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TSPY26P Gene

pseudogene   GIFtS: 33
GCID: GC20M030777

Testis Specific Protein, Y-Linked 26, Pseudogene

(Previous names: TSPY-like 3, TSPY-like 3 (pseudogene))
(Previous symbol: TSPYL3)
  Search for TSPY26P
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Testis Specific Protein, Y-Linked 26, Pseudogene1 2     bA392M18.12
TSPYL31 2 3     Testis-Specific Y-Encoded Protein 26 Pseudogene3
TSPY-Like 31     TSPY-Like Protein 33
TSPY-Like 3 (Pseudogene)1     

External Ids:    HGNC: 162561   Entrez Gene: 1288542   Ensembl: ENSG000002352177   UniProtKB: Q9H4893   
ORGUL members:         

Export aliases for TSPY26P gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TSPY26P Gene:
TSPY26P (testis specific protein, Y-linked 26, pseudogene) is a pseudogene, and is affiliated with the lncRNA class.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000020.11  NC_018931.2  NT_011362.11  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TSPY26P
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TSPY26P


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

Entrez Gene cytogenetic band: 20q11.21   Ensembl cytogenetic band:  20q11.21   HGNC cytogenetic band: 20q11.21

TSPY26P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TSPY26P gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M030777:  view genomic region     (about GC identifiers)

Start:
30,774,280 bp from pter      End:
30,778,330 bp from pter
Size:
4,051 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TSY26_HUMAN, Q9H489 (See protein sequence)
Recommended Name: Putative testis-specific Y-encoded-like protein 3  
Size: 355 amino acids; 39573 Da
Caution: Could be the product of a pseudogene
Secondary accessions: Q3MJ63 Q3MJ65

Explore the universe of human proteins at neXtProt for TSPY26P: NX_Q9H489


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR002164 NAP_family

Graphical View of Domain Structure for InterPro Entry Q9H489

ProtoNet protein and cluster: Q9H489

1 Blocks protein domain: IPB002164 Nucleosome assembly protein (NAP)

UniProtKB/Swiss-Prot: TSY26_HUMAN, Q9H489
Similarity: Belongs to the nucleosome assembly protein (NAP) family


TSPY26P 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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     1 GenomeRNAi human phenotype for TSPY26P:
 Synthetic lethal with Ras 

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

TSPY26P for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TSPY26P
Interactions:

    Search GeneGlobe Interaction Network for TSPY26P

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006334nucleosome assembly IEA--

TSPY26P for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for TSPY26P (TSY26)



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for TSPY26P:

Testis specific protein, Y-linked 26, pseudogene
Hs.647447  [show with all ESTs]
Unigene Representative Sequence: BC101558
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000565928(uc002wxm.1) ENST00000476365 ENST00000400643
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Additional mRNA sequence: 

BC101556.1 BC101558.1 NR_002781.1 

1 DOTS entry:

DT.70104967 

21 AceView cDNA sequences:

BQ432315 BQ772232 CA390378 AW261825 AI963739 AI826378 NM_178465 AI375984 
AI824863 BX647159 BE466406 BE504055 BX113258 AI971189 AI383654 AL935106 
BE253715 BE252372 AW196551 BE254800 AW294670 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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TSPY26P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TSPY26P Expression
About this image


TSPY26P expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Neurons
         GABAergic Amacrine Cells Inner Nuclear Layer
 
 Eye (Sensory Organs)
         GABAergic Amacrine Cells Inner Nuclear Layer
TSPY26P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.647447
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In Situ
Assay Products:
 

 
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(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)
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This gene was present in the common ancestor of human and mouse.

Orthologs for TSPY26P gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tspyl35 TSPY-like 3   --   2 (75.41 cM) 153222370 


ENSEMBL Gene Tree for TSPY26P (if available)
TreeFam Gene Tree for TSPY26P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TSPY26P gene
15 SIMAP similar genes for TSPY26P using alignment to 1 protein entry:     TSY26_HUMAN:
LOC728395    SET    TSPYL4    TSPYL    TSPYL1    TSPYL6
TSPY8    TSPY3    TSPY1    TSPY6P    TSPY2    TSPY10
TSPY4    TSPYL2    TSPYL5

TSPY26P 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for TSPY26P (see all 45)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1419164291,2
--27565072(+) GAGCAC/TGACCA 1 -- ds50010--------
rs1165587961,2
C--27565154(+) TGACTG/TGTGGG 1 -- ds50010--------
rs60612091,2
C,F--27565216(+) AAGATT/CATGGC 1 -- ds50016Minor allele frequency- C:0.34NA WA CSA 128
rs1918071991,2
--27565385(+) GAGTGA/CACAGA 1 -- ds50010--------
rs1147670451,2
F--27565441(+) CACCAT/CGGGCC 1 -- ds50011Minor allele frequency- C:0.05WA 118
rs1400534561,2
C--27565464(+) CGCCAA/CCCGTA 1 -- nc-transcript-variant0--------
rs1830592301,2
--27565491(+) TTATGA/TAGGCC 1 -- nc-transcript-variant0--------
rs60612101,2
C--27565659(+) GGCAAC/TCCTGT 1 -- nc-transcript-variant0--------
rs38139221,2,,4
C,F,H--27565847(-) CAACCC/ACTACT 1 -- nc-transcript-variant23Minor allele frequency- A:0.25EA NS NA CSA WA 4036
rs1160739831,2
C,F--27566022(+) GATGAT/CGAAGC 1 -- nc-transcript-variant1Minor allele frequency- C:0.03WA 118

HapMap Linkage Disequilibrium report for TSPY26P (30774280 - 30778330 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for TSPY26P:    About this table    
Variant IDTypeSubtypePubMed ID
nsv833954CNV Loss17160897
nsv833953CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(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)
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PubMed articles for TSPY26P gene integrated from 10 sources:
(articles sorted by number of sources associating them with TSPY26P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 128854 HGNC: 16256 AceView: TSPYL3 Ensembl:ENSG00000235217 euGenes: HUgn128854
ECgene: TSPY26P H-InvDB: TSPY26P

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for TSPY26P Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TSPY26P gene:
Search GeneIP for patents involving TSPY26P

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



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes      Disease genes      TSPY26P gene at Home site.
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