CALCOCO1 calcium binding and coiled-coil domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CALCOCO1provided by HGNC
Official Full Name: calcium binding and coiled-coil domain 1provided by HGNC
Primary source: HGNC:HGNC:29306
See related: Ensembl:ENSG00000012822 AllianceGenome:HGNC:29306
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Cocoa; PP13275; calphoglin
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Involved in positive regulation of DNA-templated transcription and positive regulation of gene expression. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in skin (RPKM 52.1), lung (RPKM 44.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.13

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (53708517..53727452, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (53674269..53693205, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54102301..54121236, complement)

Chromosome 12 - NC_000012.12 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: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RTN3L and CALCOCO1 function in parallel to maintain proteostasis in the endoplasmic reticulum.
Title: RTN3L and CALCOCO1 function in parallel to maintain proteostasis in the endoplasmic reticulum.
CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
Title: CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes.
Title: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide association study of panic disorder in the Japanese population.
CoCoA uses different combinations of functional domains in its synergistic coactivator function with beta-catenin or GRIP1
Title: Differential use of functional domains by coiled-coil coactivator in its synergistic coactivator function with beta-catenin or GRIP1.
Results report a novel human protein, calphoglin, which activates inorganic pyrophosphatase (IPP) and enhances phosphoglucomutase activity through the activated IPP.
Title: Cellular signaling mediated by calphoglin-induced activation of IPP and PGM.
The N terminus of CoCoA contains another activation domain , which is necessary and sufficient for synergistic activation of LEF1-mediated transcription by CoCoA and beta-catenin.
Title: Role of the N-terminal activation domain of the coiled-coil coactivator in mediating transcriptional activation by beta-catenin.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of panic disorder in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of selenium concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of calcium binding and coiled-coil domain 1 (CALCOCO1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11261 (e-PCR)
- UniSTS:42253

RH8151 (e-PCR)
- UniSTS:90663

ksks136 (e-PCR)
- UniSTS:514161

STS-T71651 (e-PCR)
- UniSTS:41720

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coregulator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in nuclear receptor-mediated steroid hormone signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
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	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info

General protein information

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

Names: coiled-coil coactivator protein; coiled-coil leucine zipper coactivator 1; inorganic pyrophosphatase activator; sarcoma antigen NY-SAR-3

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_001143682.2 → NP_001137154.1 calcium-binding and coiled-coil domain-containing protein 1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) omits an inframe coding exon and uses an alternate (in-frame) splice acceptor site, compared to variant 2. This results in a shorter protein (isoform 2).

Source sequence(s)

AC076968, AK122773, BC003177, DB060684

Consensus CDS

CCDS44908.1

UniProtKB/TrEMBL

B3KS47

Related

ENSP00000397189.2, ENST00000430117.6

Conserved Domains (3) summary

pfam07888
Location:13 → 511

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

cl02193
Location:114 → 290

VirB5_like; VirB5 protein family

cl23720
Location:335 → 425

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_020898.3 → NP_065949.1 calcium-binding and coiled-coil domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_065949.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer protein isoform (1).

Source sequence(s)

AC076968, AK315578, AL136895, BC003177

Consensus CDS

CCDS8864.1

UniProtKB/Swiss-Prot

B3KVA8, Q6FI59, Q71RC3, Q86WF8, Q96JU3, Q9H090, Q9P1Z2

UniProtKB/TrEMBL

B3KS47

Related

ENSP00000449960.1, ENST00000550804.6

Conserved Domains (2) summary

pfam07888
Location:13 → 596

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

cl23720
Location:238 → 346

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RNA

NR_026554.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) omits the second coding exon resulting in a frameshift and premature stop codon. The transcript is a candidate for nonsense-mediated decay (NMD) and is inferred to not encode a protein.

Source sequence(s)

AC076968, AK296497, AL136895, BC003177

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

53708517..53727452 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011538601.2 → XP_011536903.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_011536903.1

UniProtKB/TrEMBL

B3KS47

Conserved Domains (2) summary

pfam07888
Location:13 → 596

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

cl23720
Location:238 → 346

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_011538602.2 → XP_011536904.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_011536904.1

UniProtKB/TrEMBL

B3KS47

Conserved Domains (2) summary

pfam07888
Location:13 → 596

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

cl23720
Location:238 → 346

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_011538604.3 → XP_011536906.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_011536906.1

UniProtKB/TrEMBL

B3KS47

Conserved Domains (2) summary

pfam07888
Location:13 → 596

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

cl23720
Location:238 → 346

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_011538603.3 → XP_011536905.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_011536905.1

UniProtKB/TrEMBL

B3KS47

Conserved Domains (2) summary

pfam07888
Location:13 → 596

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

cl23720
Location:238 → 346

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

53674269..53693205 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372674.1 → XP_054228649.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1
XM_054372675.1 → XP_054228650.1 calcium-binding and coiled-coil domain-containing protein 1 isoform X1