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Aliases for SPATA7 Gene

Aliases for SPATA7 Gene

  • Spermatogenesis Associated 7 2 3 5
  • Spermatogenesis-Associated Protein HSD3 3 4
  • HSD-3.1 3 4
  • HSD3 3 4
  • Spermatogenesis-Associated Protein 7 3
  • Epididymis Secretory Protein Li 296 3
  • Leber Congenital Amaurosis 3 2
  • HEL-S-296 3
  • LCA3 3

External Ids for SPATA7 Gene

Previous HGNC Symbols for SPATA7 Gene

  • LCA3

Previous GeneCards Identifiers for SPATA7 Gene

  • GC14P082668
  • GC14P086842
  • GC14P087921
  • GC14P088852
  • GC14P069023
  • GC14P088897

Summaries for SPATA7 Gene

Entrez Gene Summary for SPATA7 Gene

  • 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]

GeneCards Summary for SPATA7 Gene

SPATA7 (Spermatogenesis Associated 7) is a Protein Coding gene. Diseases associated with SPATA7 include Leber Congenital Amaurosis 3 and Leber Congenital Amaurosis.

UniProtKB/Swiss-Prot for SPATA7 Gene

  • Involved in photoreceptor cells maintenance (By similarity). It is required for recruitment and proper localization of RPGRIP1 to the photoreceptor connecting cilium (CC), as well as protein trafficking across the CC to the outer segments (By similarity).

Gene Wiki entry for SPATA7 Gene

Additional gene information for SPATA7 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPATA7 Gene

Genomics for SPATA7 Gene

GeneHancer (GH) Regulatory Elements for SPATA7 Gene

Promoters and enhancers for SPATA7 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J088384 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.8 824 1.9 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B E2F8 SPATA7 LOC105370614
GH14J088550 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 17.4 +166.7 166703 2.3 ARNT SIN3A YY1 ELK1 ZNF143 ZFP91 KLF13 DEK NCOA1 ZC3H11A PTPN21 ENSG00000258789 SPATA7 LOC105370614 FAM35CP GC14M092413
GH14J088553 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 14.8 +169.6 169612 2.3 NFRKB ARID4B SIN3A BMI1 ZNF48 ETS1 ZNF335 EGR1 ATF7 THAP11 PTPN21 SPATA7 ENSG00000258789 GC14M092413
GH14J088791 Promoter/Enhancer 1.3 Ensembl ENCODE 9.3 +407.8 407770 1.9 SIN3A DEAF1 DMAP1 ZNF48 ZNF335 ZNF121 CREM ZBTB25 ZEB2 ZNF217 EML5 SPATA7 GC14M092413 PIR31268
GH14J088467 Enhancer 0.6 ENCODE 17.7 +84.0 83977 2.3 SMARCE1 NCOA3 GATAD2B DPF2 FOXA1 JUND GATA3 CUX1 FOS FOSL2 RNU4-22P SPATA7 LOC105370614 PTPN21 GC14M092413
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPATA7 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPATA7 gene promoter:
  • Nkx3-1 v4
  • Nkx3-1 v3
  • Nkx3-1 v2
  • Nkx3-1 v1
  • Nkx3-1
  • POU2F1a
  • POU2F1
  • NCX

Genomic Locations for SPATA7 Gene

Genomic Locations for SPATA7 Gene
chr14:88,384,924-88,470,350
(GRCh38/hg38)
Size:
85,427 bases
Orientation:
Plus strand
chr14:88,851,268-88,936,694
(GRCh37/hg19)
Size:
85,427 bases
Orientation:
Plus strand

Genomic View for SPATA7 Gene

Genes around SPATA7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPATA7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPATA7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPATA7 Gene

Proteins for SPATA7 Gene

  • Protein details for SPATA7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P0W8-SPAT7_HUMAN
    Recommended name:
    Spermatogenesis-associated protein 7
    Protein Accession:
    Q9P0W8
    Secondary Accessions:
    • Q5BKY5
    • Q8WX30
    • Q96HF3
    • Q9H0X0
    • Q9P0W7

    Protein attributes for SPATA7 Gene

    Size:
    599 amino acids
    Molecular mass:
    67719 Da
    Quaternary structure:
    • Interacts with RPGRIP1 (PubMed:25398945). Found in a complex with C21orf2, NEK1 and SPATA7 (PubMed:26167768). Interacts with NEK1 (PubMed:26167768).

    Alternative splice isoforms for SPATA7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPATA7 Gene

Post-translational modifications for SPATA7 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPATA7 Gene

Domains & Families for SPATA7 Gene

Gene Families for SPATA7 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SPATA7 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPATA7 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SPATA7: view

No data available for UniProtKB/Swiss-Prot for SPATA7 Gene

Function for SPATA7 Gene

Molecular function for SPATA7 Gene

UniProtKB/Swiss-Prot Function:
Involved in photoreceptor cells maintenance (By similarity). It is required for recruitment and proper localization of RPGRIP1 to the photoreceptor connecting cilium (CC), as well as protein trafficking across the CC to the outer segments (By similarity).

Phenotypes From GWAS Catalog for SPATA7 Gene

Gene Ontology (GO) - Molecular Function for SPATA7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25398945
genes like me logo Genes that share ontologies with SPATA7: view
genes like me logo Genes that share phenotypes with SPATA7: view

Human Phenotype Ontology for SPATA7 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPATA7 Gene

MGI Knock Outs for SPATA7:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SPATA7 Gene

Localization for SPATA7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPATA7 Gene

Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton. Note=Localizes to the microtubule network (PubMed:25398945). In the retinal photoreceptor cell layer, localizes at the connecting cilium (By similarity). {ECO:0000250 UniProtKB:Q80VP2, ECO:0000269 PubMed:25398945}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPATA7 gene
Compartment Confidence
cytoskeleton 5
mitochondrion 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPATA7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with SPATA7: view

Pathways & Interactions for SPATA7 Gene

SuperPathways for SPATA7 Gene

No Data Available

Interacting Proteins for SPATA7 Gene

Gene Ontology (GO) - Biological Process for SPATA7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0045494 photoreceptor cell maintenance ISS --
GO:0050896 response to stimulus IEA --
GO:1903546 protein localization to photoreceptor outer segment ISS --
GO:1903621 protein localization to photoreceptor connecting cilium ISS --
genes like me logo Genes that share ontologies with SPATA7: view

No data available for Pathways by source and SIGNOR curated interactions for SPATA7 Gene

Drugs & Compounds for SPATA7 Gene

No Compound Related Data Available

Transcripts for SPATA7 Gene

Unigene Clusters for SPATA7 Gene

Spermatogenesis associated 7:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPATA7 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12 ^ 13 ^
SP1: - - - - - -
SP2: - - - -
SP3: - - -
SP4: - -
SP5: - - -
SP6: - - - - -
SP7: - - - - -
SP8: - - -
SP9: - - - -
SP10: - - - - - - -
SP11: - - - - -
SP12:
SP13:

ExUns: 14a · 14b ^ 15 ^ 16 ^ 17
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for SPATA7 Gene

GeneLoc Exon Structure for
SPATA7
ECgene alternative splicing isoforms for
SPATA7

Expression for SPATA7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPATA7 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPATA7 Gene

This gene is overexpressed in Testis (x5.9).

Protein differential expression in normal tissues from HIPED for SPATA7 Gene

This gene is overexpressed in Adrenal (27.7), Esophagus (12.8), Retina (8.6), and CD8 Tcells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SPATA7 Gene



Protein tissue co-expression partners for SPATA7 Gene

NURSA nuclear receptor signaling pathways regulating expression of SPATA7 Gene:

SPATA7

SOURCE GeneReport for Unigene cluster for SPATA7 Gene:

Hs.525518

Evidence on tissue expression from TISSUES for SPATA7 Gene

  • Nervous system(4.6)
  • Intestine(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPATA7 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • olfactory bulb
  • outer ear
  • skull
Abdomen:
  • liver
Pelvis:
  • penis
  • testicle
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with SPATA7: view

No data available for mRNA Expression by UniProt/SwissProt for SPATA7 Gene

Orthologs for SPATA7 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPATA7 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPATA7 34 33
  • 99.12 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPATA7 34 33
  • 86.18 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPATA7 34 33
  • 82.64 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Spata7 33
  • 77.6 (n)
mouse
(Mus musculus)
Mammalia Spata7 16 34 33
  • 77.28 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 74 (a)
OneToMany
-- 34
  • 42 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia SPATA7 34
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPATA7 34 33
  • 55.94 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPATA7 34
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia spata7 33
  • 50.62 (n)
zebrafish
(Danio rerio)
Actinopterygii spata7 34
  • 29 (a)
OneToOne
Species where no ortholog for SPATA7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SPATA7 Gene

ENSEMBL:
Gene Tree for SPATA7 (if available)
TreeFam:
Gene Tree for SPATA7 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPATA7: view image

Paralogs for SPATA7 Gene

No data available for Paralogs for SPATA7 Gene

Variants for SPATA7 Gene

Sequence variations from dbSNP and Humsavar for SPATA7 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs10139784 likely-benign, Leber congenital amaurosis, Retinitis Pigmentosa, Recessive 88,438,223(+) G/A/T coding_sequence_variant, intron_variant, missense_variant
rs139510848 uncertain-significance, Retinitis Pigmentosa, Recessive, Leber congenital amaurosis 88,438,244(+) T/A/C coding_sequence_variant, intron_variant, missense_variant
rs140192398 uncertain-significance, not specified, Retinitis Pigmentosa, Recessive, Leber congenital amaurosis 88,438,050(+) G/A coding_sequence_variant, intron_variant, synonymous_variant
rs140287375 pathogenic, Leber congenital amaurosis 3 88,416,725(+) C/G/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant, stop_gained
rs142913613 uncertain-significance, Leber congenital amaurosis, Retinitis Pigmentosa, Recessive 88,396,172(+) G/A 5_prime_UTR_variant, coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SPATA7 Gene

Variant ID Type Subtype PubMed ID
dgv1119n106 CNV deletion 24896259
esv2276274 CNV deletion 18987734
esv2568808 CNV deletion 19546169
esv2619552 CNV deletion 19546169
esv2748992 CNV deletion 23290073
esv2748993 CNV deletion 23290073
esv3303743 CNV mobile element insertion 20981092
esv3308826 CNV mobile element insertion 20981092
esv3308884 CNV mobile element insertion 20981092
esv3382164 CNV insertion 20981092
esv3402490 CNV insertion 20981092
esv3409385 CNV insertion 20981092
esv3410641 CNV insertion 20981092
esv3551937 CNV deletion 23714750
esv3753 CNV loss 18987735
esv994338 CNV deletion 20482838
nsv1071161 CNV deletion 25765185
nsv456391 CNV gain 19166990
nsv565512 CNV gain 21841781
nsv84810 CNV deletion 16902084
nsv958753 CNV deletion 24416366

Variation tolerance for SPATA7 Gene

Residual Variation Intolerance Score: 84% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.13; 93.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPATA7 Gene

Human Gene Mutation Database (HGMD)
SPATA7
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPATA7

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPATA7 Gene

Disorders for SPATA7 Gene

MalaCards: The human disease database

(7) MalaCards diseases for SPATA7 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
leber congenital amaurosis 3
  • lca3
leber congenital amaurosis
  • lca
severe early-childhood-onset retinal dystrophy
  • eosrd
retinitis pigmentosa
  • retinitis pigmentosa 1
hereditary retinal dystrophy
  • hereditary retinal dystrophies
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPAT7_HUMAN
  • Leber congenital amaurosis 3 (LCA3) [MIM:604232]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269 PubMed:19268277}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa autosomal recessive (ARRP) [MIM:268000]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa 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. {ECO:0000269 PubMed:19268277}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SPATA7

genes like me logo Genes that share disorders with SPATA7: view

No data available for Genatlas for SPATA7 Gene

Publications for SPATA7 Gene

  1. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. (PMID: 19268277) Wang H … Chen R (American journal of human genetics 2009) 2 3 4 58
  2. Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina. (PMID: 25398945) Eblimit A … Chen R (Human molecular genetics 2015) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The DNA sequence and analysis of human chromosome 14. (PMID: 12508121) Heilig R … Weissenbach J (Nature 2003) 3 4 58
  5. A novel gene, RSD-3/HSD-3.1, encodes a meiotic-related protein expressed in rat and human testis. (PMID: 12736779) Zhang X … Koide SS (Journal of molecular medicine (Berlin, Germany) 2003) 3 4 58

Products for SPATA7 Gene

Sources for SPATA7 Gene

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