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

    Gene ID: 26010, updated on 3-Nov-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, Nov 2024]
    Expression
    Ubiquitous expression in gall bladder (RPKM 14.3), heart (RPKM 9.6) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (200305879..200482264)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (200789476..200965756)
    RS_2024_09 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 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. 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
    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. 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
    4. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Schmidt N, et al. Cell, 2023 Oct 26. PMID 37794589, Free PMC Article
    5. 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

    See all (88) 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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    NEW Try the new Transcript table

    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_2024_08

    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

    Gene LinkOut

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

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