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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ST13P4 Gene

pseudogene   GIFtS: 34
GCID: GC13P050747

Suppression Of Tumorigenicity 13 (Colon Carcinoma) (Hsp7...

(Previous names: family with sequence similarity 10, member A4 pseudogene)
(Previous symbol: FAM10A4)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 10

Aliases
Suppression Of Tumorigenicity 13 (Colon Carcinoma) (Hsp70 Interacting
Protein) Pseudogene 41 2
FAM10A41 2 3
Family With Sequence Similarity 10, Member A4 Pseudogene1
FAM10A4P2
Suppression Of Tumorigenicity 13 Pseudogene 43

External Ids:    HGNC: 184871   Entrez Gene: 1451652   Ensembl: ENSG000002321507   UniProtKB: Q8IZP23   
ORGUL members:    fRNAdb10:FR162557 FR063253 FR314868 FR023517 FR001451      
H-InvDB12:HIT000247600 HIT000247610 HIT000247591 HIT000247585    
NCBI13:AJ412058 AJ412019 AJ411992 AJ412000 AJ412056 see all 55    
NONCODE14:n373557 n373560 n382042 n386051 n386054 see all 31      
RNAdb15:LIT1875 LIT1936 LIT1973 LIT1965 LIT1884 see all 58    

Export aliases for ST13P4 gene to outside databases

Previous GC identifer: GC13P031541


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ST13P4 Gene: 
ST13P4 (suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) pseudogene 4) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with ST13P4 include b-cell chronic lymphocytic leukemia, and multiple myeloma.

fRNAdb sequence ontologies for ST13P4 - the ORGUL cluster for this gene includes several descriptions:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
mature_transcript - A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.

View fRNAdb secondary structures for ST13P4

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.2  NT_024524.14  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ST13P4
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ST13P4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q14.3   Ensembl cytogenetic band:  13q14.2   HGNC cytogenetic band: 13q14

ST13P4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ST13P4 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P050747:  view genomic region     (about GC identifiers)

Start:
50,746,154 bp from pter      End:
50,747,752 bp from pter
Size:
1,599 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for ST13P4

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ST134_HUMAN, Q8IZP2 (See protein sequence)
Recommended Name: Putative protein FAM10A4  
Size: 240 amino acids; 27407 Da
Subcellular location: Cytoplasm (Probable)
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for ST13P4: NX_Q8IZP2

ST13P4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--

ST13P4 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
4 InterPro protein domains:
 IPR011990 TPR-like_helical
 IPR013105 TPR_2
 IPR013026 TPR-contain_dom
 IPR019734 TPR_repeat

Graphical View of Domain Structure for InterPro Entry Q8IZP2

ProtoNet protein and cluster: Q8IZP2

UniProtKB/Swiss-Prot: ST134_HUMAN, Q8IZP2
Similarity: Belongs to the FAM10 family
Similarity: Contains 3 TPR repeats


ST13P4 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Phenotypes:
     1 GenomeRNAi human phenotype for ST13P4:
 Decreased Wnt reporter activit 

Animal Models:
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ST13P4

1 Interacting protein for ST13P4 (Q8IZP22, 3) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
MAP3K3Q997592, 3MINT-48499 I2D: score=2 
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for ST13P4 (ST134)

Search CenterWatch for drugs/clinical trials and news about ST13P4

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
5/38 fRNAdb Secondary structures (see all 38):


REFSEQ mRNAs for ST13P4 gene: 
NM_153290.1  

Unigene Cluster for ST13P4:

Suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) pseudogene 4
Hs.511834  [show with all ESTs]
Unigene Representative Sequence: AF539468
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000495613(uc001vej.3)
miRNA
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Additional mRNA sequence: 

AF539468.1 NR_002183.1 

12 DOTS entries:

DT.100000399  DT.100892017  DT.456282  DT.120774954  DT.99998054  DT.100034556  DT.100892030  DT.100892026 
DT.100678206  DT.100757889  DT.100892025  DT.100892042 

7 AceView cDNA sequences:

NM_153290 AF539468 BF089934 AI929839 AW604071 CD579790 BX407161 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

ST13P4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
ST13P4 Expression
About this image


SOURCE GeneReport for Unigene cluster: Hs.511834

UniProtKB/Swiss-Prot: ST134_HUMAN, Q8IZP2
Tissue specificity: Highly expressed in bone marrow and weakly in placenta, pancreas, heart and HeLa cell line

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ST13P4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for ST13P4 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
tropical clawed frog
(Xenopus tropicalis)
Amphibia Str.21232 Transcribed sequence with weak similarity to protein more 77.91(n)    AL775197.2 


ENSEMBL Gene Tree for ST13P4 (if available)
TreeFam Gene Tree for ST13P4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for ST13P4 gene
2 SIMAP similar genes for ST13P4 using alignment to 1 protein entry:     ST134_HUMAN:
ST13    ST13P5

ST13P4 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/63 SNPs in ST13P4 are shown (see all 63)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 13 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0236444
----see VAR_0236442 S L mis40--------
rs773461481,2
C--50744245(+) ATACAA/GTGTGT 1 -- us2k12Minor allele frequency- G:0.03WA 120
rs740765621,2
C--50744605(+) CAGCAC/GTTGTC 1 -- us2k13Minor allele frequency- G:0.03WA EA 240
rs7905341,2
C,F,O,A,H--50744791(+) AAATAC/GTGTAA 1 -- us2k117Minor allele frequency- N:0.00NS EA NA WA CSA 1004
rs1889730271,2
--50744890(+) CTAAGA/CAAGGA 1 -- us2k10--------
rs1817275541,2
--50745016(+) CATAGA/GAGTCA 1 -- us2k10--------
rs1875063091,2
--50745022(+) AGTCAC/TAAAAG 1 -- us2k10--------
rs20666111,2
C,F,H--50745062(+) GAGCCG/AACATG 1 -- us2k14Minor allele frequency- A:0.00NS EA 418
rs20666121,2
C,F,A,H--50745395(+) TAATCG/AGCCGG 1 -- us2k117Minor allele frequency- A:0.37NS EA NA WA 2120
rs1906515001,2
--50745399(+) CGGCCC/GGGCGC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for ST13P4 (50746154 - 50747752 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for ST13P4:    About this table     
Variant IDTypeSubtypePubMed ID
nsv900076CNV Loss21882294
nsv832608CNV Gain17160897

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM information: 605766    
9 diseases for ST13P4:    About MalaCards
b-cell chronic lymphocytic leukemia    multiple myeloma    chronic lymphocytic leukemia    celiac disease
myeloma    t-cell leukemia    prostate cancer    leukemia
prostatitis


ST13P4 for disorders           About GeneDecksing

Genetic Association Database (GAD): ST13P4

Export disorders for ST13P4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for ST13P4 gene, integrated from 9 sources (see all 15):
(articles sorted by number of sources associating them with ST13P4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Multiple common variants for celiac disease influenci ng immune gene expression. (PubMed id 20190752)1, 4 Dubois P.C....van Heel D.A. (2010)
  2. Characterization of FAM10A4, a member of the ST13 tumor suppressor gene family that maps to the 13q14.3 region associated with B-Cell leukemia, multiple myeloma, and prostate cancer. (PubMed id 12079276)1, 2 Sossey-Alaoui K.... Cowell J.K. (2002)
  3. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
  4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
  5. Genome-wide meta-analysis identifies novel multiple sc lerosis susceptibility loci. (PubMed id 22190364)4 Patsopoulos N.A....de Bakker P.I. (2011)
  6. Genetic risk and a primary role for cell-mediated immu ne mechanisms in multiple sclerosis. (PubMed id 21833088)4  ....Compston A. (2011)
  7. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1 Olsen J.V....Mann M. (2006)
  8. Phosphoproteomic analysis of the human pituitary. (PubMed id 16807684)1 Beranova-Giorgianni S.... Giorgianni F. (2006)
  9. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)2 Dunham A.... Ross M.T. (2004)
  10. RFP2, c13ORF1, and FAM10A4 are the most likely tumor suppressor gene candidates for B-cell chronic lymphocytic leukemia. (PubMed id 14499696)9 van Everdink W.J.... Buys C.H. (2003)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 145165 HGNC: 18487 AceView: FAM10A4 Ensembl:ENSG00000232150 euGenes: HUgn145165
ECgene: ST13P4 H-InvDB: ST13P4

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for ST13P4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for ST13P4 gene:
Search GeneIP for patents involving ST13P4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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