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

Summary

Official Symbol: Cicprovided by RGD
Official Full Name: capicua transcriptional repressorprovided by RGD
Primary source: RGD:1310706
See related: Ensembl: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 transcription, DNA-templated; 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 mental retardation 45. Orthologous to human CIC (capicua transcriptional repressor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 61.4), Adrenal (RPKM 60.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

suggesting differential mechanisms in the Cic gene regulation by different polyunsaturated fatty acids
Title: Functional analysis of rat liver citrate carrier promoter: differential responsiveness to polyunsaturated fatty acids.
Expression analysis of the human and mouse Cic orthologs in tumor cells.
Title: CIC, a gene involved in cerebellar development and ErbB signaling, is significantly expressed in medulloblastomas.

Submit: New GeneRIF Correction

General gene information

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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

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Preferred Names: protein capicua homolog

Names: capicua homolog

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)

NM_001107490.4 → NP_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:732 → 1288

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:156 → 315

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:646 → 788

PRK07003; DNA polymerase III subunit gamma/tau

PRK07764
Location:45 → 151

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd01388
Location:199 → 270

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 ...
NM_001372079.1 → NP_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, ENSRNOT00000101741.1

Conserved Domains (5) summary

PHA03247
Location:1638 → 2180

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:1077 → 1221

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:1552 → 1694

PRK07003; DNA polymerase III subunit gamma/tau

cd01388
Location:1105 → 1176

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:252 → 346

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

NC_086019.1 Reference GRCr8

Range

89980660..90008357

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008758933.4 → XP_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:1638 → 2180

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:1077 → 1221

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:1552 → 1694

PRK07003; DNA polymerase III subunit gamma/tau

cd01388
Location:1105 → 1176

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:252 → 346

DUF4819; Domain of unknown function (DUF4819)
XM_008758936.4 → XP_008757158.1 protein capicua homolog isoform X2

Conserved Domains (3) summary

COG5648
Location:1077 → 1221

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

cd01388
Location:1105 → 1176

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:252 → 343

DUF4819; Domain of unknown function (DUF4819)
XM_008758937.4 → XP_008757159.1 protein capicua homolog isoform X3

Conserved Domains (3) summary

COG5648
Location:1077 → 1221

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

cd01388
Location:1105 → 1176

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:252 → 343

DUF4819; Domain of unknown function (DUF4819)
XM_063261360.1 → XP_063117430.1 protein capicua homolog isoform X6
XM_008758935.4 → XP_008757157.1 protein capicua homolog isoform X4

Conserved Domains (3) summary

COG5648
Location:1077 → 1221

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

cd01388
Location:1105 → 1176

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:252 → 343

DUF4819; Domain of unknown function (DUF4819)
XM_063261359.1 → XP_063117429.1 protein capicua homolog isoform X5
XM_063261361.1 → XP_063117431.1 protein capicua homolog isoform X7
XM_017590018.3 → XP_017445507.1 protein capicua homolog isoform X8
XM_039111447.2 → XP_038967375.1 protein capicua homolog isoform X14

Conserved Domains (5) summary

PHA03247
Location:721 → 1263

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:145 → 304

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:635 → 777

PRK07003; DNA polymerase III subunit gamma/tau

PRK07764
Location:7 → 140

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd01388
Location:188 → 259

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 ...
XM_039111415.2 → XP_038967343.1 protein capicua homolog isoform X11

Conserved Domains (5) summary

PHA03247
Location:732 → 1290

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:156 → 315

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:646 → 788

PRK07003; DNA polymerase III subunit gamma/tau

PRK07764
Location:45 → 151

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd01388
Location:199 → 270

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 ...
XM_039111425.2 → XP_038967353.1 protein capicua homolog isoform X12

Conserved Domains (5) summary

PHA03247
Location:732 → 1289

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:156 → 315

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:646 → 788

PRK07003; DNA polymerase III subunit gamma/tau

PRK07764
Location:45 → 151

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd01388
Location:199 → 270

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 ...
XM_039111436.2 → XP_038967364.1 protein capicua homolog isoform X13

Conserved Domains (5) summary

PHA03247
Location:732 → 1288

PHA03247; large tegument protein UL36; Provisional

COG5648
Location:156 → 315

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

PRK07003
Location:646 → 788

PRK07003; DNA polymerase III subunit gamma/tau

PRK07764
Location:45 → 151

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd01388
Location:199 → 270

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 ...
XM_008758938.4 → XP_008757160.1 protein capicua homolog isoform X9

UniProtKB/TrEMBL

D4A853

Related

ENSRNOP00000073956.2

Conserved Domains (2) summary

COG5648
Location:156 → 315

NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

cd01388
Location:199 → 270

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 ...
XM_063261362.1 → XP_063117432.1 protein capicua homolog isoform X10