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    GTF2A1L general transcription factor IIA subunit 1 like [ Homo sapiens (human) ]

    Gene ID: 11036, updated on 5-Mar-2024

    Summary

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    Official Symbol
    GTF2A1Lprovided by HGNC
    Official Full Name
    general transcription factor IIA subunit 1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:30727
    See related
    Ensembl:ENSG00000242441 MIM:605358; AllianceGenome:HGNC:30727
    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
    Summary
    The assembly and stability of the RNA polymerase II transcription pre-initiation complex on a eukaryotic core promoter involve the effects of transcription factor IIA (TFIIA) on the interaction between TATA-binding protein (TBP) and DNA. This gene encodes a germ cell-specific counterpart of the large (alpha/beta) subunit of general transcription factor TFIIA that is able to stabilize the binding of TBP to DNA and may be uniquely important to testis biology. Alternative splicing for this locus has been observed and two variants, encoding distinct isoforms, have been identified. Co-transcription of this gene and the neighboring upstream gene generates a rare transcript (SALF), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Mar 2014]
    Expression
    Biased expression in testis (RPKM 30.5), endometrium (RPKM 1.9) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p16.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (48617856..48679604)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (48620659..48675632)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (48844995..48906743)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes 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 STON1-GTF2A1L readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48757286-48757833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:48787383-48787921 Neighboring gene stonin 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:48812672-48813306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48841993-48842496 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

    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. Regulatory factor interactions and somatic silencing of the germ cell-specific ALF gene. Kim M, et al. J Biol Chem, 2006 Nov 10. PMID 16966320
    2. Involvement of ALF in human spermatogenesis and male infertility. Huang M, et al. Int J Mol Med, 2006 Apr. PMID 16525715
    3. Transcription Factor IIA tau is associated with undifferentiated cells and its gene expression is repressed in primary neurons at the chromatin level in vivo. Howe ML, et al. Stem Cells Dev, 2006 Apr. PMID 16646664
    4. Regulation of ALF gene expression in somatic and male germ line tissues involves partial and site-specific patterns of methylation. Xie W, et al. J Biol Chem, 2002 May 17. PMID 11889132
    5. Association of single nucleotide polymorphisms in the USF1, GTF2A1L and OR2W3 genes with non-obstructive azoospermia in the Chinese population. Zhang Y, et al. J Assist Reprod Genet, 2015 Jan. PMID 25374392, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our results provided a new insight into susceptibility of USF1 variant with male infertility. rs11204546 of OR2W3 and rs11677854 of GTF2A1L might be additional valuable molecular predictive markers
      Title: Association of single nucleotide polymorphisms in the USF1, GTF2A1L and OR2W3 genes with non-obstructive azoospermia in the Chinese population.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Results identified ALF as a human spermatogenesis related gene, the abnormal expression of ALF might be the partial cause for human infertility.
      Title: Involvement of ALF in human spermatogenesis and male infertility.
    4. A unique CpG-specific methylation pattern at the ALF promoter precedes expression in pachytene spermatocytes.
      Title: Regulation of ALF gene expression in somatic and male germ line tissues involves partial and site-specific patterns of methylation.
    5. TFIIA tau is associated with undifferentiated cells during development, yet is down-regulated at the chromatin level upon cellular differentiation.
      Title: Transcription Factor IIA tau is associated with undifferentiated cells and its gene expression is repressed in primary neurons at the chromatin level in vivo.
    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 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

    Readthrough STON1-GTF2A1L

    Readthrough gene: STON1-GTF2A1L, Included gene: STON1

    Homology

    Clone Names

    • MGC26254

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cognition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription initiation at RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in male germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription factor TFIIA complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    TFIIA-alpha and beta-like factor
    Names
    GTF2A1-like factor
    TFIIA-alpha/beta-like factor
    general transcription factor II A, 1-like factor
    general transcription factor IIA 1-like
    testis secretory sperm-binding protein Li 230m

    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_001193487.3 → NP_001180416.1  TFIIA-alpha and beta-like factor isoform 2

      See identical proteins and their annotated locations for NP_001180416.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK302220, BG207854
      Consensus CDS
      CCDS54359.1
      UniProtKB/Swiss-Prot
      Q9UNN4
      Related
      ENSP00000387896.2, ENST00000430487.6
      Conserved Domains (2) summary
      cd07976
      Location:387 → 444
      TFIIA_alpha_beta_like; Precursor of TFIIA alpha and beta subunits and similar proteins
      pfam03153
      Location:8 → 444
      TFIIA; Transcription factor IIA, alpha/beta subunit

    2. NM_006872.5 → NP_006863.2  TFIIA-alpha and beta-like factor isoform 1

      See identical proteins and their annotated locations for NP_006863.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC025991, BG207854
      Consensus CDS
      CCDS46281.1
      UniProtKB/Swiss-Prot
      B4DY14, Q53FD9, Q5D050, Q9UNN4
      UniProtKB/TrEMBL
      A0A140VKA3
      Related
      ENSP00000384597.3, ENST00000403751.8
      Conserved Domains (1) summary
      pfam03153
      Location:10 → 478
      TFIIA; Transcription factor IIA, alpha/beta subunit

    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
      48617856..48679604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      48620659..48675632
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_172196.1: Suppressed sequence

      Description
      NM_172196.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UNN4.2 GenPept UniProtKB/Swiss-Prot:Q9UNN4

    Gene LinkOut

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

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