Calcoco1 calcium binding and coiled coil domain 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Calcoco1provided by RGD
Full Name: calcium binding and coiled coil domain 1provided by RGD
Primary source: RGD:619812
See related: EnsemblRapid:ENSRNOG00000015447 AllianceGenome:RGD:619812
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
Summary: Predicted to enable several functions, including RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Predicted to be involved in nuclear receptor-mediated steroid hormone signaling pathway; positive regulation of gene expression; and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin; cytosol; and nucleus. Orthologous to human CALCOCO1 (calcium binding and coiled-coil domain 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 204.6), Thymus (RPKM 160.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q36

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (135713208..135728044, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (133834705..133849515, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (144307562..144322253, complement)

Chromosome 7 - NC_086025.1 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 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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI010402 (e-PCR)
- UniSTS:260702

BF387379 (e-PCR)
- UniSTS:244323

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables beta-catenin binding	IEA Inferred from Electronic Annotation more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor coactivator activity	IEA Inferred from Electronic Annotation more info
enables nuclear receptor coactivator activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in nuclear receptor-mediated steroid hormone signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in nuclear receptor-mediated steroid hormone signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: calcium-binding and coiled-coil domain-containing protein 1

Names: calcium-binding and coiled-coil domain-containing protein 1-like

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_139190.2 → NP_631929.2 calcium-binding and coiled-coil domain-containing protein 1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000007

UniProtKB/Swiss-Prot

Q66HR5, Q8R443

UniProtKB/TrEMBL

A0A8L2QVZ6, A6KCX8

Related

ENSRNOP00000021522.3, ENSRNOT00000021523.8

Conserved Domains (3) summary

pfam07888
Location:122 → 584

CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like

pfam17751
Location:15 → 118

SKICH; SKICH domain

cd21967
Location:654 → 682

Zn-C2H2_CALCOCO1; C2H2-type zinc binding domain found in calcium-binding and coiled-coil domain-containing protein 1 (CALCOCO1) and similar proteins

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_086025.1 Reference GRCr8

Range

135713208..135728044 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063262991.1 → XP_063119061.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X2

UniProtKB/Swiss-Prot

Q66HR5, Q8R443

UniProtKB/TrEMBL

A6KCX8
XM_039078406.2 → XP_038934334.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A0G2K0S1, A0A8L2QVZ6

Related

ENSRNOP00000071559.1, ENSRNOT00000089290.3

Conserved Domains (3) summary

pfam07888
Location:122 → 584

CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like

pfam17751
Location:15 → 118

SKICH; SKICH domain

cd21967
Location:678 → 706

Zn-C2H2_CALCOCO1; C2H2-type zinc binding domain found in calcium-binding and coiled-coil domain-containing protein 1 (CALCOCO1) and similar proteins
XM_063262990.1 → XP_063119060.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A0G2K0S1
XM_063262992.1 → XP_063119062.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X2

UniProtKB/Swiss-Prot

Q66HR5, Q8R443

UniProtKB/TrEMBL

A6KCX8
XM_039078407.2 → XP_038934335.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A0G2K0S1, A0A8L2QVZ6

Conserved Domains (3) summary

pfam07888
Location:122 → 584

CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like

pfam17751
Location:15 → 118

SKICH; SKICH domain

cd21967
Location:678 → 706

Zn-C2H2_CALCOCO1; C2H2-type zinc binding domain found in calcium-binding and coiled-coil domain-containing protein 1 (CALCOCO1) and similar proteins