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

Gene ID: 57658, updated on 8-Jul-2018
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 Vega:OTTHUMG00000170095
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
Expression
Ubiquitous expression in skin (RPKM 52.1), lung (RPKM 44.3) and 25 other tissues See more
Orthologs
See CALCOCO1 in Genome Data Viewer
Location:
12q13.13
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (53711118..53727523, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54104902..54121307, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L31 pseudogene 51 Neighboring gene ATP synthase membrane subunit c locus 2 Neighboring gene uncharacterized LOC105369774 Neighboring gene CALCOCO1-CISTR intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene chondrogenesis-associated transcript

  • Project title: 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

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

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

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA1536

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II distal enhancer sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
armadillo repeat domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
nuclear receptor transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription coregulator activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
intracellular steroid hormone receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear chromatin IEA
Inferred from Electronic Annotation
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
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

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_001143682.1NP_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)
    AK122773, BC003177, DB060684
    Consensus CDS
    CCDS44908.1
    UniProtKB/Swiss-Prot
    Q9P1Z2
    Related
    ENSP00000397189.2, OTTHUMP00000242924, ENST00000430117.6, OTTHUMT00000407407
    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_020898.2NP_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)
    AK315578, AL136895, BC003177, CD723746
    Consensus CDS
    CCDS8864.1
    UniProtKB/Swiss-Prot
    Q9P1Z2
    UniProtKB/TrEMBL
    A0A024RAZ1
    Related
    ENSP00000449960.1, OTTHUMP00000242802, ENST00000550804.5, OTTHUMT00000407233
    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_026554.1 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)
    AK296497, AL136895, BC003177, CD723746

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    53711118..53727523 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019707.1XP_016875196.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q9P1Z2
    UniProtKB/TrEMBL
    A0A024RAZ1
    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_011538602.1XP_011536904.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011536904.1

    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_011538601.1XP_011536903.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011536903.1

    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_017019709.2XP_016875198.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X4

  5. XM_017019708.2XP_016875197.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X3

  6. XM_011538604.2XP_011536906.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011536906.1

    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)
  7. XM_011538603.2XP_011536905.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011536905.1

    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)
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