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    SPATA9 spermatogenesis associated 9 [ Homo sapiens (human) ]

    Gene ID: 83890, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SPATA9provided by HGNC
    Official Full Name
    spermatogenesis associated 9provided by HGNC
    Primary source
    HGNC:HGNC:22988
    See related
    Ensembl:ENSG00000145757 MIM:608039; AllianceGenome:HGNC:22988
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NYD-SP16
    Summary
    Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 4.4), bone marrow (RPKM 0.8) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPATA9 in Genome Data Viewer
    Location:
    5q15
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (95652181..95732102, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (96153102..96233338, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (94987885..95067806, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:94955347-94955962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16183 Neighboring gene Sharpr-MPRA regulatory region 2204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:94957159-94957658 Neighboring gene uncharacterized LOC112267933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22798 Neighboring gene G protein-coupled receptor 150 Neighboring gene Rieske Fe-S domain containing Neighboring gene uncharacterized LOC105379090 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:95051904-95052077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16187 Neighboring gene Rho related BTB domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22801 Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22806 Neighboring gene glutaredoxin

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Human testicular protein NYD-SP16 is involved in sperm capacitation and the acrosome reaction. Lu Y, et al. Fertil Steril, 2006 Oct. PMID 16963046
    2. NYD-SP16, a novel gene associated with spermatogenesis of human testis. Cheng LJ, et al. Biol Reprod, 2003 Jan. PMID 12493713
    3. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Soler Artigas M, et al. Nat Genet, 2011 Sep 25. PMID 21946350, Free PMC Article
    4. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. Wang B, et al. EBioMedicine, 2019 Mar. PMID 30745168, Free PMC Article
    5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35906

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 9
    Names
    CTD-2154I11.2
    testicular tissue protein Li 179
    testis development protein NYD-SP16

    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_001349303.2 → NP_001336232.1  spermatogenesis-associated protein 9 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC008840, HM005492
      Conserved Domains (1) summary
      pfam15824
      Location:1 → 224
      SPATA9; Spermatogenesis-associated protein 9

    2. NM_031952.4 → NP_114158.2  spermatogenesis-associated protein 9 isoform 1

      See identical proteins and their annotated locations for NP_114158.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer isoform (1).
      Source sequence(s)
      BC047333, BQ013593
      Consensus CDS
      CCDS4076.1
      UniProtKB/Swiss-Prot
      A8K8H3, Q4G122, Q86X33, Q8NA28, Q9BWV2
      UniProtKB/TrEMBL
      A0A140VJV2
      Related
      ENSP00000274432.8, ENST00000274432.13
      Conserved Domains (1) summary
      pfam15824
      Location:1 → 252
      SPATA9; Spermatogenesis-associated protein 9

    RNA

    1. NR_125327.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon, and contains multiple alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC008547, AK292338, AY027526

    2. NR_125328.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an alternate internal exon, and contains multiple alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC008547, AK093225, AK310260, BC047333

    3. NR_125329.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an alternate internal exon, and contains multiple alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK093225, BC032832, BC047333, BQ013593

    4. NR_125330.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two consecutive alternate internal exons, and contains multiple alternate 3' exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC008547, AK093225, AK292338

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      95652181..95732102 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417809.1 → XP_047273765.1  spermatogenesis-associated protein 9 isoform X1

    2. XM_011543664.1 → XP_011541966.1  spermatogenesis-associated protein 9 isoform X2

      Conserved Domains (1) summary
      pfam15824
      Location:4 → 235
      SPATA9; Spermatogenesis-associated protein 9

    3. XM_011543666.2 → XP_011541968.1  spermatogenesis-associated protein 9 isoform X4

      See identical proteins and their annotated locations for XP_011541968.1

      UniProtKB/Swiss-Prot
      Q9BWV2
      Related
      ENSP00000427257.1, ENST00000477715.5
      Conserved Domains (1) summary
      pfam15824
      Location:1 → 176
      SPATA9; Spermatogenesis-associated protein 9

    4. XM_024446230.1 → XP_024301998.1  spermatogenesis-associated protein 9 isoform X3

      Conserved Domains (1) summary
      pfam15824
      Location:1 → 190
      SPATA9; Spermatogenesis-associated protein 9

    5. XM_017009951.2 → XP_016865440.1  spermatogenesis-associated protein 9 isoform X5

      Conserved Domains (1) summary
      pfam15824
      Location:22 → 148
      SPATA9; Spermatogenesis-associated protein 9

    6. XM_011543667.3 → XP_011541969.1  spermatogenesis-associated protein 9 isoform X5

      Conserved Domains (1) summary
      pfam15824
      Location:22 → 148
      SPATA9; Spermatogenesis-associated protein 9

    RNA

    1. XR_001742295.1 RNA Sequence

    2. XR_007058645.1 RNA Sequence

    3. XR_001742296.2 RNA Sequence

    4. XR_002956184.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      96153102..96233338 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353631.1 → XP_054209606.1  spermatogenesis-associated protein 9 isoform X1

    2. XM_054353632.1 → XP_054209607.1  spermatogenesis-associated protein 9 isoform X2

    3. XM_054353634.1 → XP_054209609.1  spermatogenesis-associated protein 9 isoform X4

    4. XM_054353633.1 → XP_054209608.1  spermatogenesis-associated protein 9 isoform X3

    5. XM_054353636.1 → XP_054209611.1  spermatogenesis-associated protein 9 isoform X5

    6. XM_054353635.1 → XP_054209610.1  spermatogenesis-associated protein 9 isoform X5

    RNA

    1. XR_008487179.1 RNA Sequence

    2. XR_008487182.1 RNA Sequence

    3. XR_008487181.1 RNA Sequence

    4. XR_008487180.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_173361.1: Suppressed sequence

      Description
      NM_173361.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BWV2.2 GenPept UniProtKB/Swiss-Prot:Q9BWV2

    Gene LinkOut

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

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