CCBE1 (collagen and calcium binding EGF domains 1) - Rat Genome Database

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Gene: CCBE1 (collagen and calcium binding EGF domains 1) Pan paniscus
Analyze
Symbol: CCBE1
Name: collagen and calcium binding EGF domains 1
RGD ID: 11698710
Description: ENCODES a protein that exhibits calcium ion binding (inferred); collagen binding (inferred); protease binding (inferred); 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 (inferred); extracellular space (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen and calcium-binding EGF domain-containing protein 1; LOC117976819; uncharacterized LOC117976819
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
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
(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
(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
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


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSPPAT00000038949   ⟹   ENSPPAP00000016255
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl1856,149,036 - 56,195,618 (-)Ensembl
Ensembl Acc Id: ENSPPAT00000038953   ⟹   ENSPPAP00000016259
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl1856,150,666 - 56,412,222 (-)Ensembl
RefSeq Acc Id: XM_008952636   ⟹   XP_008950884
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v21776,974,280 - 77,237,725 (-)NCBI
NHGRI_mPanPan11862,662,702 - 62,930,251 (-)NCBI
Mhudiblu_PPA_v01852,819,591 - 53,087,770 (-)NCBI
PanPan1.11856,149,036 - 56,412,550 (-)NCBI
Sequence:
RefSeq Acc Id: XM_055102382   ⟹   XP_054958357
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v21776,977,315 - 77,237,715 (-)NCBI
NHGRI_mPanPan11862,669,918 - 62,930,251 (-)NCBI
RefSeq Acc Id: XM_055102383   ⟹   XP_054958358
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v21776,970,088 - 77,237,715 (-)NCBI
NHGRI_mPanPan11862,662,702 - 62,930,251 (-)NCBI
RefSeq Acc Id: XR_010110159
Type: NON-CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v21776,925,872 - 77,237,715 (-)NCBI
Protein Sequences
Protein RefSeqs XP_008950884 (Get FASTA)   NCBI Sequence Viewer  
  XP_054958357 (Get FASTA)   NCBI Sequence Viewer  
  XP_054958358 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000016255.1
  ENSPPAP00000016259
  ENSPPAP00000016259.1
RefSeq Acc Id: XP_008950884   ⟸   XM_008952636
- Peptide Label: isoform X3
- UniProtKB: A0A2R9AMQ9 (UniProtKB/TrEMBL),   A0A2R9AKT9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSPPAP00000016259   ⟸   ENSPPAT00000038953
Ensembl Acc Id: ENSPPAP00000016255   ⟸   ENSPPAT00000038949
RefSeq Acc Id: XP_054958358   ⟸   XM_055102383
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054958357   ⟸   XM_055102382
- Peptide Label: isoform X1
Protein Domains
EGF-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000031234 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000038949.1 UniProtKB/TrEMBL
  ENSPPAT00000038953.1 UniProtKB/TrEMBL
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
KEGG Report pps:100988531 UniProtKB/TrEMBL
NCBI Gene CCBE1 ENTREZGENE
PANTHER COLLAGEN UniProtKB/TrEMBL
  SCAVENGER RECEPTOR CLASS A MEMBER 3 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 A0A2R9AKT9 ENTREZGENE, UniProtKB/TrEMBL
  A0A2R9AMQ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-03-14 CCBE1  collagen and calcium binding EGF domains 1  LOC117976819  uncharacterized LOC117976819  Data Merged 737654 PROVISIONAL