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    Cic capicua transcriptional repressor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308435, updated on 28-Oct-2024

    Summary

    Official Symbol
    Cicprovided by RGD
    Official Full Name
    capicua transcriptional repressorprovided by RGD
    Primary source
    RGD:1310706
    See related
    EnsemblRapid:ENSRNOG00000056118 AllianceGenome:RGD:1310706
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including learning or memory; regulation of DNA-templated transcription; and social behavior. Predicted to act upstream of or within lung alveolus development and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 45. Orthologous to human CIC (capicua transcriptional repressor). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Thymus (RPKM 61.4), Adrenal (RPKM 60.3) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Cic in Genome Data Viewer
    Location:
    1q21
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (89980660..90008357)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (80853920..80880537)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (82135440..82163007)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene zinc finger protein 526 Neighboring gene glycogen synthase kinase 3 alpha Neighboring gene uncharacterized LOC134482971 Neighboring gene Ets2 repressor factor Neighboring gene platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 Neighboring gene proline rich 19

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in learning ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lung alveolus development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in memory ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in social behavior ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    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
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    protein capicua homolog
    Names
    capicua homolog

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001107490.4NP_001100960.2  protein capicua homolog 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter, lacks two exons in the 5' region, and therefore differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AI029769, JAXUCZ010000001
      Conserved Domains (5) summary
      PHA03247
      Location:7321288
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:156315
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:646788
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK07764
      Location:45151
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd01388
      Location:199270
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
    2. NM_001372079.1NP_001359008.1  protein capicua homolog 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI029769, JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A8I6APH0
      Related
      ENSRNOP00000094181.1, ENSRNOT00000101741.2
      Conserved Domains (5) summary
      PHA03247
      Location:16382180
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:10771221
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:15521694
      PRK07003; DNA polymerase III subunit gamma/tau
      cd01388
      Location:11051176
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
      pfam16090
      Location:252346
      DUF4819; Domain of unknown function (DUF4819)

    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_086019.1 Reference GRCr8

      Range
      89980660..90008357
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008758933.4XP_008757155.1  protein capicua homolog isoform X1

      See identical proteins and their annotated locations for XP_008757155.1

      UniProtKB/TrEMBL
      A0A8I6APH0
      Conserved Domains (5) summary
      PHA03247
      Location:16382180
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:10771221
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:15521694
      PRK07003; DNA polymerase III subunit gamma/tau
      cd01388
      Location:11051176
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
      pfam16090
      Location:252346
      DUF4819; Domain of unknown function (DUF4819)
    2. XM_008758936.4XP_008757158.1  protein capicua homolog isoform X2

      Conserved Domains (3) summary
      COG5648
      Location:10771221
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11051176
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
      pfam16090
      Location:252343
      DUF4819; Domain of unknown function (DUF4819)
    3. XM_008758937.4XP_008757159.1  protein capicua homolog isoform X3

      Conserved Domains (3) summary
      COG5648
      Location:10771221
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11051176
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
      pfam16090
      Location:252343
      DUF4819; Domain of unknown function (DUF4819)
    4. XM_063261360.1XP_063117430.1  protein capicua homolog isoform X6

    5. XM_008758935.4XP_008757157.1  protein capicua homolog isoform X4

      Conserved Domains (3) summary
      COG5648
      Location:10771221
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11051176
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
      pfam16090
      Location:252343
      DUF4819; Domain of unknown function (DUF4819)
    6. XM_063261359.1XP_063117429.1  protein capicua homolog isoform X5

    7. XM_063261361.1XP_063117431.1  protein capicua homolog isoform X7

    8. XM_017590018.3XP_017445507.1  protein capicua homolog isoform X8

    9. XM_039111447.2XP_038967375.1  protein capicua homolog isoform X14

      Conserved Domains (5) summary
      PHA03247
      Location:7211263
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:145304
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:635777
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK07764
      Location:7140
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd01388
      Location:188259
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
    10. XM_039111415.2XP_038967343.1  protein capicua homolog isoform X11

      Conserved Domains (5) summary
      PHA03247
      Location:7321290
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:156315
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:646788
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK07764
      Location:45151
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd01388
      Location:199270
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
    11. XM_039111425.2XP_038967353.1  protein capicua homolog isoform X12

      Conserved Domains (5) summary
      PHA03247
      Location:7321289
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:156315
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:646788
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK07764
      Location:45151
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd01388
      Location:199270
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
    12. XM_039111436.2XP_038967364.1  protein capicua homolog isoform X13

      Conserved Domains (5) summary
      PHA03247
      Location:7321288
      PHA03247; large tegument protein UL36; Provisional
      COG5648
      Location:156315
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      PRK07003
      Location:646788
      PRK07003; DNA polymerase III subunit gamma/tau
      PRK07764
      Location:45151
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd01388
      Location:199270
      SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
    13. XM_008758938.4XP_008757160.1  protein capicua homolog isoform X9

      UniProtKB/TrEMBL
      D4A853
      Related
      ENSRNOP00000073956.2, ENSRNOT00000091357.3
      Conserved Domains (2) summary
      COG5648
      Location:156315
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:199270
      SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    14. XM_063261362.1XP_063117432.1  protein capicua homolog isoform X10