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    GCFC2 GC-rich sequence DNA-binding factor 2 [ Homo sapiens (human) ]

    Gene ID: 6936, updated on 10-Dec-2024

    Summary

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    Official Symbol
    GCFC2provided by HGNC
    Official Full Name
    GC-rich sequence DNA-binding factor 2provided by HGNC
    Primary source
    HGNC:HGNC:1317
    See related
    Ensembl:ENSG00000005436 MIM:189901; AllianceGenome:HGNC:1317
    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
    GCF; TCF9; DNABF; C2orf3
    Summary
    The first mRNA transcript isolated for this gene was part of an artificial chimera derived from two distinct gene transcripts and a primer used in the cloning process (see Genbank accession M29204). A positively charged amino terminus present only in the chimera was determined to bind GC-rich DNA, thus mistakenly thought to identify a transcription factor gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.0), testis (RPKM 4.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GCFC2 in Genome Data Viewer
    Location:
    2p12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (75662705..75713122, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (75671995..75722342, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (75889831..75938041, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 13771 Neighboring gene uncharacterized LOC124906025 Neighboring gene SPT4 homolog, DSIF elongation factor subunit pseudogene Neighboring gene mitochondrial ribosomal protein L19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11683 Neighboring gene uncharacterized LOC105374813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:75938851-75939422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:75951704-75952204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:75960925-75961425 Neighboring gene NANOG hESC enhancer GRCh37_chr2:75999954-76000657 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:76096873-76097671 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:76097672-76098469 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:76098746-76099945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11684 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:76220709-76221210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16094 Neighboring gene SUCLA2 pseudogene 2 Neighboring gene PNP pseudogene 1

    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. Expression and chromosomal localization of the gene for the human transcriptional repressor GCF. Johnson AC, et al. J Biol Chem, 1992 Jan 25. PMID 1370479
    2. Molecular cloning and characterization of a human DNA binding factor that represses transcription. Kageyama R, et al. Cell, 1989 Dec 1. PMID 2556218
    3. [Revisions of the cDNA and primary protein structure of human transcription factor GCF]. Mao P. Hokkaido Igaku Zasshi, 1999 Jul. PMID 10480038
    4. Molecular analysis of the GCF gene identifies revisions to the cDNA and amino acid sequences(1). Takimoto M, et al. Biochim Biophys Acta, 1999 Oct 6. PMID 10500253
    5. A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia. Anthoni H, et al. Hum Mol Genet, 2007 Mar 15. PMID 17309879

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Authors propose the GCF regulated transcriptional activity, at least in part, contributed to the upregulation of IER5 on radiation in HepG2 cells. The present findings provide insights into understanding the regulatory mechanisms of IER5.
      Title: Transcriptional regulation of IER5 in response to radiation in HepG2.
    2. C2ORF3 protein is required for pre-mRNA splicing through its presumable role in efficient intron turnover
      Title: Identification of a novel component C2ORF3 in the lariat-intron complex: lack of C2ORF3 interferes with pre-mRNA splicing via intron turnover pathway.
    3. 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.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study of childhood acute lymphoblastic leukemia in Korea.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analysis of dyslexia candidate genes in the Raine cohort representing the general Australian population.
    6. Study refined the 2p12 candidate region in two populations and report evidence supporting MRPL19 and C2ORF3 as candidate susceptibility genes for dyslexia.
      Title: A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Multiple loci influencing hippocampal degeneration identified by genome scan.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U2-type post-mRNA release spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    intron Large complex component GCFC2
    Names
    GC binding factor
    GC bindng factor
    TCF-9
    transcription factor 9 (binds GC-rich sequences)

    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_001201334.2 → NP_001188263.1  intron Large complex component GCFC2 isoform 2

      See identical proteins and their annotated locations for NP_001188263.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC005034, AK097564, BC064559, EF158469
      UniProtKB/TrEMBL
      B3KUM5
      Conserved Domains (1) summary
      pfam07842
      Location:298 → 513
      GCFC; GC-rich sequence DNA-binding factor-like protein

    2. NM_001201335.2 → NP_001188264.1  intron Large complex component GCFC2 isoform 3

      See identical proteins and their annotated locations for NP_001188264.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC000853, BU189326, BU623860
      Consensus CDS
      CCDS62943.1
      UniProtKB/TrEMBL
      Q9BVX3
      Related
      ENSP00000474481.1, ENST00000470503.1

    3. NM_001410845.1 → NP_001397774.1  intron Large complex component GCFC2 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC005034
      Consensus CDS
      CCDS92788.1
      Related
      ENSP00000386552.3, ENST00000409857.7

    4. NM_003203.5 → NP_003194.3  intron Large complex component GCFC2 isoform 1

      See identical proteins and their annotated locations for NP_003194.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC005034, BC064559, BU189326, EF158469
      Consensus CDS
      CCDS1961.1
      UniProtKB/Swiss-Prot
      A4UHQ8, A4UHQ9, O95032, P16383, Q53TY0, Q6P2F2
      Related
      ENSP00000318690.3, ENST00000321027.8
      Conserved Domains (2) summary
      pfam07842
      Location:467 → 682
      GCFC; GC-rich sequence DNA-binding factor-like protein
      pfam15458
      Location:75 → 235
      NTR2; Nineteen complex-related protein 2

    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
      75662705..75713122 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445615.1 → XP_047301571.1  intron Large complex component GCFC2 isoform X4

      UniProtKB/TrEMBL
      B3KUM5

    2. XM_011533074.4 → XP_011531376.1  intron Large complex component GCFC2 isoform X3

      Related
      ENST00000470197.5
      Conserved Domains (1) summary
      pfam07842
      Location:392 → 607
      GCFC; GC-rich sequence DNA-binding factor-like protein

    3. XM_047445613.1 → XP_047301569.1  intron Large complex component GCFC2 isoform X2

    4. XM_005264520.5 → XP_005264577.1  intron Large complex component GCFC2 isoform X1

      Conserved Domains (2) summary
      pfam07842
      Location:475 → 690
      GCFC; GC-rich sequence DNA-binding factor-like protein
      pfam15458
      Location:125 → 243
      NTR2; Nineteen complex-related protein 2

    5. XM_011533075.3 → XP_011531377.1  intron Large complex component GCFC2 isoform X5

      Conserved Domains (1) summary
      pfam15458
      Location:125 → 243
      NTR2; Nineteen complex-related protein 2

    6. XM_017004787.3 → XP_016860276.1  intron Large complex component GCFC2 isoform X5

      Conserved Domains (1) summary
      pfam15458
      Location:125 → 243
      NTR2; Nineteen complex-related protein 2

    RNA

    1. XR_007080682.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      75671995..75722342 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343577.1 → XP_054199552.1  intron Large complex component GCFC2 isoform X4

      UniProtKB/TrEMBL
      B3KUM5

    2. XM_054343576.1 → XP_054199551.1  intron Large complex component GCFC2 isoform X3

    3. XM_054343575.1 → XP_054199550.1  intron Large complex component GCFC2 isoform X2

    4. XM_054343574.1 → XP_054199549.1  intron Large complex component GCFC2 isoform X1

    5. XM_054343578.1 → XP_054199553.1  intron Large complex component GCFC2 isoform X5

    6. XM_054343579.1 → XP_054199554.1  intron Large complex component GCFC2 isoform X5

    RNA

    1. XR_008486499.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P16383.2 GenPept UniProtKB/Swiss-Prot:P16383

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