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 Ref... See more...

Aliases for GCFC2 Gene

Aliases for GCFC2 Gene

  • GC-Rich Sequence DNA-Binding Factor 2 2 3 4 5
  • Transcription Factor 9 (Binds GC-Rich Sequences) 2 3
  • GC Binding Factor 2 3
  • C2orf3 3 4
  • TCF-9 3 4
  • TCF9 3 4
  • GCF 3 4
  • GC-Rich Sequence DNA-Binding Factor 4
  • Chromosome 2 Open Reading Frame 3 2
  • Transcription Factor 9 4
  • GC Bindng Factor 3
  • DNABF 3

External Ids for GCFC2 Gene

Previous HGNC Symbols for GCFC2 Gene

  • TCF9
  • C2orf3

Previous GeneCards Identifiers for GCFC2 Gene

  • GC02M075880

Summaries for GCFC2 Gene

Entrez Gene Summary for GCFC2 Gene

  • 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]

GeneCards Summary for GCFC2 Gene

GCFC2 (GC-Rich Sequence DNA-Binding Factor 2) is a Protein Coding gene. Diseases associated with GCFC2 include Dyslexia and Reading Disorder. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific. An important paralog of this gene is PAXBP1.

UniProtKB/Swiss-Prot Summary for GCFC2 Gene

  • Factor that represses transcription. It binds to the GC-rich sequences (5'-GCGGGGC-3') present in the epidermal growth factor receptor, beta-actin, and calcium-dependent protease promoters. Involved in pre-mRNA splicing through regulating spliceosome C complex formation. May play a role during late-stage splicing events and turnover of excised inrons.

Gene Wiki entry for GCFC2 Gene

Additional gene information for GCFC2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GCFC2 Gene

Genomics for GCFC2 Gene

GeneHancer (GH) Regulatory Elements for GCFC2 Gene

Promoters and enhancers for GCFC2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GCFC2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GCFC2

Genomic Locations for GCFC2 Gene

Genomic Locations for GCFC2 Gene
chr2:75,652,000-75,710,986
(GRCh38/hg38)
Size:
58,987 bases
Orientation:
Minus strand
chr2:75,879,126-75,938,115
(GRCh37/hg19)
Size:
58,990 bases
Orientation:
Minus strand

Genomic View for GCFC2 Gene

Genes around GCFC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GCFC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GCFC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GCFC2 Gene

Proteins for GCFC2 Gene

  • Protein details for GCFC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P16383-GCFC2_HUMAN
    Recommended name:
    GC-rich sequence DNA-binding factor 2
    Protein Accession:
    P16383
    Secondary Accessions:
    • A4UHQ8
    • A4UHQ9
    • O95032
    • Q53TY0
    • Q6P2F2

    Protein attributes for GCFC2 Gene

    Size:
    781 amino acids
    Molecular mass:
    89385 Da
    Quaternary structure:
    • Found in the Intron Large (IL) complex, a post-mRNA release spliceosomal complex containing the excised intron, U2, U5 and U6 snRNPs, and splicing factors. Interacts with TFIP11 and DHX15.
    SequenceCaution:
    • Sequence=AAA35598.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAA35598.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. The N-terminus matches the 2q37.3 region.; Evidence={ECO:0000305};

    Alternative splice isoforms for GCFC2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GCFC2 Gene

Post-translational modifications for GCFC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GCFC2 Gene

Domains & Families for GCFC2 Gene

Gene Families for GCFC2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for GCFC2 Gene

Blocks:
  • GC-rich sequence DNA-binding factor-like
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GCFC2 Gene

GenScript: Design optimal peptide antigens:
  • Chromosome 2 open reading frame 3, isoform CRA_a (A4UHQ8_HUMAN)
  • C2ORF3 variant 3 (A4UHR0_HUMAN)
  • Transcription factor 9 (GCF_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P16383

UniProtKB/Swiss-Prot:

GCFC2_HUMAN :
  • Belongs to the GCF family.
Family:
  • Belongs to the GCF family.
genes like me logo Genes that share domains with GCFC2: view

Function for GCFC2 Gene

Molecular function for GCFC2 Gene

UniProtKB/Swiss-Prot Function:
Factor that represses transcription. It binds to the GC-rich sequences (5'-GCGGGGC-3') present in the epidermal growth factor receptor, beta-actin, and calcium-dependent protease promoters. Involved in pre-mRNA splicing through regulating spliceosome C complex formation. May play a role during late-stage splicing events and turnover of excised inrons.

Phenotypes From GWAS Catalog for GCFC2 Gene

Gene Ontology (GO) - Molecular Function for GCFC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 9705290
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 9705290
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
GO:0005515 protein binding IPI 24304693
genes like me logo Genes that share ontologies with GCFC2: view
genes like me logo Genes that share phenotypes with GCFC2: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GCFC2 Gene

Localization for GCFC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GCFC2 Gene

Nucleus, nucleoplasm. Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GCFC2 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GCFC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IBA 24304693
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA,IEA 24304693
GO:0005829 cytosol IDA --
GO:0071008 U2-type post-mRNA release spliceosomal complex IDA 24304693
genes like me logo Genes that share ontologies with GCFC2: view

Pathways & Interactions for GCFC2 Gene

PathCards logo

SuperPathways for GCFC2 Gene

SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
2 Human Embryonic Stem Cell Pluripotency
.50
.50
3 ERK Signaling
.58
.49
4 PAK Pathway
.36
5 TGF-Beta Pathway
.51
genes like me logo Genes that share pathways with GCFC2: view

Pathways by source for GCFC2 Gene

7 Qiagen pathways for GCFC2 Gene
  • Epithelial Adherens Junctions
  • Factors Promoting Cardiogenesis in Vertebrates
  • Human Embryonic Stem Cell Pluripotency
  • ILK Signaling
  • JNK Pathway

Gene Ontology (GO) - Biological Process for GCFC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 9705290
GO:0000245 spliceosomal complex assembly IMP 24304693
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006355 regulation of transcription, DNA-templated NAS 10500253
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with GCFC2: view

No data available for SIGNOR curated interactions for GCFC2 Gene

Drugs & Compounds for GCFC2 Gene

(1) Drugs for GCFC2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with GCFC2: view

Transcripts for GCFC2 Gene

mRNA/cDNA for GCFC2 Gene

3 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GCFC2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2a · 2b ^ 3a · 3b · 3c · 3d · 3e · 3f ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^
SP1: - - - - - - -
SP2: - - - - -
SP3: -
SP4: - -
SP5: - - -
SP6: - - - -
SP7: - -

ExUns: 14 ^ 15 ^ 16 ^ 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for GCFC2 Gene

GeneLoc Exon Structure for
GCFC2

Expression for GCFC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GCFC2 Gene

Protein differential expression in normal tissues from HIPED for GCFC2 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (18.3) and Bone (13.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GCFC2 Gene



Protein tissue co-expression partners for GCFC2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GCFC2

SOURCE GeneReport for Unigene cluster for GCFC2 Gene:

Hs.303808

mRNA Expression by UniProt/SwissProt for GCFC2 Gene:

P16383-GCFC2_HUMAN
Tissue specificity: Widely expressed in tissues and cell lines.

Evidence on tissue expression from TISSUES for GCFC2 Gene

  • Liver(4.3)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with GCFC2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for GCFC2 Gene

Orthologs for GCFC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for GCFC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GCFC2 31 30
  • 98.98 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GCFC2 31 30
  • 87.08 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GCFC2 31 30
  • 86.4 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gcfc2 30
  • 79.43 (n)
mouse
(Mus musculus)
Mammalia Gcfc2 17 31 30
  • 79.4 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GCFC2 31
  • 51 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GCFC2 31
  • 35 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 31
  • 54 (a)
OneToMany
-- 31
  • 52 (a)
OneToMany
-- 31
  • 48 (a)
OneToMany
-- 31
  • 48 (a)
OneToMany
-- 31
  • 47 (a)
OneToMany
-- 31
  • 47 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 46 (a)
OneToMany
-- 31
  • 45 (a)
OneToMany
-- 31
  • 45 (a)
OneToMany
-- 31
  • 44 (a)
OneToMany
-- 31
  • 44 (a)
OneToMany
-- 31
  • 43 (a)
OneToMany
-- 31
  • 42 (a)
OneToMany
-- 31
  • 42 (a)
OneToMany
-- 31
  • 41 (a)
OneToMany
-- 31
  • 40 (a)
OneToMany
-- 31
  • 38 (a)
OneToMany
-- 31
  • 37 (a)
OneToMany
-- 31
  • 31 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101734739 30
  • 58.15 (n)
Str.15866 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.15559 30
zebrafish
(Danio rerio)
Actinopterygii gcfc2 31 30
  • 51.92 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG1965 31
  • 22 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F43G9.12 31
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 24 (a)
OneToMany
Species where no ortholog for GCFC2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GCFC2 Gene

ENSEMBL:
Gene Tree for GCFC2 (if available)
TreeFam:
Gene Tree for GCFC2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GCFC2: view image

Paralogs for GCFC2 Gene

Paralogs for GCFC2 Gene

(2) SIMAP similar genes for GCFC2 Gene using alignment to 6 proteins:

  • GCFC2_HUMAN
  • C9JII4_HUMAN
  • H7C335_HUMAN
  • S4R3C1_HUMAN
  • S4R461_HUMAN
  • S4R465_HUMAN
genes like me logo Genes that share paralogs with GCFC2: view

Variants for GCFC2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GCFC2 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs17690300 - p.Glu724Asp
rs6722682 - p.Thr594Ala
rs6742946 - p.Gln316Glu
rs7559767 - p.Pro32Ala
rs7560262 - p.Asn249Ser

Additional dbSNP identifiers (rs#s) for GCFC2 Gene

Structural Variations from Database of Genomic Variants (DGV) for GCFC2 Gene

Variant ID Type Subtype PubMed ID
dgv152e55 CNV gain 17911159
dgv20n14 CNV gain 18776910
dgv5n43 CNV gain 19587683
dgv706e214 CNV gain 21293372
esv1703569 CNV deletion 17803354
esv2662348 CNV deletion 23128226
esv2759063 CNV gain+loss 17122850
esv3303063 CNV tandem duplication 20981092
esv3558722 CNV deletion 23714750
esv3591304 CNV loss 21293372
esv992435 CNV deletion 20482838
nsv1138787 CNV deletion 24896259
nsv213696 CNV deletion 16902084
nsv441762 CNV gain 18776908
nsv478811 CNV novel sequence insertion 20440878
nsv514988 CNV loss 21397061
nsv819219 CNV gain 19587683
nsv834263 CNV gain 17160897

Variation tolerance for GCFC2 Gene

Residual Variation Intolerance Score: 98.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.43; 85.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GCFC2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GCFC2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GCFC2 Gene

Disorders for GCFC2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for GCFC2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
dyslexia
reading disorder
  • dyslexia
speech and communication disorders
  • communication disorder
specific language impairment
  • language impairment, specific
learning disability
  • academic skill disorder
- elite association - COSMIC cancer census association via MalaCards
Search GCFC2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GCFC2

genes like me logo Genes that share disorders with GCFC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GCFC2 Gene

Publications for GCFC2 Gene

  1. Identification of a novel component C2ORF3 in the lariat-intron complex: lack of C2ORF3 interferes with pre-mRNA splicing via intron turnover pathway. (PMID: 24304693) Yoshimoto R … Kataoka N (Genes to cells : devoted to molecular & cellular mechanisms 2014) 2 3 4 54
  2. A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia. (PMID: 17309879) Anthoni H … Peyrard-Janvid M (Human molecular genetics 2007) 2 3 4 54
  3. Molecular cloning and characterization of a human DNA binding factor that represses transcription. (PMID: 2556218) Kageyama R … Pastan I (Cell 1989) 2 3 4 54
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 54
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 54

Products for GCFC2 Gene

Sources for GCFC2 Gene