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    SPATA6 spermatogenesis associated 6 [ Homo sapiens (human) ]

    Gene ID: 54558, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SPATA6provided by HGNC
    Official Full Name
    spermatogenesis associated 6provided by HGNC
    Primary source
    HGNC:HGNC:18309
    See related
    Ensembl:ENSG00000132122 MIM:613947; AllianceGenome:HGNC:18309
    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
    HASH; SRF1; SRF-1
    Summary
    Predicted to enable myosin light chain binding activity. Predicted to be involved in motile cilium assembly and spermatogenesis. Predicted to be located in extracellular region. Predicted to be active in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 10.6), thyroid (RPKM 2.4) and 19 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    1p33
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (48261389..48472204, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (48140134..48350874, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (48761045..48937876, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2794 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48674527-48675206 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:48679855-48680592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:48697245-48697746 Neighboring gene Skint1 like (pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:48834694-48835194 Neighboring gene solute carrier family 5 member 9 Neighboring gene RNA, U6 small nuclear 723, pseudogene Neighboring gene protein phosphatase 1 regulatory subunit 8 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3042 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48907708-48908395 Neighboring gene uncharacterized LOC124904175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1010 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48945175-48946016 Neighboring gene Sharpr-MPRA regulatory region 6906 Neighboring gene STE20 related adaptor beta pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:48991897-48992398 Neighboring gene RNA, U4 small nuclear 61, pseudogene Neighboring gene ribosomal protein L21 pseudogene 25 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49110904-49111546 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49111547-49112189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:49152780-49153280 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49174571-49174927 Neighboring gene AGBL carboxypeptidase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1011 Neighboring gene BEN domain containing 5

    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
    • 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. The role of spermatogenesis-associated protein 6 in testicular germ cell tumors. Huo S, et al. Int J Clin Exp Pathol, 2015. PMID 26464655, Free PMC Article
    2. Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans. Wang X, et al. Clin Genet, 2023 Mar. PMID 36415156
    3. A novel spermatogenesis-related factor-1 gene expressed in maturing rat testis. Yamano Y, et al. Biochem Biophys Res Commun, 2001 Dec 14. PMID 11735130
    4. Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility. Sujit KM, et al. Andrology, 2020 May. PMID 31838782
    5. Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. Ficarro S, et al. J Biol Chem, 2003 Mar 28. PMID 12509440

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans.
      Title: Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans.
    2. Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
      Title: Increased DNA methylation in the spermatogenesis-associated (SPATA) genes correlates with infertility.
    3. SPATA6 may play an important role in testicular germ cell tumors, and down-regulation of SPATA6 could lead to apoptosis of testicular germ cell tumors.
      Title: The role of spermatogenesis-associated protein 6 in testicular germ cell tumors.
    Submit: New GeneRIF Correction

    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

    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

    • FLJ10007

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables myosin light chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in motile cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in motile cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sperm connecting piece IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in sperm connecting piece ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 6
    Names
    spermatogenesis-related factor-1
    testicular tissue protein Li 178

    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_001286238.2 → NP_001273167.1  spermatogenesis-associated protein 6 isoform 2

      See identical proteins and their annotated locations for NP_001273167.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The encodes isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL356968, AL359959, BC020660, BC040655
      Consensus CDS
      CCDS65535.1
      UniProtKB/TrEMBL
      B4DX17
      Related
      ENSP00000360909.3, ENST00000371843.7
      Conserved Domains (1) summary
      pfam14909
      Location:11 → 149
      SPATA6; Spermatogenesis-assoc protein 6

    2. NM_001286239.2 → NP_001273168.1  spermatogenesis-associated protein 6 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform(3) is shorter than isoform 1.
      Source sequence(s)
      AK301770, AL356968, AL359959, BC040655
      Consensus CDS
      CCDS72787.1
      UniProtKB/TrEMBL
      A8MU33, B4DX17
      Related
      ENSP00000379502.4, ENST00000396199.7
      Conserved Domains (1) summary
      pfam14909
      Location:11 → 135
      SPATA6; Spermatogenesis-assoc protein 6

    3. NM_019073.4 → NP_061946.1  spermatogenesis-associated protein 6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK000869, AL356968, AL359959, BC040655
      Consensus CDS
      CCDS551.1
      UniProtKB/Swiss-Prot
      Q5T3N7, Q8WUE6, Q9NWH7
      UniProtKB/TrEMBL
      A0A140VJV1, B4DX17
      Related
      ENSP00000360913.3, ENST00000371847.8
      Conserved Domains (1) summary
      pfam14909
      Location:11 → 149
      SPATA6; Spermatogenesis-assoc protein 6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      48261389..48472204 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422913.1 → XP_047278869.1  spermatogenesis-associated protein 6 isoform X12

    2. XM_047422901.1 → XP_047278857.1  spermatogenesis-associated protein 6 isoform X3

    3. XM_006710699.4 → XP_006710762.1  spermatogenesis-associated protein 6 isoform X1

      UniProtKB/TrEMBL
      B4DX17
      Conserved Domains (1) summary
      pfam14909
      Location:11 → 149
      SPATA6; Spermatogenesis-assoc protein 6

    4. XM_047422902.1 → XP_047278858.1  spermatogenesis-associated protein 6 isoform X6

    5. XM_047422919.1 → XP_047278875.1  spermatogenesis-associated protein 6 isoform X13

    6. XM_017001510.2 → XP_016856999.1  spermatogenesis-associated protein 6 isoform X4

      UniProtKB/TrEMBL
      B4DX17

    7. XM_011541606.3 → XP_011539908.1  spermatogenesis-associated protein 6 isoform X7

      See identical proteins and their annotated locations for XP_011539908.1

      Conserved Domains (1) summary
      pfam14909
      Location:11 → 149
      SPATA6; Spermatogenesis-assoc protein 6

    8. XM_017001511.3 → XP_016857000.1  spermatogenesis-associated protein 6 isoform X5

    9. XM_047422904.1 → XP_047278860.1  spermatogenesis-associated protein 6 isoform X9

    10. XM_011541609.3 → XP_011539911.1  spermatogenesis-associated protein 6 isoform X9

      See identical proteins and their annotated locations for XP_011539911.1

      UniProtKB/TrEMBL
      B4DX17
      Conserved Domains (1) summary
      pfam14909
      Location:1 → 41
      SPATA6; Spermatogenesis-assoc protein 6

    11. XM_047422907.1 → XP_047278863.1  spermatogenesis-associated protein 6 isoform X11

    12. XM_017001513.2 → XP_016857002.1  spermatogenesis-associated protein 6 isoform X9

      UniProtKB/TrEMBL
      B4DX17
      Conserved Domains (1) summary
      pfam14909
      Location:1 → 41
      SPATA6; Spermatogenesis-assoc protein 6

    13. XM_047422906.1 → XP_047278862.1  spermatogenesis-associated protein 6 isoform X10

    14. XM_011541607.3 → XP_011539909.1  spermatogenesis-associated protein 6 isoform X8

      UniProtKB/TrEMBL
      B4DX17

    15. XM_047422926.1 → XP_047278882.1  spermatogenesis-associated protein 6 isoform X16

    16. XM_047422900.1 → XP_047278856.1  spermatogenesis-associated protein 6 isoform X2

    17. XM_006710701.5 → XP_006710764.1  spermatogenesis-associated protein 6 isoform X15

      Conserved Domains (1) summary
      pfam14909
      Location:11 → 149
      SPATA6; Spermatogenesis-assoc protein 6

    18. XM_047422922.1 → XP_047278878.1  spermatogenesis-associated protein 6 isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      48140134..48350874 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337152.1 → XP_054193127.1  spermatogenesis-associated protein 6 isoform X12

    2. XM_054337141.1 → XP_054193116.1  spermatogenesis-associated protein 6 isoform X3

    3. XM_054337139.1 → XP_054193114.1  spermatogenesis-associated protein 6 isoform X1

    4. XM_054337144.1 → XP_054193119.1  spermatogenesis-associated protein 6 isoform X6

    5. XM_054337153.1 → XP_054193128.1  spermatogenesis-associated protein 6 isoform X13

    6. XM_054337142.1 → XP_054193117.1  spermatogenesis-associated protein 6 isoform X4

    7. XM_054337145.1 → XP_054193120.1  spermatogenesis-associated protein 6 isoform X7

    8. XM_054337143.1 → XP_054193118.1  spermatogenesis-associated protein 6 isoform X5

    9. XM_054337147.1 → XP_054193122.1  spermatogenesis-associated protein 6 isoform X9

    10. XM_054337149.1 → XP_054193124.1  spermatogenesis-associated protein 6 isoform X9

    11. XM_054337151.1 → XP_054193126.1  spermatogenesis-associated protein 6 isoform X11

    12. XM_054337148.1 → XP_054193123.1  spermatogenesis-associated protein 6 isoform X9

    13. XM_054337150.1 → XP_054193125.1  spermatogenesis-associated protein 6 isoform X10

    14. XM_054337146.1 → XP_054193121.1  spermatogenesis-associated protein 6 isoform X8

    15. XM_054337158.1 → XP_054193133.1  spermatogenesis-associated protein 6 isoform X16

    16. XM_054337157.1 → XP_054193132.1  spermatogenesis-associated protein 6 isoform X18

    17. XM_054337154.1 → XP_054193129.1  spermatogenesis-associated protein 6 isoform X17

    18. XM_054337140.1 → XP_054193115.1  spermatogenesis-associated protein 6 isoform X2

    19. XM_054337156.1 → XP_054193131.1  spermatogenesis-associated protein 6 isoform X15

    20. XM_054337155.1 → XP_054193130.1  spermatogenesis-associated protein 6 isoform X14

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NWH7.1 GenPept UniProtKB/Swiss-Prot:Q9NWH7

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