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

Gene ID: 57658, updated on 28-Sep-2024

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 several functions, including armadillo repeat domain binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Involved in positive regulation of gene expression and positive regulation of transcription, DNA-templated. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in skin (RPKM 52.1), lung (RPKM 44.3) and 25 other tissues See more
Orthologs
NEW
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Genomic context

See CALCOCO1 in Genome Data Viewer
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_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902938 Neighboring gene Sharpr-MPRA regulatory region 12722 Neighboring gene Sharpr-MPRA regulatory region 2395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6427 Neighboring gene ATP synthase membrane subunit c locus 2 Neighboring gene Sharpr-MPRA regulatory region 7415 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:54118812-54120011 Neighboring gene uncharacterized LOC105369774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54133003-54133792 Neighboring gene uncharacterized LOC105378250 Neighboring gene CALCOCO1-CISTR intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54141521-54142049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54142050-54142577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54144138-54144726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6429 Neighboring gene chondrogenesis-associated transcript Neighboring gene RN7SK pseudogene 289

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1536

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

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)

NEW Try the new Transcript table

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)

  1. NM_001143682.2NP_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:13511
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl02193
    Location:114290
    VirB5_like; VirB5 protein family
    cl23720
    Location:335425
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  2. NM_020898.3NP_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:13596
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl23720
    Location:238346
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RNA

  1. 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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53708517..53727452 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538601.2XP_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:13596
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl23720
    Location:238346
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  2. XM_011538602.2XP_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:13596
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl23720
    Location:238346
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  3. XM_011538604.3XP_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:13596
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl23720
    Location:238346
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  4. XM_011538603.3XP_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:13596
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl23720
    Location:238346
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53674269..53693205 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B3KS47
  2. XM_054372675.1XP_054228650.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B3KS47