U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 147372, updated on 2-Nov-2024

    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; AllianceGenome:HGNC:29426
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CCBE1 in Genome Data Viewer
    Location:
    18q21.32
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (59430939..59697721, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (59632718..59900788, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (57098171..57364655, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9496 Neighboring gene lectin, mannose binding 1 Neighboring gene uncharacterized LOC107985156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:57053866-57054862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:57122524-57123295 Neighboring gene meiotic recombination hotspot N Neighboring gene ReSE screen-validated silencer GRCh37_chr18:57139771-57139930 Neighboring gene meiotic recombination hotspot L Neighboring gene NANOG hESC enhancer GRCh37_chr18:57214689-57215202 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:57373821-57374004 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 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

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ30681, MGC50861

    Gene Ontology Provided by GOA

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

    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.

    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
      Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
      UniProtKB/TrEMBL
      A0A3B3IRL6
      Related
      ENSP00000404464.2, ENST00000439986.9
      Conserved Domains (1) summary
      smart00179
      Location:134175
      EGF_CA; Calcium-binding EGF-like domain

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      59430939..59697721 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451091.2XP_024306859.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
      UniProtKB/TrEMBL
      A0A3B3IRL6
      Related
      ENSP00000497183.1, ENST00000649564.1
      Conserved Domains (1) summary
      smart00179
      Location:134175
      EGF_CA; Calcium-binding EGF-like domain
    2. XM_017025557.2XP_016881046.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WKU1, A0A8Q3WKU2
      Related
      ENSP00000512259.1, ENST00000695904.1
    3. XM_047437302.1XP_047293258.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    4. XM_047437301.1XP_047293257.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WKU1
    5. XM_017025558.2XP_016881047.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3

      Related
      ENSP00000512255.1, ENST00000695903.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      59632718..59900788 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318206.1XP_054174181.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    2. XM_054318207.1XP_054174182.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    3. XM_054318208.1XP_054174183.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    4. XM_054318209.1XP_054174184.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3