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SPATS2L spermatogenesis associated serine rich 2 like [ Homo sapiens (human) ]

Gene ID: 26010, updated on 5-Mar-2024

Summary

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Official Symbol
SPATS2Lprovided by HGNC
Official Full Name
spermatogenesis associated serine rich 2 likeprovided by HGNC
Primary source
HGNC:HGNC:24574
See related
Ensembl:ENSG00000196141 MIM:613817; AllianceGenome:HGNC:24574
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
SGNP; DNAPTP6
Summary
Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in gall bladder (RPKM 14.3), heart (RPKM 9.6) and 25 other tissues See more
Orthologs
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Genomic context

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See SPATS2L in Genome Data Viewer
Location:
2q33.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (200305879..200482264)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (200789476..200965756)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (201170602..201346987)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906112 Neighboring gene uncharacterized LOC124907962 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:200874708-200874865 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:200919369-200920289 Neighboring gene uncharacterized LOC105373833 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:201022335-201023070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:201023071-201023805 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:201067941-201068746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:201073293-201073822 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:201109283-201110482 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:201167128-201168327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:201176989-201177489 Neighboring gene Sharpr-MPRA regulatory region 2520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:201243374-201243900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16957 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:201253767-201254966 Neighboring gene uncharacterized LOC101927741 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:201270083-201271282 Neighboring gene RNY4 pseudogene 34 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12225 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12226 Neighboring gene potassium channel tetramerization domain containing 18 Neighboring gene shugoshin 2

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. Spermatogenesis associated serine rich 2 like plays a prognostic factor and therapeutic target in acute myeloid leukemia by regulating the JAK2/STAT3/STAT5 axis. Li F, et al. J Transl Med, 2023 Feb 11. PMID 36774517, Free PMC Article
  2. Genome-wide association analysis in asthma subjects identifies SPATS2L as a novel bronchodilator response gene. Himes BE, et al. PLoS Genet, 2012 Jul. PMID 22792082, Free PMC Article
  3. SGNP: an essential Stress Granule/Nucleolar Protein potentially involved in 5.8s rRNA processing/transport. Zhu CH, et al. PLoS One, 2008. PMID 19005571, Free PMC Article
  4. Genetic determinants of acute asthma therapy response in children with moderate-to-severe asthma exacerbations. Tse SM, et al. Pediatr Pulmonol, 2019 Apr. PMID 30644648
  5. Respiratory traits and coal workers' pneumoconiosis: Mendelian randomisation and association analysis. Wang T, et al. Occup Environ Med, 2021 Feb. PMID 33097673

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spermatogenesis associated serine rich 2 like plays a prognostic factor and therapeutic target in acute myeloid leukemia by regulating the JAK2/STAT3/STAT5 axis.
    Title: Spermatogenesis associated serine rich 2 like plays a prognostic factor and therapeutic target in acute myeloid leukemia by regulating the JAK2/STAT3/STAT5 axis.
  2. Respiratory traits and coal workers' pneumoconiosis: Mendelian randomisation and association analysis.
    Title: Respiratory traits and coal workers' pneumoconiosis: Mendelian randomisation and association analysis.
  3. While controlling for clinical determinants, in acute asthma therapy response, SNP rs295137 in SPATS2L (OR = 1.77, 95%CI: 1.17, 2.68) was significantly associated with increased odds of emergency department (ED) management failure. Two SNPs in IL33 were associated with decreased odds of ED management failure: rs7037276 (OR = 0.55, 95%CI: 0.33, 0.90), and rs1342326 (OR = 0.52, 95%CI: 0.32, 0.86).
    Title: Genetic determinants of acute asthma therapy response in children with moderate-to-severe asthma exacerbations.
  4. Down-regulation of SPATS2L expression may be related to the etiology of poor sleep quality and chronic abdominal pain.
    Title: Sleep quality, BDNF genotype and gene expression in individuals with chronic abdominal pain.
  5. A haplotype of 23 SNPs spanning 131.6 Kb shared by all affected members of 3 linked families with restless legs syndrome was identified. The shared candidate region covers 46.9 Kb over the potassium channel-related gene KCTD18 and exons 10-13 of SPATS2L.
    Title: Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.
  6. Our results suggest that SPATS2L may be an important regulator of beta(2)-adrenergic receptor down-regulation and that there is promise in gaining a better understanding of the biological mechanisms of differential response to beta(2)-agonists through GWAS.
    Title: Genome-wide association analysis in asthma subjects identifies SPATS2L as a novel bronchodilator response gene.
  7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  9. SGNP is localized in both the cytoplasm and nucleolus and defines a non-nucleolar compartment containing 5.8S rRNA. Under oxidative stress, SGNP nucleolar localization decreases and it rapidly co-localizes with stress granules.
    Title: SGNP: an essential Stress Granule/Nucleolar Protein potentially involved in 5.8s rRNA processing/transport.
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
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Genome-wide association analysis in asthma subjects identifies SPATS2L as a novel bronchodilator response gene.
EBI GWAS Catalog
Genome-wide association study of exercise behavior in Dutch and American adults.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of discs, large (Drosophila) homolog-associated protein 1 (DLGAP1; LOC26010) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14138, DKFZp564A2416

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
SPATS2-like protein
Names
DNA polymerase-transactivated protein 6
stress granule and nucleolar 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_001100422.1 → NP_001093892.1  SPATS2-like protein isoform a

    See identical proteins and their annotated locations for NP_001093892.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2, 3 and 5 encode the same isoform a.
    Source sequence(s)
    AC012459, AK002064, BC018736, BQ030316, CN480518, DB206952
    Consensus CDS
    CCDS46483.1
    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6
    Related
    ENSP00000386931.3, ENST00000409988.7
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 368
    DUF1387; Protein of unknown function (DUF1387)

  2. NM_001100423.2 → NP_001093893.1  SPATS2-like protein isoform a

    See identical proteins and their annotated locations for NP_001093893.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2, 3 and 5 encode the same isoform a.
    Source sequence(s)
    AC012459, AF193059, AL525852, BQ030316, DB454965
    Consensus CDS
    CCDS46483.1
    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6
    Related
    ENSP00000386730.3, ENST00000409140.8
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 368
    DUF1387; Protein of unknown function (DUF1387)

  3. NM_001100424.1 → NP_001093894.1  SPATS2-like protein isoform b

    See identical proteins and their annotated locations for NP_001093894.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 5' UTR exon and lacks an in-frame coding exon, compared to variant 1. The resulting isoform (b) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AC012459, BC010848, BQ030316, CN480518, DB206952
    Consensus CDS
    CCDS46484.1
    UniProtKB/Swiss-Prot
    Q9NUQ6
    Related
    ENSP00000353989.5, ENST00000360760.9
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 299
    DUF1387; Protein of unknown function (DUF1387)

  4. NM_001282735.1 → NP_001269664.1  SPATS2-like protein isoform a

    See identical proteins and their annotated locations for NP_001269664.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an alternate splice site in the 5' UTR, which results in a longer 5' UTR, compared to variant 1. Variants 1, 2, 3 and 5 encode the same isoform a.
    Source sequence(s)
    AC012459, AK290496, AL110124, BP310992, BQ030316
    Consensus CDS
    CCDS46483.1
    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6
    Related
    ENSP00000386336.1, ENST00000409718.5
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 368
    DUF1387; Protein of unknown function (DUF1387)

  5. NM_001282743.1 → NP_001269672.1  SPATS2-like protein isoform c

    See identical proteins and their annotated locations for NP_001269672.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) has an alternate splice site in the 5' UTR, lacks an internal exon which contains the translation start codon, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AC012459, AF193059, AK090867, AK290496, BP310992, BQ030316
    Consensus CDS
    CCDS74622.1
    UniProtKB/TrEMBL
    B8ZZZ7
    Related
    ENSP00000386391.1, ENST00000409385.5
    Conserved Domains (1) summary
    pfam07139
    Location:17 → 308
    DUF1387; Protein of unknown function (DUF1387)

  6. NM_001282744.2 → NP_001269673.1  SPATS2-like protein isoform d

    See identical proteins and their annotated locations for NP_001269673.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) has an alternate 5' terminal exon which contains an upstream in-frame AUG codon, compared to variant 1. The resulting isoform (d) has a longer N-terminus, compared to isoform a.
    Source sequence(s)
    AC012459, AC074213, AK300075, BQ030316
    Consensus CDS
    CCDS74621.1
    UniProtKB/Swiss-Prot
    Q9NUQ6
    Related
    ENSP00000482515.1, ENST00000619961.4
    Conserved Domains (1) summary
    pfam07139
    Location:89 → 397
    DUF1387; Protein of unknown function (DUF1387)

  7. NM_015535.3 → NP_056350.2  SPATS2-like protein isoform a

    See identical proteins and their annotated locations for NP_056350.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) and variants 2, 3 and 5 encode the same isoform (a).
    Source sequence(s)
    AC012459, AC074213, AY450394, BC018736, BP310992, BQ030316
    Consensus CDS
    CCDS46483.1
    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6
    Related
    ENSP00000351503.4, ENST00000358677.9
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 368
    DUF1387; Protein of unknown function (DUF1387)

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    200305879..200482264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452788.2 → XP_024308556.1  SPATS2-like protein isoform X4

    Conserved Domains (1) summary
    pfam07139
    Location:59 → 299
    DUF1387; Protein of unknown function (DUF1387)

  2. XM_011510938.2 → XP_011509240.1  SPATS2-like protein isoform X1

    See identical proteins and their annotated locations for XP_011509240.1

    UniProtKB/Swiss-Prot
    Q9NUQ6
    Conserved Domains (1) summary
    pfam07139
    Location:89 → 397
    DUF1387; Protein of unknown function (DUF1387)

  3. XM_047443892.1 → XP_047299848.1  SPATS2-like protein isoform X1

  4. XM_005246459.2 → XP_005246516.1  SPATS2-like protein isoform X4

    See identical proteins and their annotated locations for XP_005246516.1

    UniProtKB/Swiss-Prot
    Q9NUQ6
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 299
    DUF1387; Protein of unknown function (DUF1387)

  5. XM_017003784.3 → XP_016859273.1  SPATS2-like protein isoform X3

  6. XM_047443894.1 → XP_047299850.1  SPATS2-like protein isoform X2

    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6

  7. XM_047443895.1 → XP_047299851.1  SPATS2-like protein isoform X4

  8. XM_005246458.3 → XP_005246515.1  SPATS2-like protein isoform X2

    See identical proteins and their annotated locations for XP_005246515.1

    UniProtKB/Swiss-Prot
    A8K381, B4DRE6, B4DT67, B7WNZ7, Q53T22, Q8WV53, Q8WYG1, Q9NTW4, Q9NUQ6
    Related
    ENSP00000386310.1, ENST00000409151.5
    Conserved Domains (1) summary
    pfam07139
    Location:59 → 368
    DUF1387; Protein of unknown function (DUF1387)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    200789476..200965756
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NUQ6.2 GenPept UniProtKB/Swiss-Prot:Q9NUQ6

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