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    PAXBP1 PAX3 and PAX7 binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 94104, updated on 5-May-2024

    Summary

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    Official Symbol
    PAXBP1provided by HGNC
    Official Full Name
    PAX3 and PAX7 binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:13579
    See related
    Ensembl:ENSG00000159086 MIM:617621; AllianceGenome:HGNC:13579
    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
    GCFC; BM020; GCFC1; FSAP105; C21orf66
    Summary
    Predicted to enable DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of histone methylation; positive regulation of myoblast proliferation; and regulation of skeletal muscle satellite cell proliferation. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in bone marrow (RPKM 19.2), ovary (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PAXBP1 in Genome Data Viewer
    Location:
    21q22.11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (32733899..32771755, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (31099918..31138061, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (34106210..34144066, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 7 subfamily E member 23 pseudogene Neighboring gene synaptojanin 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:34033532-34033721 Neighboring gene uncharacterized LOC124905011 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34099530-34100030 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34100031-34100531 Neighboring gene PAXBP1 antisense RNA 1 Neighboring gene uncharacterized LOC124905010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:34143733-34144722 Neighboring gene EPCIP antisense RNA 1 Neighboring gene exosomal polycystin 1 interacting protein Neighboring gene small nucleolar RNA SNORA70

    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. A homozygous potentially pathogenic variant in the PAXBP1 gene in a large family with global developmental delay and myopathic hypotonia. Alharby E, et al. Clin Genet, 2017 Dec. PMID 28542722
    2. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mudge JM, et al. Mol Biol Evol, 2011 Oct. PMID 21551269, Free PMC Article
    3. Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21. Slavov D, et al. Gene, 2000 Apr 18. PMID 10773462
    4. Pax3/7BP is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Diao Y, et al. Cell Stem Cell, 2012 Aug 3. PMID 22862948
    5. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. Reymond A, et al. Genomics, 2001 Nov. PMID 11707072

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A homozygous potentially pathogenic variant in the PAXBP1 gene in a large family with global developmental delay and myopathic hypotonia has been reported.
      Title: A homozygous potentially pathogenic variant in the PAXBP1 gene in a large family with global developmental delay and myopathic hypotonia.
    2. The GCFC1/C21orf66 distal promoter contains an inhibitory cis-regulatory element that is responsive to Trichostatin A (TSA) treatment according to promoter reporter assays in HEK 293 cells.
      Title: Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
    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

    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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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, GC-rich sequence DNA-binding factor 1 (GCFC1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa 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

    • FLJ90561

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of myoblast proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of skeletal muscle satellite cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PAX3- and PAX7-binding protein 1
    Names
    GC-rich sequence DNA-binding factor 1
    GC-rich sequence DNA-binding factor candidate
    functional spliceosome-associated protein 105

    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_013329.4 → NP_037461.2  PAX3- and PAX7-binding protein 1 isoform 2

      See identical proteins and their annotated locations for NP_037461.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AF153208, BC005213, BC030539, BC062992
      Consensus CDS
      CCDS33541.1
      UniProtKB/Swiss-Prot
      Q9Y5B6
      UniProtKB/TrEMBL
      Q8N6E6
      Related
      ENSP00000290178.4, ENST00000290178.4
      Conserved Domains (1) summary
      pfam07842
      Location:595 → 771
      GCFC; GC-rich sequence DNA-binding factor-like protein

    2. NM_016631.4 → NP_057715.2  PAX3- and PAX7-binding protein 1 isoform 1

      See identical proteins and their annotated locations for NP_057715.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BC030539, BC062992
      Consensus CDS
      CCDS13619.1
      UniProtKB/Swiss-Prot
      D3DSE7, Q96DU8, Q9NYQ0, Q9Y5B6
      Related
      ENSP00000328992.4, ENST00000331923.9
      Conserved Domains (1) summary
      pfam07842
      Location:595 → 806
      GCFC; GC-rich sequence DNA-binding factor-like protein

    RNA

    1. NR_027873.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AY033906, BC062992

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      32733899..32771755 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006724066.3 → XP_006724129.1  PAX3- and PAX7-binding protein 1 isoform X1

      Conserved Domains (1) summary
      pfam07842
      Location:595 → 771
      GCFC; GC-rich sequence DNA-binding factor-like protein

    2. XM_047441051.1 → XP_047297007.1  PAX3- and PAX7-binding protein 1 isoform X2

    3. XM_011529804.4 → XP_011528106.1  PAX3- and PAX7-binding protein 1 isoform X3

      Conserved Domains (1) summary
      pfam07842
      Location:595 → 641
      GCFC; GC-rich sequence DNA-binding factor-like protein

    4. XM_047441052.1 → XP_047297008.1  PAX3- and PAX7-binding protein 1 isoform X4

      Related
      ENSP00000393038.1, ENST00000443785.5

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315969.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      727..2677 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      31099918..31138061 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324958.1 → XP_054180933.1  PAX3- and PAX7-binding protein 1 isoform X1

    2. XM_054324959.1 → XP_054180934.1  PAX3- and PAX7-binding protein 1 isoform X2

    3. XM_054324960.1 → XP_054180935.1  PAX3- and PAX7-binding protein 1 isoform X3

    4. XM_054324961.1 → XP_054180936.1  PAX3- and PAX7-binding protein 1 isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_058191.3: Suppressed sequence

      Description
      NM_058191.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_145328.1: Suppressed sequence

      Description
      NM_145328.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5B6.2 GenPept UniProtKB/Swiss-Prot:Q9Y5B6

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