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

    Gene ID: 55064, updated on 28-Oct-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 head-tail coupling apparatus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 1.8), gall bladder (RPKM 0.4) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPATA6L in Genome Data Viewer
    Location:
    9p24.2-p24.1
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (4588821..4666480, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (4592492..4670154, complement)
    RS_2024_09 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 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. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article
    4. 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
    5. 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

    See all (13) 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 head-tail coupling apparatus 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_2024_08

    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

    Gene LinkOut

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

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