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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
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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)

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

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