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    Gcfc2 GC-rich sequence DNA-binding factor 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 312474, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Gcfc2provided by RGD
    Official Full Name
    GC-rich sequence DNA-binding factor 2provided by RGD
    Primary source
    RGD:1304792
    See related
    Ensembl:ENSRNOG00000006888 AllianceGenome:RGD:1304792
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1304792
    Summary
    Predicted to enable DNA binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in cytosol; nucleolus; and nucleoplasm. Predicted to be part of U2-type post-mRNA release spliceosomal complex. Predicted to be active in nucleus. Orthologous to human GCFC2 (GC-rich sequence DNA-binding factor 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 22.9), Kidney (RPKM 20.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    4q34
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (116039432..116076330)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (114481613..114519268)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (112662556..112700505)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100911370 Neighboring gene uncharacterized LOC134486807 Neighboring gene mitochondrial ribosomal protein L19 Neighboring gene eva-1 homolog A, regulator of programmed cell death

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and characterization of a transcription regulator with homology to GC-binding factor. Reed AL, et al. J Biol Chem, 1998 Aug 21. PMID 9705290
    2. Identification of a novel component C2ORF3 in the lariat-intron complex: lack of C2ORF3 interferes with pre-mRNA splicing via intron turnover pathway. Yoshimoto R, et al. Genes Cells, 2014 Jan. PMID 24304693
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of U2-type post-mRNA release spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    intron Large complex component GCFC2
    Names
    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_001134554.1 → NP_001128026.1  intron Large complex component GCFC2

      See identical proteins and their annotated locations for NP_001128026.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473957
      UniProtKB/TrEMBL
      A0A8I6AVA2, A6IAH1, D4A3Z4
      Related
      ENSRNOP00000009104.5, ENSRNOT00000009104.6
      Conserved Domains (1) summary
      pfam07842
      Location:416 → 630
      GCFC; GC-rich sequence DNA-binding factor-like protein

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      116039432..116076330
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286052.1 → XP_063142122.1  intron Large complex component GCFC2 isoform X5

    2. XM_006236702.5 → XP_006236764.1  intron Large complex component GCFC2 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AVA2
      Related
      ENSRNOP00000092144.1
      Conserved Domains (1) summary
      pfam07842
      Location:459 → 673
      GCFC; GC-rich sequence DNA-binding factor-like protein

    3. XM_006236703.5 → XP_006236765.1  intron Large complex component GCFC2 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AHL1, A0A8I6AVA2
      Related
      ENSRNOP00000087910.1
      Conserved Domains (1) summary
      pfam07842
      Location:459 → 673
      GCFC; GC-rich sequence DNA-binding factor-like protein

    4. XM_039107583.2 → XP_038963511.1  intron Large complex component GCFC2 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AVA2
      Conserved Domains (1) summary
      pfam07842
      Location:459 → 673
      GCFC; GC-rich sequence DNA-binding factor-like protein

    5. XM_039107584.2 → XP_038963512.1  intron Large complex component GCFC2 isoform X4

      Conserved Domains (1) summary
      pfam07842
      Location:142 → 356
      GCFC; GC-rich sequence DNA-binding factor-like protein

    RNA

    1. XR_005503212.2 RNA Sequence

    2. XR_005503213.2 RNA Sequence

    3. XR_005503214.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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