Ccbe1 (collagen and calcium binding EGF domains 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ccbe1 (collagen and calcium binding EGF domains 1) Heterocephalus glaber
Analyze
Symbol: Ccbe1
Name: collagen and calcium binding EGF domains 1
RGD ID: 18908962
Description: ENCODES a protein that exhibits collagen binding (ortholog); protease binding (ortholog); INVOLVED IN endothelial cell migration (ortholog); lung development (ortholog); lymph vessel development (ortholog); ASSOCIATED WITH Distal Renal Tubular Acidosis 4 with Hemolytic Anemia (ortholog); Facies (ortholog); genetic disease (ortholog); FOUND IN extracellular matrix (ortholog); extracellular space (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen and calcium-binding EGF domain-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247924,867,858 - 5,146,839 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247924,863,978 - 5,146,907 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
Ccbe1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247924,867,858 - 5,146,839 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247924,863,978 - 5,146,907 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
CCBE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381859,430,939 - 59,697,721 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1859,430,939 - 59,697,662 (-)EnsemblGRCh38hg38GRCh38
GRCh371857,098,171 - 57,364,655 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361855,252,124 - 55,515,570 (-)NCBINCBI36Build 36hg18NCBI36
Build 341855,252,128 - 55,515,570NCBI
Celera1853,815,992 - 54,082,692 (-)NCBICelera
Cytogenetic Map18q21.32NCBI
HuRef1853,807,272 - 54,074,065 (-)NCBIHuRef
CHM1_11857,093,481 - 57,360,274 (-)NCBICHM1_1
T2T-CHM13v2.01859,632,718 - 59,900,788 (-)NCBIT2T-CHM13v2.0
Ccbe1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391866,189,926 - 66,424,909 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1866,178,373 - 66,435,812 (-)EnsemblGRCm39 Ensembl
GRCm381866,056,855 - 66,291,838 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1866,045,302 - 66,302,741 (-)EnsemblGRCm38mm10GRCm38
MGSCv371866,216,510 - 66,451,492 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361866,186,267 - 66,417,201 (-)NCBIMGSCv36mm8
Celera1867,332,660 - 67,571,414 (-)NCBICelera
Cytogenetic Map18E1NCBI
cM Map1839.13NCBI
Ccbe1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81861,849,821 - 62,093,876 (-)NCBIGRCr8
mRatBN7.21859,579,851 - 59,823,977 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1859,580,768 - 59,824,400 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01861,758,754 - 62,013,194 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1861,759,289 - 61,788,863 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01860,953,314 - 61,204,084 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41862,407,265 - 62,442,194 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11862,444,950 - 62,516,306 (+)NCBI
Celera1857,703,958 - 57,944,773 (-)NCBICelera
Cytogenetic Map18q12.1NCBI
Ccbe1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540243,555,924 - 43,819,706 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540243,551,810 - 43,819,731 (-)NCBIChiLan1.0ChiLan1.0
CCBE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21776,925,872 - 77,237,725 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11862,662,702 - 62,930,251 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01852,819,591 - 53,087,772 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11856,149,036 - 56,412,550 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1856,149,036 - 56,412,222 (-)Ensemblpanpan1.1panPan2
CCBE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1116,597,389 - 16,819,888 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl116,597,334 - 16,819,894 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha117,573,095 - 17,795,588 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0116,468,211 - 16,697,179 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl116,468,224 - 16,697,173 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1116,503,987 - 16,732,917 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0116,430,870 - 16,653,326 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0116,686,056 - 16,915,078 (+)NCBIUU_Cfam_GSD_1.0
Ccbe1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494430,049,305 - 30,083,693 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364975,290,077 - 5,321,876 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364975,290,068 - 5,321,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCBE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1161,321,273 - 161,556,537 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11161,320,627 - 161,556,539 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21178,904,622 - 179,130,264 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCBE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11820,054,281 - 20,363,024 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1820,271,874 - 20,309,784 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660605,250,942 - 5,540,578 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_021239199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_021239200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AHKG01066024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01066036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GEBF01006446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSHGLT00000026347   ⟹   ENSHGLP00000026115
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247924,867,858 - 5,146,839 (-)Ensembl
RefSeq Acc Id: XM_021239199   ⟹   XP_021094858
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247924,863,978 - 5,146,907 (-)NCBI
RefSeq Acc Id: XM_021239200   ⟹   XP_021094859
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247924,863,978 - 5,146,907 (-)NCBI
Protein Sequences
Protein RefSeqs XP_021094858 (Get FASTA)   NCBI Sequence Viewer  
  XP_021094859 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000026115
GenBank Protein JAN97186 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_021094859   ⟸   XM_021239200
- Peptide Label: isoform X2
- UniProtKB: A0A0P6J1T6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_021094858   ⟸   XM_021239199
- Peptide Label: isoform X1
Ensembl Acc Id: ENSHGLP00000026115   ⟸   ENSHGLT00000026347


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000018589 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000026347 ENTREZGENE
Gene3D-CATH Laminin UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  Nematode_Cuticular_Collagen UniProtKB/TrEMBL
  NOTCH1_EGF-like UniProtKB/TrEMBL
NCBI Gene Ccbe1 ENTREZGENE
PANTHER COLLAGEN UniProtKB/TrEMBL
  GENE, 37797-RELATED UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
UniProt A0A0P6J1T6 ENTREZGENE, UniProtKB/TrEMBL