Human Gene PASD1 (uc004fev.4) Description and Page Index
  Description: Homo sapiens PAS domain containing 1 (PASD1), mRNA.
RefSeq Summary (NM_173493): This gene encodes a protein that is thought to function as a transcription factor. The protein is a cancer-associated antigen that can stimulate autologous T-cell responses, and it is therefore considered to be a potential immunotherapeutic target for the treatment of various hematopoietic malignancies, including diffuse large B-cell lymphoma. [provided by RefSeq, May 2010]. ##Evidence-Data-START## Transcript exon combination :: AK097552.1, BC040301.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2148093 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000370357.5/ ENSP00000359382.4 RefSeq Select criteria :: based on expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chrX:150,732,007-150,845,211 Size: 113,205 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chrX:150,770,026-150,844,615 Size: 74,590 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:150,732,007-150,845,211)mRNA (may differ from genome)Protein (773 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PASD1_HUMAN
DESCRIPTION: RecName: Full=PAS domain-containing protein 1; AltName: Full=Cancer/testis antigen 63; Short=CT63; AltName: Full=OX-TES-1;
FUNCTION: May function as a transcription factor.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Testis-specific. Found in histologically normal tissues from patients with uterus, lung and small intestine cancers. Widespread expression seen in solid tumors and diffuse large B-cell lymphoma (DLBCL)-derived cell lines. Isoform 2 is expressed in all DLBCL-derived cell lines, while isoform 1 is preferentially expressed in cell lines derived from non-germinal center DLBCL.
SIMILARITY: Contains 1 PAS (PER-ARNT-SIM) domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: PASD1
Diseases sorted by gene-association score: diffuse large b-cell lymphoma (16)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 13.66 RPKM in Testis
Total median expression: 13.66 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 -106.10332-0.320 Picture PostScript Text
3' UTR -192.06596-0.322 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
IPR000014 - PAS

Pfam Domains:
PF13426 - PAS domain

SCOP Domains:
55785 - PYP-like sensor domain (PAS domain)

ModBase Predicted Comparative 3D Structure on Q8IV76
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001223 transcription coactivator binding

Biological Process:
GO:0042754 negative regulation of circadian rhythm
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process

Cellular Component:
GO:0005634 nucleus
GO:0016607 nuclear speck
GO:1990512 Cry-Per complex


-  Descriptions from all associated GenBank mRNAs
  AK097552 - Homo sapiens cDNA FLJ40233 fis, clone TESTI2023085, weakly similar to CIRCADIAN LOCOMOTER OUTPUT CYCLES KAPUT PROTEIN.
BC040301 - Homo sapiens PAS domain containing 1, mRNA (cDNA clone MGC:42664 IMAGE:4826573), complete cds.
AY270020 - Homo sapiens PAS domain containing protein 1 (PASD1) mRNA, complete cds.
JD251608 - Sequence 232632 from Patent EP1572962.
JD408618 - Sequence 389642 from Patent EP1572962.
JD486313 - Sequence 467337 from Patent EP1572962.
JD519713 - Sequence 500737 from Patent EP1572962.
AB463159 - Synthetic construct DNA, clone: pF1KB8584, Homo sapiens PASD1 gene for PAS domain containing 1, without stop codon, in Flexi system.
AM393031 - Synthetic construct Homo sapiens clone IMAGE:100002018 for hypothetical protein (PASD1 gene).
KJ900184 - Synthetic construct Homo sapiens clone ccsbBroadEn_09578 PASD1 gene, encodes complete protein.
AY623425 - Homo sapiens hypothetical protein LOC139135 mRNA, partial cds.
JD094242 - Sequence 75266 from Patent EP1572962.
JD166741 - Sequence 147765 from Patent EP1572962.
JD481779 - Sequence 462803 from Patent EP1572962.
JD167367 - Sequence 148391 from Patent EP1572962.
JD496318 - Sequence 477342 from Patent EP1572962.
JD562465 - Sequence 543489 from Patent EP1572962.
JD314020 - Sequence 295044 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_173493, NP_775764, PASD1_HUMAN, Q3MNE0, Q69HD7, Q8IV76, Q8N7X9
UCSC ID: uc004fev.4
RefSeq Accession: NM_173493
Protein: Q8IV76 (aka PASD1_HUMAN)
CCDS: CCDS35431.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173493.2
exon count: 16CDS single in 3' UTR: no RNA size: 3250
ORF size: 2322CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3237.00frame 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.