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    STON1-GTF2A1L STON1-GTF2A1L readthrough [ Homo sapiens (human) ]

    Gene ID: 286749, updated on 2-Nov-2024

    Summary

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    Official Symbol
    STON1-GTF2A1Lprovided by HGNC
    Official Full Name
    STON1-GTF2A1L readthroughprovided by HGNC
    Primary source
    HGNC:HGNC:30651
    See related
    Ensembl:ENSG00000068781 AllianceGenome:HGNC:30651
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALF; SALF; GTF2A1L; GTF2A1LF
    Summary
    STON1-GTF2A1L mRNAs are infrequent but naturally occurring read-through products of the neighboring STON1 and GTF2A1L genes. These transcripts encode fusion proteins composed of the vast majority of each of the individual elements, stonin 1 and general transcription factor IIA, 1-like. Alternative splicing results in multiple transcript variants. The significance of these read-through variants and the function of the resulting protein products have not yet been determined. [provided by RefSeq, Oct 2010]
    Expression
    Broad expression in testis (RPKM 13.2), endometrium (RPKM 9.3) and 20 other tissues See more
    Orthologs
    all
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    Genomic context

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    See STON1-GTF2A1L in Genome Data Viewer
    Location:
    2p16.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (48529925..48776519)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (48535810..48772541)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (48757064..49003658)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11479 Neighboring gene forkhead box N2 Neighboring gene RNA, U4 small nuclear 49, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48617307-48617446 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48628408-48628554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48674501-48675002 Neighboring gene protein phosphatase 1 regulatory subunit 21 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48734957-48735731 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48735732-48736506 Neighboring gene RNA, U6 small nuclear 282, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48757286-48757833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48787383-48787921 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48812672-48813306 Neighboring gene stonin 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48841993-48842496 Neighboring gene general transcription factor IIA subunit 1 like Neighboring gene TPT1 pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15747 Neighboring gene luteinizing hormone/choriogonadotropin receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48982421-48983197 Neighboring gene uncharacterized LOC105374594 Neighboring gene elongin B pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:49067851-49069050 Neighboring gene CTBP2 pseudogene 5

    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. A genome-wide association study identified a novel genetic loci STON1-GTF2A1L/LHCGR/FSHR for bilaterality of neovascular age-related macular degeneration. Kawashima-Kumagai K, et al. Sci Rep, 2017 Aug 3. PMID 28775256, Free PMC Article
    2. Identification of a general transcription factor TFIIAalpha/beta homolog selectively expressed in testis. Upadhyaya AB, et al. J Biol Chem, 1999 Jun 18. PMID 10364255
    3. Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3. Chen ZJ, et al. Nat Genet, 2011 Jan. PMID 21151128
    4. Human stoned B interacts with AP-2 and synaptotagmin and facilitates clathrin-coated vesicle uncoating. Walther K, et al. EMBO Rep, 2001 Jul. PMID 11454741, Free PMC Article
    5. TFIIAalpha/beta-like factor is encoded by a germ cell-specific gene whose expression is up-regulated with other general transcription factors during spermatogenesis in the mouse. Han SY, et al. Biol Reprod, 2001 Feb. PMID 11159353

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GWAS for neovascular age-related macular degeneration bilaterality found new genetic loci STON1-GTF2A1L/LHCGR/FSHR
      Title: A genome-wide association study identified a novel genetic loci STON1-GTF2A1L/LHCGR/FSHR for bilaterality of neovascular age-related macular degeneration.
    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
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome.
    EBI GWAS Catalog
    Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC126821, MGC126823

    General protein information

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    Preferred Names
    STON1-GTF2A1L protein
    Names
    General transcription factor II A, 1-like factor
    TFIIA-alpha and beta-like factor
    stoned B/TFIIA-alpha/beta-like factor

    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.

    Genomic

    1. NG_033050.2 RefSeqGene

      Range
      5001..251593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198593.2 → NP_001185522.1  STON1-GTF2A1L protein isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC073082, AC091788, AK309740, BG191372
      UniProtKB/TrEMBL
      Q3MIM1
      Related
      ENSP00000385701.1, ENST00000402114.6
      Conserved Domains (3) summary
      cd07976
      Location:712 → 760
      TFIIA_alpha_beta_like; Precursor of TFIIA alpha and beta subunits and similar proteins
      cd09262
      Location:403 → 716
      AP_stonin-1_MHD; Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor)
      pfam03153
      Location:714 → 1147
      TFIIA; Transcription factor IIA, alpha/beta subunit

    2. NM_001198594.1 → NP_001185523.1  STON1-GTF2A1L protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons, resulting in a loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1. The 5' UTR is incomplete due to a lack of 5'-complete transcript support for this variant and the presence of splicing ambiguity further upstream.
      Source sequence(s)
      AC073082, BC143520
      UniProtKB/TrEMBL
      A0A0A6YYG5, Q3MIM1
      Related
      ENSP00000378234.3, ENST00000394751.5
      Conserved Domains (3) summary
      cd07976
      Location:1078 → 1135
      TFIIA_alpha_beta_like; Precursor of TFIIA alpha and beta subunits and similar proteins
      cd09262
      Location:403 → 716
      AP_stonin-1_MHD; Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor)
      pfam03153
      Location:714 → 1135
      TFIIA; Transcription factor IIA, alpha/beta subunit

    3. NM_172311.3 → NP_758515.1  STON1-GTF2A1L protein isoform 1

      See identical proteins and their annotated locations for NP_758515.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC073082, AF026169, BC101774
      UniProtKB/TrEMBL
      Q3MIM1, Q53S48
      Related
      ENSP00000378236.1, ENST00000394754.5
      Conserved Domains (3) summary
      cd07976
      Location:1125 → 1182
      TFIIA_alpha_beta_like; Precursor of TFIIA alpha and beta subunits and similar proteins
      cd09262
      Location:403 → 716
      AP_stonin-1_MHD; Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor)
      pfam03153
      Location:714 → 1182
      TFIIA; Transcription factor IIA, alpha/beta subunit

    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
      48529925..48776519
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      48535810..48772541
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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