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    Spata7 spermatogenesis associated 7 [ Mus musculus (house mouse) ]

    Gene ID: 104871, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Spata7provided by MGI
    Official Full Name
    spermatogenesis associated 7provided by MGI
    Primary source
    MGI:MGI:2144877
    See related
    Ensembl:ENSMUSG00000021007 AllianceGenome:MGI:2144877
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    HSD3; B230306G18Rik
    Summary
    Involved in microtubule cytoskeleton organization; photoreceptor cell maintenance; and protein localization to non-motile cilium. Located in photoreceptor distal connecting cilium. Is active in rod photoreceptor outer segment. Is expressed in several structures, including blood vessel; central nervous system; and retina layer. Used to study Leber congenital amaurosis 3. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 3. Orthologous to human SPATA7 (spermatogenesis associated 7). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis adult (RPKM 77.4), frontal lobe adult (RPKM 5.1) and 4 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    12 E; 12 49.88 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (98594169..98636078)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (98628129..98669819)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene potassium channel, subfamily K, member 10 Neighboring gene predicted gene, 40893 Neighboring gene STARR-seq mESC enhancer starr_32997 Neighboring gene STARR-positive B cell enhancer mm9_chr12:99839121-99839422 Neighboring gene STARR-seq mESC enhancer starr_32998 Neighboring gene predicted gene, 25486 Neighboring gene STARR-seq mESC enhancer starr_33000 Neighboring gene protein tyrosine phosphatase, non-receptor type 21 Neighboring gene STARR-positive B cell enhancer ABC_E9861 Neighboring gene zinc finger CCCH type containing 14 Neighboring gene echinoderm microtubule associated protein like 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. Eblimit A, et al. Exp Eye Res, 2018 Jan. PMID 29100828, Free PMC Article
    2. Spata7 is required for maintenance of the retinal connecting cilium. Lu J, et al. Sci Rep, 2022 Apr 2. PMID 35368022, Free PMC Article
    3. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Wang H, et al. Am J Hum Genet, 2009 Mar. PMID 19268277, Free PMC Article
    4. Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina. Eblimit A, et al. Hum Mol Genet, 2015 Mar 15. PMID 25398945, Free PMC Article
    5. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. Dharmat R, et al. J Cell Biol, 2018 Aug 6. PMID 29899041, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Spata7 is required for maintenance of the retinal connecting cilium.
      Title: Spata7 is required for maintenance of the retinal connecting cilium.
    2. The absence of Spata7 results in the mislocalization of DCC proteins without affecting the proximal connecting cilium (PCC) protein complexes.
      Title: SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium.
    3. Spata7 is expressed in the mature mouse retina.
      Title: Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (5)  1 citation
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in microtubule cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in microtubule cytoskeleton organization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in microtubule cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photoreceptor cell maintenance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to photoreceptor connecting cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to photoreceptor outer segment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axoneme ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor connecting cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in photoreceptor distal connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in photoreceptor distal connecting cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in photoreceptor distal connecting cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in rod photoreceptor outer segment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in rod photoreceptor outer segment IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    is_active_in rod photoreceptor outer segment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 7 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001289572.1 → NP_001276501.1  spermatogenesis-associated protein 7 homolog isoform 2

      See identical proteins and their annotated locations for NP_001276501.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded protein (isoform 2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK153698, AK161308, BY252962
      Consensus CDS
      CCDS70413.1
      UniProtKB/TrEMBL
      Q3TTL3
      Related
      ENSMUSP00000098705.4, ENSMUST00000101146.4
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 376
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    2. NM_001289573.1 → NP_001276502.1  spermatogenesis-associated protein 7 homolog isoform 3

      See identical proteins and their annotated locations for NP_001276502.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons, compared to variant 1. The encoded protein (isoform 3) is shorter, compared to isoform 1.
      Source sequence(s)
      AK153698, BY252962
      Consensus CDS
      CCDS79145.1
      UniProtKB/TrEMBL
      Q3U5D0
      Related
      ENSMUSP00000098704.4, ENSMUST00000101144.10
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 241
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    3. NM_001289574.1 → NP_001276503.1  spermatogenesis-associated protein 7 homolog isoform 4

      See identical proteins and their annotated locations for NP_001276503.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate exon and lacks an alternate exon in the 5' coding region, and uses an alternate downstream translation start codon, compared to variant 1. The encoded protein (isoform 4) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC124516
      Conserved Domains (1) summary
      pfam15244
      Location:1 → 302
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    4. NM_178914.4 → NP_849245.2  spermatogenesis-associated protein 7 homolog isoform 1

      See identical proteins and their annotated locations for NP_849245.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AK153698, BC046960, BY252962
      Consensus CDS
      CCDS26097.1
      UniProtKB/Swiss-Prot
      Q80VP2, Q8BK23
      Related
      ENSMUSP00000045827.6, ENSMUST00000048402.12
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 408
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      98594169..98636078
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030246503.2 → XP_030102363.1  spermatogenesis-associated protein 7 homolog isoform X3

      Conserved Domains (1) summary
      pfam15244
      Location:1 → 302
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    2. XM_006515358.5 → XP_006515421.1  spermatogenesis-associated protein 7 homolog isoform X1

      See identical proteins and their annotated locations for XP_006515421.1

      Conserved Domains (1) summary
      pfam15244
      Location:3 → 369
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    3. XM_011243979.4 → XP_011242281.1  spermatogenesis-associated protein 7 homolog isoform X2

      See identical proteins and their annotated locations for XP_011242281.1

      UniProtKB/Swiss-Prot
      Q80VP2
      Conserved Domains (1) summary
      pfam15244
      Location:1 → 357
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    4. XM_030246504.2 → XP_030102364.1  spermatogenesis-associated protein 7 homolog isoform X3

      Conserved Domains (1) summary
      pfam15244
      Location:1 → 302
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    5. XM_030246502.2 → XP_030102362.1  spermatogenesis-associated protein 7 homolog isoform X1

      Conserved Domains (1) summary
      pfam15244
      Location:3 → 369
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    6. XM_030246505.2 → XP_030102365.1  spermatogenesis-associated protein 7 homolog isoform X3

      Conserved Domains (1) summary
      pfam15244
      Location:1 → 302
      HSD3; Spermatogenesis-associated protein 7, or HSD3
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80VP2.1 GenPept UniProtKB/Swiss-Prot:Q80VP2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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