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CCBE1 collagen and calcium binding EGF domains 1 [ Homo sapiens (human) ]

Gene ID: 147372, updated on 13-Mar-2020

Summary

Official Symbol
CCBE1provided by HGNC
Official Full Name
collagen and calcium binding EGF domains 1provided by HGNC
Primary source
HGNC:HGNC:29426
See related
Ensembl:ENSG00000183287 MIM:612753
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HKLLS1
Summary
This gene is thought to function in extracellular matrix remodeling and migration. It is predominantly expressed in the ovary, but down regulated in ovarian cancer cell lines and primary carcinomas, suggesting its role as a tumour suppressor. Mutations in this gene have been associated with Hennekam lymphangiectasia-lymphedema syndrome, a generalized lymphatic dysplasia in humans. [provided by RefSeq, Mar 2010]
Expression
Biased expression in ovary (RPKM 14.7), lung (RPKM 5.5) and 8 other tissues See more
Orthologs

Genomic context

See CCBE1 in Genome Data Viewer
Location:
18q21.32
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (59430939..59698181, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (57098171..57364860, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene lectin, mannose binding 1 Neighboring gene uncharacterized LOC107985156 Neighboring gene meiotic recombination hotspot N Neighboring gene meiotic recombination hotspot L Neighboring gene ACTB pseudogene 3 Neighboring gene ribosomal protein S26 pseudogene 54 Neighboring gene glutamate dehydrogenase 1 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hennekam lymphangiectasia-lymphedema syndrome 1
MedGen: C4012050 OMIM: 235510 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association analysis accounting for environmental factors through propensity-score matching: application to stressful live events in major depressive disorder.
NHGRI GWA Catalog
Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30681, MGC50861

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
lung development IEA
Inferred from Electronic Annotation
more info
 
lymphangiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
lymphangiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of endothelial cell migration IEA
Inferred from Electronic Annotation
more info
 
positive regulation of lymphangiogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein processing IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of vascular endothelial growth factor production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of vascular endothelial growth factor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
respiratory system process IEA
Inferred from Electronic Annotation
more info
 
sprouting angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
venous blood vessel morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
collagen and calcium-binding EGF domain-containing protein 1
Names
full of fluid protein homolog

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_016990.1 RefSeqGene

    Range
    4990..271474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1209

mRNA and Protein(s)

  1. NM_133459.4NP_597716.1  collagen and calcium-binding EGF domain-containing protein 1 precursor

    See identical proteins and their annotated locations for NP_597716.1

    Status: REVIEWED

    Source sequence(s)
    AB075863, AC010776, AC016229
    Consensus CDS
    CCDS32838.1
    UniProtKB/Swiss-Prot
    Q6UXH8
    Related
    ENSP00000404464.2, ENST00000439986.9
    Conserved Domains (1) summary
    smart00179
    Location:134175
    EGF_CA; Calcium-binding EGF-like domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    59430939..59698181 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451091.1XP_024306859.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    Related
    ENSP00000497183.1, ENST00000649564.1
    Conserved Domains (1) summary
    smart00179
    Location:134175
    EGF_CA; Calcium-binding EGF-like domain
  2. XM_017025557.1XP_016881046.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

  3. XM_017025556.1XP_016881045.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

  4. XM_017025558.1XP_016881047.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3

RNA

  1. XR_001753142.1 RNA Sequence

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