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SPATA20 spermatogenesis associated 20 [ Homo sapiens (human) ]

Gene ID: 64847, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in testis (RPKM 59.2), thyroid (RPKM 34.4) and 25 other tissues See more
Orthologs
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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: 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. 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)

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

  • 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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