Human Gene SPATA7 (ENST00000356583.9) from GENCODE V44
  Description: Homo sapiens spermatogenesis associated 7 (SPATA7), transcript variant 2, mRNA. (from RefSeq NM_001040428)
RefSeq Summary (NM_001040428): This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010].
Gencode Transcript: ENST00000356583.9
Gencode Gene: ENSG00000042317.17
Transcript (Including UTRs)
   Position: hg38 chr14:88,385,668-88,438,458 Size: 52,791 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg38 chr14:88,385,819-88,438,422 Size: 52,604 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:88,385,668-88,438,458)mRNA (may differ from genome)Protein (567 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPAT7_HUMAN
DESCRIPTION: RecName: Full=Spermatogenesis-associated protein 7; AltName: Full=HSD-3.1; AltName: Full=Spermatogenesis-associated protein HSD3;
FUNCTION: May be involved in retinal function.
DISEASE: Defects in SPATA7 are the cause of Leber congenital amaurosis type 3 (LCA3) [MIM:604232]. LCA designates a clinically and genetically heterogeneous group of childhood retinal degenerations, generally inherited in an autosomal recessive manner. Affected infants have little or no retinal photoreceptor function as tested by electroretinography. LCA represents the most common genetic cause of congenital visual impairment in infants and children.
DISEASE: Defects in SPATA7 are a cause of retinitis pigmentosa autosomal recessive (ARRP) [MIM:268000]. ARRP is a retinal dystrophy belonging to the group of pigmentary retinopathies. RP is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SPATA7
Diseases sorted by gene-association score: leber congenital amaurosis 3* (937), severe early-childhood-onset retinal dystrophy* (202), leber congenital amaurosis* (113), spata7-related leber congenital amaurosis* (100), spata7-related retinitis pigmentosa* (100), retinitis pigmentosa* (50), hereditary retinal dystrophy (9), fundus dystrophy (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.24 RPKM in Testis
Total median expression: 179.70 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 -63.80151-0.423 Picture PostScript Text
3' UTR -1.1036-0.031 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
  ModBase Predicted Comparative 3D Structure on Q9P0W8
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007601 visual perception
GO:0045494 photoreceptor cell maintenance
GO:0050896 response to stimulus
GO:1903546 protein localization to photoreceptor outer segment
GO:1903621 protein localization to photoreceptor connecting cilium

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005930 axoneme
GO:0015630 microtubule cytoskeleton
GO:0032391 photoreceptor connecting cilium
GO:0036064 ciliary basal body
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  BC090875 - Homo sapiens spermatogenesis associated 7, mRNA (cDNA clone MGC:102934 IMAGE:30383306), complete cds.
LF384875 - JP 2014500723-A/192378: Polycomb-Associated Non-Coding RNAs.
MA620452 - JP 2018138019-A/192378: Polycomb-Associated Non-Coding RNAs.
AL136604 - Homo sapiens mRNA; cDNA DKFZp564F2122 (from clone DKFZp564F2122).
AF144487 - Homo sapiens clone HSD-3.1 unknown mRNA.
GQ891487 - Homo sapiens clone HEL-S-208 epididymis secretory sperm binding protein mRNA, complete cds.
EU668353 - Homo sapiens epididymis secretory protein Li 296 (HEL-S-296) mRNA, complete cds.
AK225746 - Homo sapiens mRNA for Spermatogenesis associated protein 7 variant, clone: TST06008.
AK290631 - Homo sapiens cDNA FLJ76119 complete cds.
JD057719 - Sequence 38743 from Patent EP1572962.
AK293007 - Homo sapiens cDNA FLJ78263 complete cds.
CR936777 - Homo sapiens mRNA; cDNA DKFZp686D07199 (from clone DKFZp686D07199).
AK055864 - Homo sapiens cDNA FLJ31302 fis, clone LIVER1000079, highly similar to Spermatogenesis-associated protein 7.
JD227026 - Sequence 208050 from Patent EP1572962.
AB463283 - Synthetic construct DNA, clone: pF1KB8656, Homo sapiens SPATA7 gene for spermatogenesis associated 7, without stop codon, in Flexi system.
AM393238 - Synthetic construct Homo sapiens clone IMAGE:100001633 for hypothetical protein (SPATA7 gene).
CR533563 - Homo sapiens full open reading frame cDNA clone RZPDo834G0821D for gene SPATA7, spermatogenesis associated 7; complete cds, incl. stopcodon.
AF144488 - Homo sapiens clone HSD-3.2 unknown mRNA.
BC034635 - Homo sapiens cDNA clone IMAGE:4831226, **** WARNING: chimeric clone ****.
BC037809 - Homo sapiens spermatogenesis associated 7, mRNA (cDNA clone IMAGE:4797676), with apparent retained intron.
BC008656 - Homo sapiens spermatogenesis associated 7, mRNA (cDNA clone IMAGE:3854920), partial cds.
GQ891486 - Homo sapiens clone HEL-S-207 epididymis secretory sperm binding protein mRNA, partial cds.
CU679017 - Synthetic construct Homo sapiens gateway clone IMAGE:100018798 5' read SPATA7 mRNA.
KJ902884 - Synthetic construct Homo sapiens clone ccsbBroadEn_12278 SPATA7 gene, encodes complete protein.
JD177984 - Sequence 159008 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000356583.1, ENST00000356583.2, ENST00000356583.3, ENST00000356583.4, ENST00000356583.5, ENST00000356583.6, ENST00000356583.7, ENST00000356583.8, HSD3, NM_001040428, Q5BKY5, Q8WX30, Q96HF3, Q9H0X0, Q9P0W7, Q9P0W8, SPAT7_HUMAN, uc001xwr.1, uc001xwr.2, uc001xwr.3, uc001xwr.4, uc001xwr.5
UCSC ID: ENST00000356583.9
RefSeq Accession: NM_001040428
Protein: Q9P0W8 (aka SPAT7_HUMAN or SAT7_HUMAN)
CCDS: CCDS32132.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SPATA7:
lca-ov (Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview)
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.