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

Gene ID: 94104, updated on 5-Mar-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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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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