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CCBE1 Gene(Protein Coding)

Collagen And Calcium Binding EGF Domains 1

GCID:
GC18M059430
GIFtS:
54
Genes Participants
UDN Logo

Aliases for CCBE1 Gene

Aliases for CCBE1 Gene

  • Collagen And Calcium Binding EGF Domains 1 2 3 5
  • Full Of Fluid Protein Homolog 3 4
  • Collagen And Calcium-Binding EGF Domain-Containing Protein 1 3
  • KIAA1983 4
  • HKLLS1 3

External Ids for CCBE1 Gene

Previous GeneCards Identifiers for CCBE1 Gene

  • GC18M055253
  • GC18M057101
  • GC18M053807

Summaries for CCBE1 Gene

Entrez Gene Summary for CCBE1 Gene

  • 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]

GeneCards Summary for CCBE1 Gene

CCBE1 (Collagen And Calcium Binding EGF Domains 1) is a Protein Coding gene. Diseases associated with CCBE1 include Hennekam Lymphangiectasia-Lymphedema Syndrome 1 and Hennekam Syndrome. GO annotations related to this gene include calcium ion binding and collagen binding.

UniProtKB/Swiss-Prot for CCBE1 Gene

  • Required for lymphangioblast budding and angiogenic sprouting from venous endothelium during embryogenesis.

Gene Wiki entry for CCBE1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCBE1 Gene

Genomics for CCBE1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for CCBE1 Gene

Enhancers for CCBE1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G059714 1.2 Ensembl ENCODE dbSUPER 18.8 -20.1 -20107 6.3 CTCF JUN SIN3A RAD21 ZEB1 GATA3 POLR2A RCOR1 FOS NFE2L2 CCBE1 ENSG00000273664 GC18P059755
GH18G059515 1.3 Ensembl ENCODE 8.2 +181.3 181349 2.2 FOXA2 MLX ARID4B FEZF1 FOS SP3 SP5 MIER3 SMARCA4 GLIS1 CCBE1 PIR51986 ENSG00000267000
GH18G059501 1.1 Ensembl ENCODE 9.1 +195.0 194957 2.8 PKNOX1 INSM2 FEZF1 RAD21 ZEB1 ZNF121 ZNF366 FOS EGR2 ZNF263 CCBE1 PIR51986 ENSG00000267000
GH18G059742 0.9 ENCODE dbSUPER 9.8 -46.5 -46523 3.4 GATAD2A BHLHE40 HLF CEBPB CEBPG KAT2B JUND CEBPA FOS CCBE1 GC18P059755 ENSG00000273664
GH18G059513 1 Ensembl ENCODE 8.4 +183.5 183474 1.4 MXI1 SAP130 MAX KLF17 FEZF1 ZNF600 FOS PRDM10 ZNF680 ZNF280D CCBE1 PIR51986 ENSG00000267000
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CCBE1 on UCSC Golden Path with GeneCards custom track

Promoters for CCBE1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000104148 443 1601 ZNF76 SIN3A ZNF2 RAD21 ZEB1 ZNF121 GLIS2 SCRT2 ZNF263 ZNF654

Transcription factor binding sites by QIAGEN in the CCBE1 gene promoter:

Genomic Location for CCBE1 Gene

Chromosome:
18
Start:
59,430,939 bp from pter
End:
59,697,643 bp from pter
Size:
266,705 bases
Orientation:
Minus strand

Genomic View for CCBE1 Gene

Genes around CCBE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCBE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCBE1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CCBE1 Gene

Proteins for CCBE1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CCBE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UXH8-CCBE1_HUMAN
    Recommended name:
    Collagen and calcium-binding EGF domain-containing protein 1
    Protein Accession:
    Q6UXH8
    Secondary Accessions:
    • Q6MZX5
    • Q86SS2
    • Q8TF19

    Protein attributes for CCBE1 Gene

    Size:
    406 amino acids
    Molecular mass:
    44103 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB85569.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CCBE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCBE1 Gene

Protein Expression for CCBE1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CCBE1 Gene

  • Glycosylation at Asn142 and Asn182
  • Modification sites at PhosphoSitePlus

Other Protein References for CCBE1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CCBE1 Gene

Domains & Families for CCBE1 Gene

Protein Domains for CCBE1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CCBE1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6UXH8

UniProtKB/Swiss-Prot:

CCBE1_HUMAN :
  • Belongs to the CCBE1 family.
Family:
  • Belongs to the CCBE1 family.
genes like me logo Genes that share domains with CCBE1: view

No data available for Gene Families for CCBE1 Gene

Function for CCBE1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for CCBE1 Gene

UniProtKB/Swiss-Prot Function:
Required for lymphangioblast budding and angiogenic sprouting from venous endothelium during embryogenesis.

Gene Ontology (GO) - Molecular Function for CCBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002020 protease binding IPI 24552833
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0005518 collagen binding IDA 21778431
genes like me logo Genes that share ontologies with CCBE1: view
genes like me logo Genes that share phenotypes with CCBE1: view

Human Phenotype Ontology for CCBE1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CCBE1 Gene

MGI Knock Outs for CCBE1:

Animal Model Products

  • Taconic Biosciences Mouse Models for CCBE1

CRISPR Products

miRNA for CCBE1 Gene

miRTarBase miRNAs that target CCBE1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CCBE1 Gene

Localization for CCBE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCBE1 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCBE1 gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytosol 3
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CCBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IDA 21778431
GO:0005581 collagen trimer IEA --
GO:0005615 extracellular space IDA 24552833
genes like me logo Genes that share ontologies with CCBE1: view

Pathways & Interactions for CCBE1 Gene

SuperPathways for CCBE1 Gene

PathCards logo More details on SuperPathways for CCBE1
No Data Available

Gene Ontology (GO) - Biological Process for CCBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001945 lymph vessel development IEA --
GO:0001946 lymphangiogenesis IEA,ISS --
GO:0002040 sprouting angiogenesis ISS --
GO:0003016 respiratory system process IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with CCBE1: view

No data available for Pathways by source and SIGNOR curated interactions for CCBE1 Gene

Drugs & Compounds for CCBE1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for CCBE1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for CCBE1 Gene

(4) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(54) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CCBE1 Gene

Collagen and calcium binding EGF domains 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCBE1 Gene

No ASD Table

Relevant External Links for CCBE1 Gene

GeneLoc Exon Structure for
CCBE1
ECgene alternative splicing isoforms for
CCBE1

Expression for CCBE1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCBE1 Gene

mRNA expression in normal human tissues for CCBE1 Gene
mRNA expression by BioGPS for CCBE1 GenemRNA expression by GTEx for CCBE1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCBE1 Gene

This gene is overexpressed in Colon - Sigmoid (x5.5) and Ovary (x4.8).

Protein differential expression in normal tissues from HIPED for CCBE1 Gene

This gene is overexpressed in Heart (64.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCBE1 Gene



Protein tissue co-expression partners for CCBE1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CCBE1 Gene:

CCBE1

SOURCE GeneReport for Unigene cluster for CCBE1 Gene:

Hs.34333

mRNA Expression by UniProt/SwissProt for CCBE1 Gene:

Q6UXH8-CCBE1_HUMAN
Tissue specificity: Not expressed in blood or lymphatic endothelial cells.

Evidence on tissue expression from TISSUES for CCBE1 Gene

  • Lung(4.2)
  • Liver(4.1)
  • Nervous system(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CCBE1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • thyroid
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • intestine
  • kidney
  • large intestine
  • small intestine
  • spleen
Pelvis:
  • anus
  • pelvis
  • rectum
  • testicle
  • ureter
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • lymph node
  • lymph vessel
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with CCBE1: view

Primer Products

Orthologs for CCBE1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCBE1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia CCBE1 34 35
  • 99.59 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 89 (a)
 OneToMany
-- 35
  • 84 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia CCBE1 34 35
  • 88.06 (n)
mouse
(Mus musculus)
 Mammalia Ccbe1 34 16 35
  • 86.62 (n)
rat
(Rattus norvegicus)
 Mammalia Ccbe1 34
  • 86.45 (n)
cow
(Bos Taurus)
 Mammalia CCBE1 34 35
  • 86.29 (n)
oppossum
(Monodelphis domestica)
 Mammalia CCBE1 35
  • 83 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CCBE1 34 35
  • 74.56 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 35
  • 78 (a)
 OneToMany
-- 35
  • 77 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia ccbe1 34
  • 72.57 (n)
zebrafish
(Danio rerio)
 Actinopterygii ccbe1 34 35
  • 66.39 (n)
Species where no ortholog for CCBE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CCBE1 Gene

ENSEMBL:
Gene Tree for CCBE1 (if available)
TreeFam:
Gene Tree for CCBE1 (if available)

Paralogs for CCBE1 Gene

No data available for Paralogs for CCBE1 Gene

Variants for CCBE1 Gene

Sequence variations from dbSNP and Humsavar for CCBE1 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs121908250 Pathogenic, Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510] 59,480,228(-) AGTGC(A/T)GCAAA nc-transcript-variant, reference, missense
rs121908251 Pathogenic, Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510] 59,469,568(-) GCAGT(C/G)CACGG nc-transcript-variant, reference, missense
rs121908252 Pathogenic, Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510] 59,438,119(-) CCAGA(C/G)GGTCT nc-transcript-variant, reference, missense
rs121908253 Pathogenic, Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510] 59,466,820(-) GCTAC(C/G/T)GCTGC nc-transcript-variant, reference, missense
rs121908254 Pathogenic, Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510] 59,466,772(-) AGACA(C/T)GTACC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CCBE1 Gene

Variant ID Type Subtype PubMed ID
dgv1617n106 CNV deletion 24896259
dgv3365n100 CNV gain 25217958
dgv3366n100 CNV gain 25217958
esv1302581 CNV insertion 17803354
esv2344726 CNV deletion 18987734
esv2507425 CNV insertion 19546169
esv2578250 CNV deletion 19546169
esv2659149 CNV deletion 23128226
esv2717167 CNV deletion 23290073
esv2717168 CNV deletion 23290073
esv2717169 CNV deletion 23290073
esv274875 CNV gain+loss 21479260
esv275221 CNV loss 21479260
esv3303248 CNV mobile element insertion 20981092
esv3336754 CNV insertion 20981092
esv3391683 CNV insertion 20981092
esv3397864 CNV insertion 20981092
esv3427131 CNV duplication 20981092
esv3555474 CNV deletion 23714750
esv3642663 CNV loss 21293372
esv3642664 CNV loss 21293372
esv3642665 CNV loss 21293372
esv3642666 CNV loss 21293372
esv3642667 CNV loss 21293372
esv3893108 CNV loss 25118596
esv4345 CNV loss 18987735
esv8710 CNV loss 19470904
nsv1055437 CNV gain 25217958
nsv1055632 CNV loss 25217958
nsv1055873 CNV gain 25217958
nsv1066670 CNV loss 25217958
nsv1071853 CNV deletion 25765185
nsv1142239 CNV tandem duplication 24896259
nsv1146850 CNV deletion 26484159
nsv470420 CNV gain 18288195
nsv513499 CNV insertion 21212237
nsv522624 CNV loss 19592680
nsv577052 CNV loss 21841781
nsv577053 CNV gain 21841781
nsv828251 CNV loss 20364138

Variation tolerance for CCBE1 Gene

Residual Variation Intolerance Score: 50.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.75; 46.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CCBE1 Gene

Human Gene Mutation Database (HGMD)
CCBE1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCBE1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCBE1 Gene

Disorders for CCBE1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CCBE1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hennekam lymphangiectasia-lymphedema syndrome 1
  • hennekam syndrome
hennekam syndrome
  • hennekam lymphangiectasia-lymphedema syndrome
lymphedema
  • lymphatic edema
immune hydrops fetalis
  • ihf
cholestasis-lymphedema syndrome
  • aagenaes syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CCBE1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CCBE1_HUMAN
  • Hennekam lymphangiectasia-lymphedema syndrome 1 (HKLLS1) [MIM:235510]: A generalized lymph-vessels dysplasia characterized by intestinal lymphangiectasia with severe lymphedema of the limbs, genitalia and face. In addition, affected individuals have unusual facies and severe mental retardation. {ECO:0000269 PubMed:19911200, ECO:0000269 PubMed:19935664}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CCBE1

Genetic Association Database (GAD)
CCBE1
Human Genome Epidemiology (HuGE) Navigator
CCBE1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CCBE1
genes like me logo Genes that share disorders with CCBE1: view

No data available for Genatlas for CCBE1 Gene

Publications for CCBE1 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 2 3 4 64
  2. Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PMID: 11853319) Nagase T. … Ohara O. (DNA Res. 2001) 2 3 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Linkage and sequence analysis indicate that CCBE1 is mutated in recessively inherited generalised lymphatic dysplasia. (PMID: 19911200) Connell F. … Jeffery S. (Hum. Genet. 2010) 3 4 64
  5. ccbe1 is required for embryonic lymphangiogenesis and venous sprouting. (PMID: 19287381) Hogan B.M. … Schulte-Merker S. (Nat. Genet. 2009) 3 4 64

Products for CCBE1 Gene

Sources for CCBE1 Gene

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