Cdcp1 (CUB domain containing protein 1) - Rat Genome Database

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Gene: Cdcp1 (CUB domain containing protein 1) Rattus norvegicus
Analyze
Symbol: Cdcp1
Name: CUB domain containing protein 1
RGD ID: 1305578
Description: Predicted to be located in membrane. Orthologous to human CDCP1 (CUB domain containing protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CUB domain-containing protein 1; LOC301082; RGD1305578; similar to CUB domain containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28122,828,685 - 122,865,345 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,828,685 - 122,865,388 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,418,976 - 128,455,475 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08126,617,915 - 126,654,422 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08124,446,097 - 124,482,633 (-)NCBIRnor_WKY
Rnor_6.08132,260,007 - 132,296,661 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,260,029 - 132,296,661 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,412,926 - 131,449,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,951,811 - 127,988,666 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18127,974,156 - 128,008,282 (-)NCBI
Celera8121,941,452 - 121,978,261 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-dichloroaniline  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
crocidolite asbestos  (ISO)
diazinon  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
lipopolysaccharide  (ISO)
nickel atom  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
pentanal  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sotorasib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trametinib  (ISO)
trichloroethene  (EXP)
triclosan  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Cdcp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28122,828,685 - 122,865,345 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8122,828,685 - 122,865,388 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8128,418,976 - 128,455,475 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08126,617,915 - 126,654,422 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08124,446,097 - 124,482,633 (-)NCBIRnor_WKY
Rnor_6.08132,260,007 - 132,296,661 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8132,260,029 - 132,296,661 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08131,412,926 - 131,449,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,951,811 - 127,988,666 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18127,974,156 - 128,008,282 (-)NCBI
Celera8121,941,452 - 121,978,261 (-)NCBICelera
Cytogenetic Map8q32NCBI
CDCP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38345,082,277 - 45,146,482 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl345,082,277 - 45,146,422 (-)EnsemblGRCh38hg38GRCh38
GRCh37345,123,769 - 45,187,870 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36345,098,773 - 45,162,918 (-)NCBINCBI36Build 36hg18NCBI36
Celera345,061,726 - 45,126,310 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef345,167,190 - 45,231,748 (-)NCBIHuRef
CHM1_1345,073,764 - 45,137,892 (-)NCBICHM1_1
T2T-CHM13v2.0345,098,021 - 45,162,812 (-)NCBIT2T-CHM13v2.0
Cdcp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399122,999,870 - 123,045,175 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9122,999,889 - 123,045,103 (-)EnsemblGRCm39 Ensembl
GRCm389123,170,805 - 123,216,110 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9123,170,824 - 123,216,038 (-)EnsemblGRCm38mm10GRCm38
MGSCv379123,081,403 - 123,125,156 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369123,020,983 - 123,064,736 (-)NCBIMGSCv36mm8
Celera9123,623,251 - 123,665,086 (-)NCBICelera
Cytogenetic Map9F4NCBI
Cdcp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542026,596,932 - 26,636,207 (+)NCBIChiLan1.0ChiLan1.0
CDCP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1346,094,033 - 46,130,131 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl346,097,391 - 46,130,929 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0344,982,974 - 45,048,814 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CDCP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12043,234,981 - 43,293,840 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2043,234,387 - 43,289,765 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2043,150,958 - 43,205,664 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02043,719,850 - 43,774,525 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2043,719,856 - 43,774,525 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12042,959,256 - 43,013,675 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02043,366,560 - 43,421,075 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02043,642,438 - 43,697,205 (+)NCBIUU_Cfam_GSD_1.0
Cdcp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118198,305,476 - 198,353,833 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936695657,865 - 706,186 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936695657,934 - 705,447 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDCP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1328,257,417 - 28,319,215 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11328,258,593 - 28,319,365 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21331,136,251 - 31,197,528 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDCP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,559,500 - 6,619,952 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl226,557,046 - 6,619,827 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041160,548,997 - 160,611,935 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdcp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473075,493,350 - 75,516,730 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473075,490,278 - 75,518,744 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdcp1
216 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:840
Count of miRNA genes:298
Interacting mature miRNAs:405
Transcripts:ENSRNOT00000006272
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
RH125864  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,828,706 - 122,828,935 (+)MAPPERmRatBN7.2
Rnor_6.08132,260,051 - 132,260,279NCBIRnor6.0
Rnor_5.08131,412,970 - 131,413,198UniSTSRnor5.0
RGSC_v3.48127,951,833 - 127,952,061UniSTSRGSC3.4
Celera8121,941,474 - 121,941,702UniSTS
Cytogenetic Map8q32UniSTS
AU046595  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,841,327 - 122,841,520 (+)MAPPERmRatBN7.2
Rnor_6.08132,272,647 - 132,272,839NCBIRnor6.0
Rnor_5.08131,425,566 - 131,425,758UniSTSRnor5.0
RGSC_v3.48127,964,652 - 127,964,844UniSTSRGSC3.4
Celera8121,954,247 - 121,954,439UniSTS
Cytogenetic Map8q32UniSTS
RH130398  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,828,792 - 122,828,980 (+)MAPPERmRatBN7.2
Rnor_6.08132,260,137 - 132,260,324NCBIRnor6.0
Rnor_5.08131,413,056 - 131,413,243UniSTSRnor5.0
RGSC_v3.48127,951,919 - 127,952,106UniSTSRGSC3.4
Celera8121,941,560 - 121,941,747UniSTS
RH 3.4 Map81276.79UniSTS
Cytogenetic Map8q32UniSTS
BI293852  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28122,830,992 - 122,831,154 (+)MAPPERmRatBN7.2
Rnor_6.08132,262,337 - 132,262,498NCBIRnor6.0
Rnor_5.08131,415,256 - 131,415,417UniSTSRnor5.0
RGSC_v3.48127,954,119 - 127,954,280UniSTSRGSC3.4
Celera8121,943,760 - 121,943,921UniSTS
RH 3.4 Map81334.6UniSTS
Cytogenetic Map8q32UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 4 1 3
Low 2 16 6 10 6 4 31 31 8
Below cutoff 25 37 31 9 31 7 7 36 4 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006272   ⟹   ENSRNOP00000006272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8122,828,685 - 122,865,388 (-)Ensembl
Rnor_6.0 Ensembl8132,260,029 - 132,296,661 (-)Ensembl
RefSeq Acc Id: NM_001106869   ⟹   NP_001100339
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28122,828,685 - 122,865,345 (-)NCBI
Rnor_6.08132,260,029 - 132,296,661 (-)NCBI
Rnor_5.08131,412,926 - 131,449,580 (-)NCBI
RGSC_v3.48127,951,811 - 127,988,666 (-)RGD
Celera8121,941,452 - 121,978,261 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100339 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76763 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100339   ⟸   NM_001106869
- Peptide Label: precursor
- UniProtKB: D3ZVA1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006272   ⟸   ENSRNOT00000006272

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVA1-F1-model_v2 AlphaFold D3ZVA1 1-833 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696406
Promoter ID:EPDNEW_R6931
Type:initiation region
Name:Cdcp1_1
Description:CUB domain containing protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08132,296,596 - 132,296,656EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305578 AgrOrtholog
BioCyc Gene G2FUF-28617 BioCyc
Ensembl Genes ENSRNOG00000004743 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006272 ENTREZGENE
  ENSRNOP00000006272.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006272 ENTREZGENE
  ENSRNOT00000006272.6 UniProtKB/TrEMBL
InterPro CDCP1 UniProtKB/TrEMBL
  sperma_CUB_dom UniProtKB/TrEMBL
KEGG Report rno:301082 UniProtKB/TrEMBL
NCBI Gene 301082 ENTREZGENE
PANTHER PTHR14477 UniProtKB/TrEMBL
PhenoGen Cdcp1 PhenoGen
Superfamily-SCOP SSF49854 UniProtKB/TrEMBL
UniProt D3ZVA1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cdcp1  CUB domain containing protein 1   Cdcp1_predicted  CUB domain containing protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Cdcp1_predicted  CUB domain containing protein 1 (predicted)  RGD1305578_predicted  similar to CUB domain containing protein 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1305578_predicted  similar to CUB domain containing protein 1 (predicted)  LOC301082_predicted  similar to CUB domain containing protein 1 (predicted)  Symbol and Name status set to approved 1331353 APPROVED
2005-01-20 RGD1305578_predicted  similar to CUB domain containing protein 1 (predicted)  LOC301082_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC301082_predicted  similar to CUB domain containing protein 1 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL