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    SPATA20 spermatogenesis associated 20 [ Homo sapiens (human) ]

    Gene ID: 64847, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPATA20provided by HGNC
    Official Full Name
    spermatogenesis associated 20provided by HGNC
    Primary source
    HGNC:HGNC:26125
    See related
    Ensembl:ENSG00000006282 MIM:613939; AllianceGenome:HGNC:26125
    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
    SSP411; Tisp78; HEL-S-98
    Summary
    Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 59.2), thyroid (RPKM 34.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPATA20 in Genome Data Viewer
    Location:
    17q21.33
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50547174..50555852)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51414308..51422988)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48624535..48633213)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8701 Neighboring gene MYCBP associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48610962-48611638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48611639-48612315 Neighboring gene uncharacterized LOC105371824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48620417-48620917 Neighboring gene epsin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8704 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:48626222-48626443 Neighboring gene CACNA1G antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12387 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48639035-48639624 Neighboring gene calcium voltage-gated channel subunit alpha1 G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48646614-48647600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48670255-48671063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48673674-48674174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48686338-48686945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48702910-48703682 Neighboring gene uncharacterized LOC101927253

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Comparative proteomic profiling of human bile reveals SSP411 as a novel biomarker of cholangiocarcinoma. Shen J, et al. PLoS One, 2012. PMID 23118872, 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. Cloning and characterization of rat spermatid protein SSP411: a thioredoxin-like protein. Shi HJ, et al. J Androl, 2004 Jul-Aug. PMID 15223837
    4. p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors. Karras P, et al. Cancer Cell, 2019 Jan 14. PMID 30581152
    5. A protein interaction framework for human mRNA degradation. Lehner B, et al. Genome Res, 2004 Jul. PMID 15231747, Free PMC Article

    See all (24) 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. SSP411 has potential as a biomarker for the diagnosis of Cholangiocarcinoma
      Title: Comparative proteomic profiling of human bile reveals SSP411 as a novel biomarker of cholangiocarcinoma.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21347, FLJ21969, MGC111032, DKFZp686H1839

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    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
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 20
    Names
    epididymis secretory protein Li 98
    sperm protein SSP411
    sperm-specific protein 411
    transcript increased in spermiogenesis 78

    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_001258372.2 → NP_001245301.1  spermatogenesis-associated protein 20 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001245301.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC025255, BC111029, BM787432
      Consensus CDS
      CCDS58563.1
      UniProtKB/Swiss-Prot
      Q2TA99, Q2XUZ6, Q6P0P1, Q8TB22, Q8WVW3, Q9H747
      UniProtKB/TrEMBL
      A0A0K0K1J9
      Related
      ENSP00000348878.4, ENST00000356488.8
      Conserved Domains (3) summary
      COG1331
      Location:57 → 784
      YyaL; Uncharacterized conserved protein YyaL, SSP411 family, contains thoiredoxin and six-hairpin glycosidase-like domains [General function prediction only]
      pfam03190
      Location:62 → 223
      Thioredox_DsbH; Protein of unknown function, DUF255
      cl23840
      Location:276 → 395
      AGE; AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is ...

    2. NM_001258373.2 → NP_001245302.1  spermatogenesis-associated protein 20 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to variant 1.
      Source sequence(s)
      BC025255, BC065526, DA295930
      Consensus CDS
      CCDS58564.1
      UniProtKB/TrEMBL
      A8K6Z0, B3KS41
      Conserved Domains (3) summary
      COG1331
      Location:13 → 740
      YyaL; Uncharacterized conserved protein YyaL, SSP411 family, contains thoiredoxin and six-hairpin glycosidase-like domains [General function prediction only]
      pfam03190
      Location:18 → 179
      Thioredox_DsbH; Protein of unknown function, DUF255
      cl23840
      Location:232 → 351
      AGE; AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is ...

    3. NM_022827.4 → NP_073738.2  spermatogenesis-associated protein 20 isoform 1 precursor

      See identical proteins and their annotated locations for NP_073738.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC025255, BM787432
      Consensus CDS
      CCDS11571.1
      UniProtKB/TrEMBL
      A0A0K0K1J9
      Related
      ENSP00000006658.6, ENST00000006658.11
      Conserved Domains (3) summary
      COG1331
      Location:73 → 800
      YyaL; Uncharacterized conserved protein YyaL, SSP411 family, contains thoiredoxin and six-hairpin glycosidase-like domains [General function prediction only]
      pfam03190
      Location:78 → 239
      Thioredox_DsbH; Protein of unknown function, DUF255
      cl23840
      Location:292 → 411
      AGE; AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is ...

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      50547174..50555852
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      51414308..51422988
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TB22.3 GenPept UniProtKB/Swiss-Prot:Q8TB22

    Gene LinkOut

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