Human Gene EBAG9 (uc003ynf.3) Description and Page Index
  Description: Homo sapiens estrogen receptor binding site associated, antigen, 9 (EBAG9), transcript variant 2, mRNA.
RefSeq Summary (NM_198120): This gene was identified as an estrogen-responsive gene. Regulation of transcription by estrogen is mediated by estrogen receptor, which binds to the estrogen-responsive element found in the 5'-flanking region of this gene. The encoded protein is a tumor-associated antigen that is expressed at high frequency in a variety of cancers. Alternate splicing results in multiple transcript variants. A pseudogene of this gene has been defined on chromosome 10. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chr8:110,551,929-110,577,391 Size: 25,463 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr8:110,563,054-110,576,788 Size: 13,735 Coding Exon Count: 6 

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 (chr8:110,551,929-110,577,391)mRNA (may differ from genome)Protein (213 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RCAS1_HUMAN
DESCRIPTION: RecName: Full=Receptor-binding cancer antigen expressed on SiSo cells; AltName: Full=Cancer-associated surface antigen RCAS1; AltName: Full=Estrogen receptor-binding fragment-associated gene 9 protein;
FUNCTION: May participate in suppression of cell proliferation and induces apoptotic cell death through activation of interleukin-1- beta converting enzyme (ICE)-like proteases.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type III membrane protein. Note=According to PubMed:10426319, it also exists as a soluble form which has the same biological activities. The existence of such soluble form is however uncertain.
TISSUE SPECIFICITY: Widely expressed. Expressed in ovary, testis, prostate, thymus, muscle and heart, but not in small intestine, colon, lymph nodes, or peripherical blood lymphocytes. The protein is not detected in any of the above organs.
INDUCTION: By estrogen.
DOMAIN: The coiled coil domain is necessary for the homodimerization.
MISCELLANEOUS: May serve as a prognostic marker for cancers such as adenocarcinomas of the lung and breast cancers. It is present and overexpressed in many patients suffering from breast carcinomas, its level of expression correlates with tumor grade, suggesting that it may be involved in cancer immune escape. According to PubMed:12672804, it is however not directly a tumor- associated antigen, but it rather modulates surface expression of tumor-associated O-linked glycan Tn when it is overexpressed, suggesting that it contributes indirectly to the antigenicity of tumor cells.
CAUTION: It was initially reported to be a ligand for some putative receptor present on T-, B-, natural killer (NK) cells and various human cell lines. However, PubMed:12672804 showed that it does not bind any receptor.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/EBAG9ID40393ch8q23.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EBAG9
CDC HuGE Published Literature: EBAG9
Positive Disease Associations: early-stage breast cancers
Related Studies:
  1. early-stage breast cancers
    Tsuneizumi M et al. 2001, Overrepresentation of the EBAG9 gene at 8q23 associated with early-stage breast cancers., Clinical cancer research. 2001 Nov;7(11):3526-32. [PubMed 11705872]

-  MalaCards Disease Associations
  MalaCards Gene Search: EBAG9
Diseases sorted by gene-association score: placental abruption (9), bile duct carcinoma (6), paget disease, extramammary (5), endometrial cancer (4)

-  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: 9.96 RPKM in Thyroid
Total median expression: 294.68 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 -121.00235-0.515 Picture PostScript Text
3' UTR -119.41603-0.198 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
IPR017025 - Cancer-assoc_antigen_RCAS1

ModBase Predicted Comparative 3D Structure on O00559
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016505 peptidase activator activity involved in apoptotic process

Biological Process:
GO:0001558 regulation of cell growth
GO:0006915 apoptotic process

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030141 secretory granule


-  Descriptions from all associated GenBank mRNAs
  AK290651 - Homo sapiens cDNA FLJ75919 complete cds, highly similar to Homo sapiens estrogen receptor binding site associated, antigen, 9 (EBAG9), transcript variant 1, mRNA.
BC017729 - Homo sapiens estrogen receptor binding site associated, antigen, 9, mRNA (cDNA clone MGC:21461 IMAGE:3453385), complete cds.
BC005249 - Homo sapiens estrogen receptor binding site associated, antigen, 9, mRNA (cDNA clone MGC:12283 IMAGE:3930583), complete cds.
BC022506 - Homo sapiens estrogen receptor binding site associated, antigen, 9, mRNA (cDNA clone MGC:26497 IMAGE:4815654), complete cds.
AK308950 - Homo sapiens cDNA, FLJ98991.
AB007619 - Homo sapiens mRNA for EBAG9, complete cds.
AF006265 - Homo sapiens cancer associated surface antigen (RCAS1) mRNA, complete cds.
AY515724 - Homo sapiens receptor-binding cancer antigen expressed on SiSo cells (RCAS1) mRNA, partial cds.
DQ894642 - Synthetic construct Homo sapiens clone IMAGE:100009102; FLH177171.01L; RZPDo839D12123D estrogen receptor binding site associated, antigen, 9 (EBAG9) gene, encodes complete protein.
DQ891464 - Synthetic construct clone IMAGE:100004094; FLH177174.01X; RZPDo839D12124D estrogen receptor binding site associated, antigen, 9 (EBAG9) gene, encodes complete protein.
CU675065 - Synthetic construct Homo sapiens gateway clone IMAGE:100020167 5' read EBAG9 mRNA.
CU676036 - Synthetic construct Homo sapiens gateway clone IMAGE:100016780 5' read EBAG9 mRNA.
KJ892701 - Synthetic construct Homo sapiens clone ccsbBroadEn_02095 EBAG9 gene, encodes complete protein.
KJ897975 - Synthetic construct Homo sapiens clone ccsbBroadEn_07369 EBAG9 gene, encodes complete protein.
AY653072 - Homo sapiens placenta derived apoptotic factor (PDAF) mRNA, complete cds.
CR456984 - Homo sapiens full open reading frame cDNA clone RZPDo834D035D for gene EBAG9, estrogen receptor binding site associated, antigen, 9; complete cds, incl. stopcodon.
JD328675 - Sequence 309699 from Patent EP1572962.
JD251192 - Sequence 232216 from Patent EP1572962.

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

Protein O00559 (Reactome details) participates in the following event(s):

R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-8939211 ESR-mediated signaling
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_198120, NP_936056, O00559, Q6IB20, Q9BS76, RCAS1, RCAS1_HUMAN
UCSC ID: uc003ynf.3
RefSeq Accession: NM_198120
Protein: O00559 (aka RCAS1_HUMAN or RCAS_HUMAN)
CCDS: CCDS6313.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198120.1
exon count: 7CDS single in 3' UTR: no RNA size: 1494
ORF size: 642CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1335.00frame shift in genome: no % Coverage: 99.06
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.