SPATA20 spermatogenesis associated 20 [Homo sapiens (human)] - Gene

Summary

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. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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

Location:: 17q21.33

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (50547174..50555852)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (51414308..51422988)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (48624535..48633213)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans.
Title: Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans.
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.

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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

RH12494 (e-PCR)
- UniSTS:71792

G31146 (e-PCR)
- UniSTS:73378

MARC_11627-11628:1002815904:1 (e-PCR)
- UniSTS:267250

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

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)

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 ...
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 ...
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 ...