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SPATA24 Gene

protein-coding   GIFtS: 42
GCID: GC05M138732

Spermatogenesis Associated 24

  See related disease
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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Aliases
Spermatogenesis Associated 241 2
Coiled-Coil Domain Containing 1611 2
Testis Protein T6441 Homolog2 3
CCDC1612
T64412
Spermatogenesis-Associated Protein 242

External Ids:    HGNC: 273221   Entrez Gene: 2020512   Ensembl: ENSG000001704697   UniProtKB: Q86W543   

Export aliases for SPATA24 gene to outside databases

Previous GC identifers: GC05M138762 GC05M133922


(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 SPATA24 Gene:
SPATA24 (spermatogenesis associated 24) is a protein-coding gene. Diseases associated with SPATA24 include myelodysplastic syndromes. GO annotations related to this gene include protein homodimerization activity.

UniProtKB/Swiss-Prot: SPA24_HUMAN, Q86W54
Function: Binds DNA with high affinity but does not bind to TATA boxes. Synergises with GMNN and TBP in activation
of TATA box-containing promoters and with GMNN and TBPL1 in activation of the NF1 TATA-less promoter. May play a
role in cytoplasm movement and removal during spermiogenesis (By similarity)




(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_000005.10  NT_034772.7  NC_018916.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SPATA24
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SPATA24

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPATA24


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

Entrez Gene cytogenetic band: 5q31.2   Ensembl cytogenetic band:  5q31.2   HGNC cytogenetic band: 5q31.2

SPATA24 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA24 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M138732:  view genomic region     (about GC identifiers)

Start:
138,732,252 bp from pter      End:
138,739,777 bp from pter
Size:
7,526 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: SPA24_HUMAN, Q86W54 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 24  
Size: 205 amino acids; 23587 Da
Subunit: Homodimer. Interacts with CBX3, CBX5, GMNN, GTF2B, TBPL1 and the polycomb proteins PHCF2, RNF2 and SCMH1
but not with CBX1 or PCGF2 (By similarity)
Alternative splicing: 2 isoforms:  Q86W54-1   Q86W54-2   

Explore the universe of human proteins at neXtProt for SPATA24: NX_Q86W54

Explore proteomics data for SPATA24 at MOPED


See SPATA24 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_919272.1  
ENSEMBL proteins: 
 ENSP00000302917   ENSP00000414920   ENSP00000426748   ENSP00000423424   ENSP00000424248  
 ENSP00000400524   ENSP00000423226  

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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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ProtoNet protein and cluster: Q86W54

UniProtKB/Swiss-Prot: SPA24_HUMAN, Q86W54
Similarity: Belongs to the SPATA24 family


(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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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SPA24_HUMAN, Q86W54
Function: Binds DNA with high affinity but does not bind to TATA boxes. Synergises with GMNN and TBP in activation
of TATA box-containing promoters and with GMNN and TBPL1 in activation of the NF1 TATA-less promoter. May play a
role in cytoplasm movement and removal during spermiogenesis (By similarity)

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0005515protein binding ----
GO:0042803protein homodimerization activity IEA--
     
SPATA24 for ontologies           About GeneDecksing


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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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Subcellular locations from UniProtKB/Swiss-Prot
SPA24_HUMAN, Q86W54: Cytoplasm. Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Associated with chromatin (By
similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol3
extracellular1

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA--
GO:0005654nucleoplasm IEA--
GO:0005730nucleolus IEA--
GO:0005737cytoplasm IDA--

SPATA24 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 SPATA24
Interactions:

    Search GeneGlobe Interaction Network for SPATA24

STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

Selected Interacting proteins for SPATA24 (Q86W543 ENSP000004149204) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
InteractantInteraction Details
GeneCardExternal ID(s)
RNF2Q994963, ENSP000003564804I2D: score=1 STRING: ENSP00000356480
TBPP202263, ENSP000002303544I2D: score=1 STRING: ENSP00000230354
TBPL1P623803, ENSP000002372644I2D: score=1 STRING: ENSP00000237264
GMNNO754963, ENSP000002300564I2D: score=1 STRING: ENSP00000230056
GTF2BQ004033, ENSP000003595314I2D: score=1 STRING: ENSP00000359531
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Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated IEA--
GO:0007275multicellular organismal development IEA--
GO:0007283spermatogenesis IEA--
GO:0030154cell differentiation IEA--

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(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for SPATA24 (SPA24)



(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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REFSEQ mRNAs for SPATA24 gene: 
NM_194296.1  

Unigene Cluster for SPATA24:

Spermatogenesis associated 24
Hs.373612  [show with all ESTs]
Unigene Representative Sequence: BQ067292
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000302091(uc003lek.2 uc003lel.4) ENST00000450845 ENST00000512761
ENST00000514983 ENST00000509959 ENST00000451821(uc003lem.2) ENST00000507779

miRNA
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Additional mRNA sequence: 

AK098740.1 BC040037.1 BC050563.1 

7 DOTS entries:

DT.105704  DT.91692000  DT.206319  DT.120823307  DT.40120641  DT.75116236  DT.426022 

Selected AceView cDNA sequences (see all 30):

BX089584 BC050563 CD674203 AW663380 AW015836 AA999881 AK098740 AI989587 
BE743887 AI671015 AW082238 BI261744 AI650574 BE044369 AA758652 BM746879 
BM785501 BQ426104 BQ067292 AI692888 AA922602 BC040037 BP872735 AI200935 

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for SPATA24    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c
SP1:                                -                           
SP2:                                -           -               
SP3:                                                            


ECgene alternative splicing isoforms for SPATA24

(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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SPATA24 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCAAAACCAA
SPATA24 Expression
About this image

SPATA24 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SPATA24 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.373612
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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 SPATA24 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Spata241 , 5 spermatogenesis associated 241, 5 91.22(n)1
90.73(a)1
  18 (19.20 cM)5
712421  NM_029485.21  NP_083761.11 
 356566905 


ENSEMBL Gene Tree for SPATA24 (if available)
TreeFam Gene Tree for SPATA24 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 SPATA24 (see all 153)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1893399601,2
C--138733021(+) GGATTG/TTTGTC 1 -- int10--------
rs1420351121,2
--138733077(+) CAGGAA/GAAGGT 1 -- int10--------
rs1930230011,2
--138733092(+) GGAGAC/GAAGTG 1 -- int10--------
rs68659701,2
C,H--138733108(+) GCCTGC/ACCAAA 1 -- int19Minor allele frequency- A:0.00NA WA CSA EA 253
rs1856570681,2
--138733132(+) ATGGCA/GCCTGC 1 -- int10--------
rs2015935681,2
--138733238(+) TGCTT-/TCTCTCT 1 -- int10--------
rs572660901,2
C--138733243(+) TCTCTC/-TTTTT 1 -- int11Minor allele frequency- -:0.50CSA 2
rs68875551,2
C,F,A,H--138733244(+) tctctC/Tttttt 1 -- int1 trp316Minor allele frequency- T:0.40NS EA NA CSA 2222
rs1901831931,2
--138733386(+) TTACAG/TGCGCC 1 -- int10--------
rs1817150921,2
--138733514(+) GCTGGG/TATTAC 1 -- int10--------

HapMap Linkage Disequilibrium report for SPATA24 (138732252 - 138739777 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for SPATA24:    About this table    
Variant IDTypeSubtypePubMed ID
esv2730828CNV Deletion23290073
esv1917494CNV Deletion18987734
esv2568140CNV Deletion19546169
esv2669016CNV Deletion23128226
nsv328925CNV Loss16902084
nsv519808CNV Loss19592680

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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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1 disease for SPATA24:    
About MalaCards
myelodysplastic syndromes


SPATA24 for disorders           About GeneDecksing

Human Genome Epidemiology (HuGE) Navigator: SPATA24 (0 documents)

Export disorders for SPATA24 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)
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PubMed articles for SPATA24 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with SPATA24)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Cloning and characterization of a novel spermiogenesis-related gene, T6441, in rat testis. (PubMed id 16146721)1, 3 Song X.X....Liu Y.X. (Front. Biosci. 2006)
  2. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
  3. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
  4. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. (PubMed id 21565611)1 Sang L.... Jackson P.K. (Cell 2011)
  5. Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis. (PubMed id 19240791)1 Graubert T.A....Walter M.J. (PLoS ONE 2009)
  6. TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation. (PubMed id 19515240)2 Pitulescu M.E.... Kessel M. (BMC Biochem. 2009)
  7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  9. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
  10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

(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: 202051 HGNC: 27322 AceView: LOC202051 Ensembl:ENSG00000170469 euGenes: HUgn202051
ECgene: SPATA24 H-InvDB: SPATA24

(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 SPATA24 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 SPATA24 gene:
Search GeneIP for patents involving SPATA24

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Custom PCR Arrays for SPATA24 Search Chromatin IP Primers for SPATA24
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 Search Tocris compounds for SPATA24 (SPA24)
 Browse Sino Biological Proteins
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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 See all of Abcam's Antibodies, Kits and Proteins for SPATA24
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPATA24
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPATA24
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 LSBio Antibodies in human, mouse, rat for SPATA24
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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