Human Gene SPATA24 (ENST00000450845.7_10) from GENCODE V47lift37
  Description: spermatogenesis associated 24 (from RefSeq NM_194296.2)
Gencode Transcript: ENST00000450845.7_10
Gencode Gene: ENSG00000170469.11_20
Transcript (Including UTRs)
   Position: hg19 chr5:138,732,456-138,739,778 Size: 7,323 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr5:138,732,489-138,739,749 Size: 7,261 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:138,732,456-138,739,778)mRNA (may differ from genome)Protein (205 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPA24_HUMAN
DESCRIPTION: RecName: Full=Spermatogenesis-associated protein 24; AltName: Full=Testis protein T6441 homolog;
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).
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).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Associated with chromatin (By similarity).
SIMILARITY: Belongs to the SPATA24 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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: 74.16 RPKM in Testis
Total median expression: 153.07 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 -4.3029-0.148 Picture PostScript Text
3' UTR -6.4033-0.194 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
  Pfam Domains:
PF15175 - Spermatogenesis-associated protein 24

SCOP Domains:
111474 - Coronavirus S2 glycoprotein

ModBase Predicted Comparative 3D Structure on Q86W54
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK098740 - Homo sapiens cDNA FLJ25874 fis, clone CBR02446.
LF211007 - JP 2014500723-A/18510: Polycomb-Associated Non-Coding RNAs.
BC040037 - Homo sapiens, Similar to RIKEN cDNA 5133400G04 gene, clone IMAGE:6155722, mRNA.
JD476129 - Sequence 457153 from Patent EP1572962.
LF343167 - JP 2014500723-A/150670: Polycomb-Associated Non-Coding RNAs.
LF343168 - JP 2014500723-A/150671: Polycomb-Associated Non-Coding RNAs.
BC050563 - Homo sapiens hypothetical protein LOC202051, mRNA (cDNA clone MGC:57735 IMAGE:5751687), complete cds.
HQ448612 - Synthetic construct Homo sapiens clone IMAGE:100072051; CCSB011642_02 hypothetical protein LOC202051 (LOC202051) gene, encodes complete protein.
KJ903998 - Synthetic construct Homo sapiens clone ccsbBroadEn_13392 SPATA24 gene, encodes complete protein.
MA578744 - JP 2018138019-A/150670: Polycomb-Associated Non-Coding RNAs.
MA578745 - JP 2018138019-A/150671: Polycomb-Associated Non-Coding RNAs.
MA446584 - JP 2018138019-A/18510: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000450845.1, ENST00000450845.2, ENST00000450845.3, ENST00000450845.4, ENST00000450845.5, ENST00000450845.6, NM_194296, Q86W54, SPA24_HUMAN, uc320sfy.1, uc320sfy.2
UCSC ID: ENST00000450845.7_10
RefSeq Accession: NM_194296.2
Protein: Q86W54 (aka SPA24_HUMAN)

-  Gene Model Information
  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.