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SPATA6L spermatogenesis associated 6 like [ Homo sapiens (human) ]

Gene ID: 55064, updated on 3-Apr-2024

Summary

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Official Symbol
SPATA6Lprovided by HGNC
Official Full Name
spermatogenesis associated 6 likeprovided by HGNC
Primary source
HGNC:HGNC:25472
See related
Ensembl:ENSG00000106686 AllianceGenome:HGNC:25472
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
C9orf68; bA6J24.2
Summary
Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 1.8), gall bladder (RPKM 0.4) and 16 other tissues See more
Orthologs
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Genomic context

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Location:
9p24.2-p24.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (4588821..4666480, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (4592492..4670154, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (4588821..4666480, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene GLIS family zinc finger 3 Neighboring gene RNA, U6 small nuclear 694, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28147 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:4514651-4515591 Neighboring gene solute carrier family 1 member 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:4605494-4606693 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:4630798-4631350 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:4647337-4647509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28148 Neighboring gene ribosomal protein S6 pseudogene 11 Neighboring gene CDC37L1 divergent transcript Neighboring gene cell division cycle 37 like 1, HSP90 cochaperone Neighboring gene phospholipid phosphatase 6

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. Genetics of coronary artery calcification among African Americans, a meta-analysis. Wojczynski MK, et al. BMC Med Genet, 2013 Jul 19. PMID 23870195, Free PMC Article
  2. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  3. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
  4. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article
  5. UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Liu J, et al. Nat Cell Biol, 2020 Sep. PMID 32807901

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

EBI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis.
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

  • FLJ10058

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables myosin light chain binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in sperm connecting piece IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
spermatogenesis associated 6-like protein

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_001039395.4 → NP_001034484.3  spermatogenesis associated 6-like protein isoform d

    See identical proteins and their annotated locations for NP_001034484.3

    Status: VALIDATED

    Source sequence(s)
    AK295831, AL136231, H05132
    Consensus CDS
    CCDS43785.2
    UniProtKB/Swiss-Prot
    Q8N4H0
    Related
    ENSP00000417063.1, ENST00000475086.5
    Conserved Domains (1) summary
    pfam14909
    Location:7 → 73
    SPATA6; Spermatogenesis-assoc protein 6

  2. NM_001353484.2 → NP_001340413.1  spermatogenesis associated 6-like protein isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1), as well as variant 2, encodes isoform a.
    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    A0AA34QVF8
    Related
    ENSP00000516766.1, ENST00000707147.1
    Conserved Domains (1) summary
    pfam14909
    Location:7 → 145
    SPATA6; Spermatogenesis-assoc protein 6

  3. NM_001353485.2 → NP_001340414.1  spermatogenesis associated 6-like protein isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2), as well as variant 1, encodes isoform a.
    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    A0AA34QVF8
    Conserved Domains (1) summary
    pfam14909
    Location:7 → 145
    SPATA6; Spermatogenesis-assoc protein 6

  4. NM_001353486.2 → NP_001340415.1  spermatogenesis associated 6-like protein isoform b

    Status: VALIDATED

    Source sequence(s)
    AL136231
    Consensus CDS
    CCDS6453.1
    UniProtKB/Swiss-Prot
    B4DIY4, Q5JVJ5, Q8IY90, Q8N4H0
    Related
    ENSP00000506787.1, ENST00000682582.1
    Conserved Domains (1) summary
    pfam14909
    Location:7 → 131
    SPATA6; Spermatogenesis-assoc protein 6

  5. NM_001353487.1 → NP_001340416.1  spermatogenesis associated 6-like protein isoform c

    Status: VALIDATED

    Source sequence(s)
    AL136231
    Conserved Domains (1) summary
    pfam14909
    Location:1 → 98
    SPATA6; Spermatogenesis-assoc protein 6

  6. NM_001353488.1 → NP_001340417.1  spermatogenesis associated 6-like protein isoform e

    Status: VALIDATED

    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    B4DX33
    Conserved Domains (1) summary
    pfam14909
    Location:1 → 40
    SPATA6; Spermatogenesis-assoc protein 6

  7. NM_001353489.1 → NP_001340418.1  spermatogenesis associated 6-like protein isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7), as well as variant 8, encodes isoform f.
    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    B4DX33
    Conserved Domains (1) summary
    pfam14909
    Location:1 → 22
    SPATA6; Spermatogenesis-assoc protein 6

  8. NM_001353490.1 → NP_001340419.1  spermatogenesis associated 6-like protein isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8), as well as variant 7, encodes isoform f.
    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    B4DX33
    Conserved Domains (1) summary
    pfam14909
    Location:1 → 22
    SPATA6; Spermatogenesis-assoc protein 6

  9. NM_001353491.2 → NP_001340420.1  spermatogenesis associated 6-like protein isoform g

    Status: VALIDATED

    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    B4DX33

  10. NM_001416130.1 → NP_001403059.1  spermatogenesis associated 6-like protein isoform a

    Status: VALIDATED

    Source sequence(s)
    AL136231
    UniProtKB/TrEMBL
    A0AA34QVF8
    Related
    ENSP00000516765.1, ENST00000707146.1

RNA

  1. NR_148443.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231

  2. NR_148444.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231
    Related
    ENST00000486047.5

  3. NR_148445.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231

  4. NR_148446.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231

  5. NR_148447.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231

  6. NR_148448.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL136231

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    4588821..4666480 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423558.1 → XP_047279514.1  spermatogenesis associated 6-like protein isoform X1

  2. XM_047423557.1 → XP_047279513.1  spermatogenesis associated 6-like protein isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    4592492..4670154 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363213.1 → XP_054219188.1  spermatogenesis associated 6-like protein isoform X1

  2. XM_054363212.1 → XP_054219187.1  spermatogenesis associated 6-like protein isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017985.3: Suppressed sequence

    Description
    NM_017985.3: 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
Q8N4H0.2 GenPept UniProtKB/Swiss-Prot:Q8N4H0

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