Cc2d1a coiled-coil and C2 domain containing 1A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cc2d1aprovided by RGD
Official Full Name: coiled-coil and C2 domain containing 1Aprovided by RGD
Primary source: RGD:1306108
See related: Ensembl:ENSRNOG00000006747 AllianceGenome:RGD:1306108
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
Also known as: RGD1306108
Summary: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of snRNA transcription by RNA polymerase II; positive regulation of canonical NF-kappaB signal transduction; and regulation of postsynapse assembly. Predicted to act upstream of or within several processes, including apical dendrite arborization; negative regulation of transcription by RNA polymerase II; and regulation of respiratory gaseous exchange by nervous system process. Located in nucleus. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 3 and intellectual disability. Orthologous to human CC2D1A (coiled-coil and C2 domain containing 1A). [provided by Alliance of Genome Resources, Apr 2025]
Expression: Biased expression in Kidney (RPKM 82.3), Lung (RPKM 68.6) and 9 other tissues See more
Orthologs: all
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Genomic context

Location:: 19q11

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (40916587..40931702)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (24011897..24026937)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (25246912..25261965, complement)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Freud-1 and Freud-2 levels were different in rats selectively bred for 85 generations for either high level of fear-induced aggression or its absence. Freud-1 protein level was decreased in the hippocampus, whereas Freud-2 protein level was increased in the frontal cortex of highly aggressive rats. There no differences in 5-HT1A receptor gene expression were found in the brains of highly aggressive and nonaggressive rats.
Title: 5-HT1A receptor gene silencers Freud-1 and Freud-2 are differently expressed in the brain of rats with genetically determined high level of fear-induced aggression or its absence.
In pregnancy stress, prefrontal cortex Cc2d1a levels were reduced in rats.
Title: Stress-induced alterations in 5-HT1A receptor transcriptional modulators NUDR and Freud-1.
chronic social defeat stress downregulates the 5-HT1A receptor mRNA but does not significantly alter the levels of Freud-1 and NUDR in PFC; this stress paradigm could offer a useful rodent model for depression and other stress related disorders
Title: Chronic social defeat downregulates the 5-HT1A receptor but not Freud-1 or NUDR in the rat prefrontal cortex.
results point to the importance of understanding the mechanism for the differential regulation of 5-HT1AR, Freud-1 and NUDR in the prefrontal cortex as a basis for understanding the related effects of chronic stress and stress-related disorders
Title: Differential regulation of the serotonin 1 A transcriptional modulators five prime repressor element under dual repression-1 and nuclear-deformed epidermal autoregulatory factor by chronic stress.

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 DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within apical dendrite arborization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendrite arborization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endosome organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of snRNA transcription by RNA polymerase II	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 postsynapse assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of respiratory gaseous exchange	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of respiratory gaseous exchange by nervous system process	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

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: coiled-coil and C2 domain-containing protein 1A

Names: FRE under dual repression-binding protein 1; five prime repressor element under dual repression-binding protein 1; five repressor element under dual repression-binding protein 1; freud-1

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_001013869.2 → NP_001013891.1 coiled-coil and C2 domain-containing protein 1A isoform 1

See identical proteins and their annotated locations for NP_001013891.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A6IYA7

Conserved Domains (2) summary

smart00685
Location:296 → 354

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:601 → 755

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)
NM_001433990.1 → NP_001420919.1 coiled-coil and C2 domain-containing protein 1A isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/Swiss-Prot

Q66HA5

UniProtKB/TrEMBL

A6IYA7
NM_001433991.1 → NP_001420920.1 coiled-coil and C2 domain-containing protein 1A isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A0A8L2QP71, A6IYA7
NM_001433992.1 → NP_001420921.1 coiled-coil and C2 domain-containing protein 1A isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A6IYA7

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_086037.1 Reference GRCr8

Range

40916587..40931702

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039097531.2 → XP_038953459.1 coiled-coil and C2 domain-containing protein 1A isoform X1

UniProtKB/TrEMBL

A6IYA7

Conserved Domains (3) summary

smart00685
Location:341 → 399

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:644 → 801

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

PHA03247
Location:217 → 486

PHA03247; large tegument protein UL36; Provisional
XM_006255233.4 → XP_006255295.1

Related

ENSRNOP00000045667.4, ENSRNOT00000045180.6

Conserved Domains (3) summary

smart00685
Location:341 → 399

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:647 → 801

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

pfam07404
Location:420 → 495

TEBP_beta; Telomere-binding protein beta subunit (TEBP beta)
XM_039097532.2 → XP_038953460.1

Conserved Domains (3) summary

smart00685
Location:341 → 399

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:643 → 800

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

PHA03247
Location:217 → 485

PHA03247; large tegument protein UL36; Provisional
XM_006255234.4 → XP_006255296.1

Conserved Domains (2) summary

smart00685
Location:341 → 399

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:646 → 800

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)
XM_039097533.2 → XP_038953461.1 coiled-coil and C2 domain-containing protein 1A isoform X3

UniProtKB/TrEMBL

A6IYA7

Conserved Domains (3) summary

smart00685
Location:309 → 367

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:612 → 769

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)

PHA03247
Location:185 → 454

PHA03247; large tegument protein UL36; Provisional