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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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See SPATA6 in Genome Data Viewer
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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