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    CIC capicua transcriptional repressor [ Homo sapiens (human) ]

    Gene ID: 23152, updated on 17-Jun-2019

    Summary

    Official Symbol
    CICprovided by HGNC
    Official Full Name
    capicua transcriptional repressorprovided by HGNC
    Primary source
    HGNC:HGNC:14214
    See related
    Ensembl:ENSG00000079432 MIM:612082
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MRD45
    Summary
    The protein encoded by this gene is an ortholog of the Drosophila melanogaster capicua gene, and is a member of the high mobility group (HMG)-box superfamily of transcriptional repressors. This protein contains a conserved HMG domain that is involved in DNA binding and nuclear localization, and a conserved C-terminus. Studies suggest that the N-terminal region of this protein interacts with Atxn1 (GeneID:6310), to form a transcription repressor complex, and in vitro studies suggest that polyglutamine-expansion of ATXN1 may alter the repressor activity of this complex. Mutations in this gene have been associated with olidogdendrogliomas (PMID:21817013). In addition, translocation events resulting in gene fusions of this gene with both DUX4 (GeneID:100288687) and FOXO4 (GeneID:4303) have been associated with round cell sarcomas. There are multiple pseudogenes of this gene found on chromosomes 1, 4, 6, 7, 16, 20, and the Y chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]
    Expression
    Ubiquitous expression in testis (RPKM 16.0), endometrium (RPKM 12.0) and 25 other tissues See more
    Orthologs

    Genomic context

    See CIC in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (42268537..42295796)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (42788734..42799949)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene glycogen synthase kinase 3 alpha Neighboring gene ETS2 repressor factor Neighboring gene ZFP161 motif-containing MPRA enhancer 284/285 Neighboring gene platelet activating factor acetylhydrolase 1b catalytic subunit 3 Neighboring gene proline rich 19 Neighboring gene transmembrane protein 145

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    MENTAL RETARDATION, AUTOSOMAL DOMINANT 45
    MedGen: C4539848 OMIM: 617600 GeneReviews: Not available
    not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2018-06-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2018-06-27)

    ClinGen Genome Curation PagePubMed

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0306

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific ISM
    Inferred from Sequence Model
    more info
    PubMed 
    DNA-binding transcription factor activity, RNA polymerase II-specific NAS
    Non-traceable Author Statement
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
     
    memory ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    social behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     

    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.

    Genomic

    1. NG_042060.1 RefSeqGene

      Range
      5001..32260
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_999

    mRNA and Protein(s)

    1. NM_001304815.1NP_001291744.1  protein capicua homolog isoform CIC-L

      See identical proteins and their annotated locations for NP_001291744.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (CIC-L, PMID:17190598).
      Source sequence(s)
      AC006486, AF363689, AK025939, BF848448
      UniProtKB/Swiss-Prot
      Q96RK0
      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    2. NM_015125.4NP_055940.3  protein capicua homolog isoform CIC-S

      See identical proteins and their annotated locations for NP_055940.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (CIC-S, PMID:17190598) has a distinct N-terminus and is shorter than isoform CIC-L.
      Source sequence(s)
      AC006486, AF363689, AK025939
      Consensus CDS
      CCDS12601.1
      UniProtKB/Swiss-Prot
      Q96RK0
      Related
      ENSP00000458663.2, ENST00000575354.6
      Conserved Domains (2) summary
      COG5648
      Location:171315
      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 ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      42268537..42295796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526660.2XP_011524962.1  protein capicua homolog isoform X1

      See identical proteins and their annotated locations for XP_011524962.1

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    2. XM_011526665.2XP_011524967.1  protein capicua homolog isoform X7

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    3. XM_011526663.2XP_011524965.1  protein capicua homolog isoform X4

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    4. XM_011526666.2XP_011524968.1  protein capicua homolog isoform X9

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    5. XM_011526661.2XP_011524963.1  protein capicua homolog isoform X2

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    6. XM_024451433.1XP_024307201.1  protein capicua homolog isoform X8

      Conserved Domains (5) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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)
      cl26464
      Location:17652184
      Atrophin-1; Atrophin-1 family
      cl28271
      Location:8711046
      dnaA; chromosomal replication initiation protein; Provisional
    7. XM_024451432.1XP_024307200.1  protein capicua homolog isoform X6

      Conserved Domains (5) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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)
      cl26464
      Location:17652184
      Atrophin-1; Atrophin-1 family
      cl28271
      Location:8711046
      dnaA; chromosomal replication initiation protein; Provisional
    8. XM_011526662.2XP_011524964.1  protein capicua homolog isoform X3

      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    9. XM_011526664.2XP_011524966.1  protein capicua homolog isoform X5

      Related
      ENSP00000459719.1, ENST00000572681.6
      Conserved Domains (3) summary
      COG5648
      Location:10801224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    10. XM_011526667.2XP_011524969.1  protein capicua homolog isoform X10

      Conserved Domains (3) summary
      COG5648
      Location:10651224
      NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
      cd01388
      Location:11081179
      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:252349
      DUF4819; Domain of unknown function (DUF4819)
    11. XM_005258674.2XP_005258731.1  protein capicua homolog isoform X12

      Conserved Domains (2) summary
      COG5648
      Location:171315
      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 ...
    12. XM_005258673.2XP_005258730.1  protein capicua homolog isoform X11

      UniProtKB/TrEMBL
      A0A0A0MQR4
      Related
      ENSP00000160740.3, ENST00000160740.7
      Conserved Domains (2) summary
      COG5648
      Location:171315
      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 ...
    13. XM_005258675.2XP_005258732.1  protein capicua homolog isoform X13

      Conserved Domains (2) summary
      COG5648
      Location:171315
      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 ...

    RNA

    1. XR_002958286.1 RNA Sequence

    2. XR_002958287.1 RNA Sequence

    3. XR_002958288.1 RNA Sequence

    4. XR_002958289.1 RNA Sequence

    5. XR_002958290.1 RNA Sequence

    6. XR_935778.2 RNA Sequence

    7. XR_935779.2 RNA Sequence

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