy (8), esophagus squamous cell carcinoma (6)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.37 RPKM in Spleen
Total median expression: 990.15 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 -42.8092-0.465 Picture PostScript Text
3' UTR -433.251106-0.392 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
IPR005011 - SART_1

Pfam Domains:
PF03343 - SART-1 family

ModBase Predicted Comparative 3D Structure on O43290
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 BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0000481 maturation of 5S rRNA
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0045292 mRNA cis splicing, via spliceosome
GO:0045585 positive regulation of cytotoxic T cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0016607 nuclear speck
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK309104 - Homo sapiens cDNA, FLJ99145.
AK297589 - Homo sapiens cDNA FLJ51897 complete cds, highly similar to U4/U6.U5 tri-snRNP-associated protein 1.
AK223016 - Homo sapiens mRNA for squamous cell carcinoma antigen recognized by T cells 1 variant, clone: HSI14471.
AK293200 - Homo sapiens cDNA FLJ53820 complete cds, highly similar to U4/U6.U5 tri-snRNP-associated protein 1.
AK298184 - Homo sapiens cDNA FLJ51016 complete cds, highly similar to U4/U6.U5 tri-snRNP-associated protein 1.
BC001058 - Homo sapiens squamous cell carcinoma antigen recognized by T cells, mRNA (cDNA clone MGC:2038 IMAGE:3504745), complete cds.
AB006198 - Homo sapiens mRNA for SART-1, complete cds.
AF353625 - Homo sapiens U4/U6.U5 tri-snRNP-associated 110 kDa protein mRNA, complete cds.
DQ891694 - Synthetic construct clone IMAGE:100004324; FLH180820.01X; RZPDo839G05134D squamous cell carcinoma antigen recognised by T cells (SART1) gene, encodes complete protein.
EU176645 - Synthetic construct Homo sapiens clone IMAGE:100011443; FLH180819.01L; RZPDo839B10254D squamous cell carcinoma antigen recognized by T cells (SART1) gene, encodes complete protein.
BT006637 - Homo sapiens squamous cell carcinoma antigen recognised by T cells mRNA, complete cds.
Y14314 - Homo sapiens mRNA for IgE autoantigen.
BX648500 - Homo sapiens mRNA; cDNA DKFZp686H1978 (from clone DKFZp686H1978).
BC018607 - Homo sapiens squamous cell carcinoma antigen recognized by T cells, mRNA (cDNA clone IMAGE:4347524).

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein O43290 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDN1, NM_005146, NP_005137, O43290, Q53GB5, SNUT1_HUMAN
UCSC ID: uc001ogl.3
RefSeq Accession: NM_005146
Protein: O43290 (aka SNUT1_HUMAN)
CCDS: CCDS31611.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005146.4
exon count: 20CDS single in 3' UTR: no RNA size: 3601
ORF size: 2403CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4615.00frame 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.