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

Gene ID: 6936, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (75662705..75713122, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (75671995..75722342, complement)
105.20220307 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. 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
  2. [Revisions of the cDNA and primary protein structure of human transcription factor GCF]. Mao P. Hokkaido Igaku Zasshi, 1999 Jul. PMID 10480038
  3. Molecular cloning and characterization of a human DNA binding factor that represses transcription. Kageyama R, et al. Cell, 1989 Dec 1. PMID 2556218
  4. 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
  5. Transcriptional regulation of IER5 in response to radiation in HepG2. Yang C, et al. Cancer Gene Ther, 2016 Feb-Mar. PMID 26915404

See all (44) 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)

Genotypes

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_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
    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

Gene LinkOut

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