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

Gene ID: 6936, updated on 12-Aug-2018

Summary

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; Vega:OTTHUMG00000129989
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

Genomic context

See GCFC2 in Genome Data Viewer
Location:
2p12
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (75655606..75711642, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (75889831..75938482, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927884 Neighboring gene eva-1 homolog A, regulator of programmed cell death Neighboring gene SPT4 homolog, DSIF elongation factor subunit pseudogene Neighboring gene mitochondrial ribosomal protein L19 Neighboring gene uncharacterized LOC105374813 Neighboring gene succinate-CoA ligase ADP-forming beta subunit pseudogene 2 Neighboring gene purine nucleoside phosphorylase pseudogene

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
spliceosomal complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
U2-type post-mRNA release spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
GC-rich sequence DNA-binding factor 2
Names
GC binding factor
GC bindng factor
TCF-9
transcription factor 9 (binds GC-rich sequences)

NCBI Reference Sequences (RefSeq)

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_001201334.1NP_001188263.1  GC-rich sequence DNA-binding factor 2 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/Swiss-Prot
    P16383
    UniProtKB/TrEMBL
    A4UHR0, B3KUM5
    Conserved Domains (1) summary
    pfam07842
    Location:298513
    GCFC; GC-rich sequence DNA-binding factor-like protein
  2. NM_001201335.1NP_001188264.1  GC-rich sequence DNA-binding factor 2 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, BU628451, DB455842
    Consensus CDS
    CCDS62943.1
    UniProtKB/Swiss-Prot
    P16383
    UniProtKB/TrEMBL
    Q9BVX3
    Related
    ENSP00000474481.1, OTTHUMP00000272963, ENST00000470503.1, OTTHUMT00000328714
  3. NM_003203.4NP_003194.3  GC-rich sequence DNA-binding factor 2 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, DB455842, EF158469
    Consensus CDS
    CCDS1961.1
    UniProtKB/Swiss-Prot
    P16383
    UniProtKB/TrEMBL
    A4UHR0
    Related
    ENSP00000318690.3, OTTHUMP00000160450, ENST00000321027.7, OTTHUMT00000252255
    Conserved Domains (2) summary
    pfam07842
    Location:467682
    GCFC; GC-rich sequence DNA-binding factor-like protein
    pfam15458
    Location:75235
    NTR2; Nineteen complex-related protein 2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    75655606..75711642 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533074.3XP_011531376.1  GC-rich sequence DNA-binding factor 2 isoform X2

    Conserved Domains (1) summary
    pfam07842
    Location:392607
    GCFC; GC-rich sequence DNA-binding factor-like protein
  2. XM_005264520.4XP_005264577.1  GC-rich sequence DNA-binding factor 2 isoform X1

    Conserved Domains (2) summary
    pfam07842
    Location:475690
    GCFC; GC-rich sequence DNA-binding factor-like protein
    pfam15458
    Location:125243
    NTR2; Nineteen complex-related protein 2
  3. XM_017004787.2XP_016860276.1  GC-rich sequence DNA-binding factor 2 isoform X3

    Conserved Domains (1) summary
    pfam15458
    Location:125243
    NTR2; Nineteen complex-related protein 2
  4. XM_011533075.2XP_011531377.1  GC-rich sequence DNA-binding factor 2 isoform X3

    Conserved Domains (1) summary
    pfam15458
    Location:125243
    NTR2; Nineteen complex-related protein 2

RNA

  1. XR_001738916.2 RNA Sequence

  2. XR_426995.3 RNA Sequence

  3. XR_002959327.1 RNA Sequence

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