Cubn (cubilin) - Rat Genome Database

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Gene: Cubn (cubilin) Rattus norvegicus
Analyze
Symbol: Cubn
Name: cubilin
RGD ID: 68355
Description: Exhibits several functions, including cargo receptor activity; hemoglobin binding activity; and identical protein binding activity. Involved in several processes, including cobalamin catabolic process; in utero embryonic development; and organic substance transport. Localizes to several cellular components, including brush border membrane; clathrin-coated pit; and cytoplasmic vesicle. Orthologous to human CUBN (cubilin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 460 kDa receptor; cubilin (intrinsic factor-cobalamin receptor); glycoprotein 280; GP280; IFCR; intrinsic factor-cobalamin receptor; intrinsic factor-vitamin B12 receptor; MGA1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cubnem1Mcwi  
Genetic Models: SS-Cubnem1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21776,385,046 - 76,593,133 (-)NCBI
Rnor_6.0 Ensembl1780,584,878 - 80,807,243 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01780,584,921 - 80,807,181 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,205,509 - 82,425,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,545,893 - 87,772,079 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,556,725 - 87,782,912 (-)NCBI
Celera1775,753,959 - 75,962,017 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Ahuja R, etal., Biochem J. 2008 Mar 1;410(2):301-8.
2. Aminoff M, etal., Nat Genet 1999 Mar;21(3):309-13.
3. Andersen CB, etal., Nature. 2010 Mar 18;464(7287):445-8. doi: 10.1038/nature08874.
4. Assemat E, etal., Biol Reprod. 2005 May;72(5):1079-86. Epub 2004 Dec 22.
5. Feng M, etal., Sichuan Da Xue Xue Bao Yi Xue Ban. 2006 Sep;37(5):738-41.
6. Fyfe JC, etal., Blood. 2004 Mar 1;103(5):1573-9. Epub 2003 Oct 23.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gburek J, etal., Am J Physiol Renal Physiol 2003 Sep;285(3):F451-8. Epub 2003 Apr 29.
9. Gburek J, etal., J Am Soc Nephrol. 2002 Feb;13(2):423-30.
10. GOA data from the GO Consortium
11. Ishida T, etal., Cell Tissue Res. 2004 Dec;318(3):533-43. Epub 2004 Oct 2.
12. MGD data from the GO Consortium
13. Moestrup SK, etal., J Biol Chem 1998 Feb 27;273(9):5235-42.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Tauris J, etal., Audiol Neurootol. 2009;14(4):267-78. doi: 10.1159/000199446. Epub 2009 Feb 6.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Yammani RR, etal., Am J Physiol Endocrinol Metab 2001 Nov;281(5):E900-7.
22. Yammani RR, etal., J Biol Chem 2001 Nov 30;276(48):44777-84.
Additional References at PubMed
PMID:6321516   PMID:9153271   PMID:9691015   PMID:10400683   PMID:10552972   PMID:10766831   PMID:10811843   PMID:11856751   PMID:12815097   PMID:15286052   PMID:15342463   PMID:15976000  
PMID:16027047   PMID:17442257   PMID:17453355   PMID:19056867   PMID:21082674   PMID:22337902   PMID:23012479   PMID:23376485   PMID:23533145   PMID:24122887   PMID:26025362   PMID:26173747  


Genomics

Comparative Map Data
Cubn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21776,385,046 - 76,593,133 (-)NCBI
Rnor_6.0 Ensembl1780,584,878 - 80,807,243 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01780,584,921 - 80,807,181 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,205,509 - 82,425,565 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,545,893 - 87,772,079 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,556,725 - 87,782,912 (-)NCBI
Celera1775,753,959 - 75,962,017 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
CUBN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1016,823,966 - 17,129,817 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1016,823,966 - 17,129,811 (-)EnsemblGRCh38hg38GRCh38
GRCh381016,823,966 - 17,130,492 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371016,865,965 - 17,171,810 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361016,905,971 - 17,211,822 (-)NCBINCBI36hg18NCBI36
Build 341016,906,543 - 17,211,796NCBI
Celera1016,799,178 - 17,105,066 (-)NCBI
Cytogenetic Map10p13NCBI
HuRef1016,779,758 - 17,084,998 (-)NCBIHuRef
CHM1_11016,866,152 - 17,171,970 (-)NCBICHM1_1
Cubn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39213,281,149 - 13,496,687 (-)NCBIGRCm39mm39
GRCm39 Ensembl213,281,149 - 13,496,624 (-)Ensembl
GRCm38213,276,338 - 13,491,876 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,276,338 - 13,491,813 (-)EnsemblGRCm38mm10GRCm38
MGSCv37213,197,965 - 13,413,503 (-)NCBIGRCm37mm9NCBIm37
MGSCv36213,194,189 - 13,409,729 (-)NCBImm8
Celera213,186,219 - 13,402,130 (-)NCBICelera
Cytogenetic Map2A1NCBI
cM Map29.86NCBI
Cubn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,788,959 - 11,038,845 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,789,674 - 11,038,297 (+)NCBIChiLan1.0ChiLan1.0
CUBN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11017,415,551 - 17,719,126 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1017,415,551 - 17,719,129 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01017,141,464 - 17,446,867 (-)NCBIMhudiblu_PPA_v0panPan3
CUBN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1219,784,125 - 20,041,840 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl219,784,198 - 20,041,839 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,887,230 - 17,151,382 (+)NCBI
ROS_Cfam_1.0220,075,720 - 20,333,544 (+)NCBI
UMICH_Zoey_3.1217,278,052 - 17,541,754 (+)NCBI
UNSW_CanFamBas_1.0218,116,485 - 18,374,283 (+)NCBI
UU_Cfam_GSD_1.0218,734,135 - 18,999,935 (+)NCBI
Cubn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934417,550,256 - 17,808,034 (-)NCBI
SpeTri2.0NW_00493652010,140,784 - 10,410,082 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CUBN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1043,102,946 - 43,414,613 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11043,102,931 - 43,414,692 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21047,746,354 - 48,023,009 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUBN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1916,774,644 - 17,079,776 (-)NCBI
ChlSab1.1 Ensembl916,774,757 - 17,079,681 (-)Ensembl
Cubn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479610,728,853 - 10,987,292 (+)NCBI

Position Markers
RH128210  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,585,051 - 80,585,237NCBIRnor6.0
Rnor_5.01782,205,639 - 82,205,825UniSTSRnor5.0
RGSC_v3.41787,546,023 - 87,546,209UniSTSRGSC3.4
Celera1775,754,089 - 75,754,275UniSTS
RH 3.4 Map17774.0UniSTS
Cytogenetic Map17q12.3UniSTS
BM387042  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,797,136 - 80,797,945NCBIRnor6.0
Rnor_5.01782,415,520 - 82,416,329UniSTSRnor5.0
RGSC_v3.41787,762,034 - 87,762,843UniSTSRGSC3.4
Celera1775,951,986 - 75,952,795UniSTS
RH 3.4 Map17807.2UniSTS
Cytogenetic Map17q12.3UniSTS
RH124704  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01780,585,005 - 80,585,384NCBIRnor6.0
Rnor_5.01782,205,593 - 82,205,972UniSTSRnor5.0
RGSC_v3.41787,545,977 - 87,546,356UniSTSRGSC3.4
Celera1775,754,043 - 75,754,422UniSTS
Cytogenetic Map17q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177485263085183543Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177570542786731080Rat


Genetic Models
This gene Cubn is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:826
Count of miRNA genes:293
Interacting mature miRNAs:376
Transcripts:ENSRNOT00000040052
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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.


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 29
Low 1 2 9 3 11 3 1 1 38 4 39 11 1
Below cutoff 40 35 25 8 25 7 9 36 2 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040052   ⟹   ENSRNOP00000048477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1780,585,303 - 80,807,181 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090064   ⟹   ENSRNOP00000075097
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1780,584,878 - 80,807,243 (-)Ensembl
RefSeq Acc Id: NM_053332   ⟹   NP_445784
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,385,046 - 76,593,133 (-)NCBI
Rnor_6.01780,584,921 - 80,807,181 (-)NCBI
Rnor_5.01782,205,509 - 82,425,565 (-)NCBI
RGSC_v3.41787,545,893 - 87,772,079 (-)RGD
Celera1775,753,959 - 75,962,017 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445784 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC71661 (Get FASTA)   NCBI Sequence Viewer  
  EDL78717 (Get FASTA)   NCBI Sequence Viewer  
  EDL78718 (Get FASTA)   NCBI Sequence Viewer  
  O70244 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445784   ⟸   NM_053332
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000075097   ⟸   ENSRNOT00000090064
RefSeq Acc Id: ENSRNOP00000048477   ⟸   ENSRNOT00000040052
Protein Domains
CUB   EGF-like

Transcriptome

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

Promoters
RGD ID:13700594
Promoter ID:EPDNEW_R11118
Type:initiation region
Name:Cubn_1
Description:cubilin
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_6.01780,807,226 - 80,807,286EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68355 AgrOrtholog
BIND 133316
Ensembl Genes ENSRNOG00000029047 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048477 UniProtKB/TrEMBL
  ENSRNOP00000075097 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040052 UniProtKB/TrEMBL
  ENSRNOT00000090064 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.290 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CUB_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cubilin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sperma_CUB_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:80848 UniProtKB/Swiss-Prot
NCBI Gene 80848 ENTREZGENE
PANTHER PTHR45656:SF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cubn PhenoGen
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49854 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC218981
UniProt CUBN_RAT UniProtKB/Swiss-Prot
  F1LNU2_RAT UniProtKB/TrEMBL
  O70244 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cubn  cubilin       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations in gene cause hereditary megaloblastic anaemia 1 61796
gene_domains NH2 terminal fragment comprised of 110 amino-acid residues followed by 8 epidermal growth factor (EGF)-like repeats and 27 CUB domains 628443
gene_expression expressed in the apical membranes of epithelial cells 61796
gene_expression expressed in the apical membranes of epithelial cells 70244
gene_function receptor for intrinsic factor-vitamin B12 complexes 61796
gene_physical_interaction binds to intrinsic factor (IF)-cobalamin (cbl, vitamin B12) complex to promote the transportation of cobalamin 628443
gene_process facilitates vitamin B12 uptake (cyanocobalamin) 61796
gene_process undergoes degradation in the intestine losing the NH2 terminal which impaires its binding affinity to megalin, the 230 kDa form may be a major intermediate during the degradation of the 460 kDa form 628443
gene_process involved in renal reabsorption of myoglobin 1299150
gene_regulation poor expression due to thyroixine defficiency results in decreased uptake and transport of cobalamin 628443