Human Gene CUBN (ENST00000377833.10_7) from GENCODE V47lift37
  Description: cubilin (from RefSeq NM_001081.4)
Gencode Transcript: ENST00000377833.10_7
Gencode Gene: ENSG00000107611.16_10
Transcript (Including UTRs)
   Position: hg19 chr10:16,865,965-17,171,810 Size: 305,846 Total Exon Count: 67 Strand: -
Coding Region
   Position: hg19 chr10:16,866,974-17,171,764 Size: 304,791 Coding Exon Count: 67 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:16,865,965-17,171,810)mRNA (may differ from genome)Protein (3623 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CUBN_HUMAN
DESCRIPTION: RecName: Full=Cubilin; AltName: Full=460 kDa receptor; AltName: Full=Intestinal intrinsic factor receptor; AltName: Full=Intrinsic factor-cobalamin receptor; AltName: Full=Intrinsic factor-vitamin B12 receptor; Flags: Precursor;
FUNCTION: Cotransporter which plays a role in lipoprotein, vitamin and iron metabolism, by facilitating their uptake. Binds to ALB, MB, Kappa and lambda-light chains, TF, hemoglobin, GC, SCGB1A1, APOA1, high density lipoprotein, and the GIF-cobalamin complex. The binding of all ligands requires calcium. Serves as important transporter in several absorptive epithelia, including intestine, renal proximal tubules and embryonic yolk sac. Interaction with LRP2 mediates its trafficking throughout vesicles and facilitates the uptake of specific ligands like GC, hemoglobin, ALB, TF and SCGB1A1. Interaction with AMN controls its trafficking to the plasma membrane and facilitates endocytosis of ligands. May play an important role in the development of the peri-implantation embryo through internalization of APOA1 and cholesterol. Binds to LGALS3 at the maternal-fetal interface.
SUBUNIT: Interacts with LRP2 in a dual-receptor complex in a calcium-dependent manner. Component of the cubam complex composed of CUBN and AMN. The cubam complex can oligomerize and form cubam trimers. Found in a complex with PID1/PCLI1, LRP1 and CUBNI. Interacts with LRP1 and PID1/PCLI1.
SUBCELLULAR LOCATION: Endosome membrane; Peripheral membrane protein (By similarity). Lysosome membrane; Peripheral membrane protein (By similarity). Note=Colocalizes with AMN and LRP2 in the endocytotic apparatus of epithelial cells (By similarity).
TISSUE SPECIFICITY: Expressed in kidney proximal tubule cells, placenta, visceral yolk-sac cells and in absorptive intestinal cells. Expressed in the epithelium of intestine and kidney.
DOMAIN: The CUB domains 5 to 8 mediate binding to GIF and ALB. CUB domains 1 and 2 mediate interaction with LRP2.
PTM: The precursor is cleaved by a trans-Golgi proteinase furin. The result is a propeptide cleaved off.
PTM: N-glycosylated.
DISEASE: Defects in CUBN are a cause of recessive hereditary megaloblastic anemia 1 (RH-MGA1) [MIM:261100]; also known as MGA1 Norwegian type or Imerslund-Grasbeck syndrome (I-GS). RH-MGA1 is due to selective malabsorption of vitamin B12. Defects in vitamin B12 absorption lead to impaired function of thymidine synthase. As a consequence DNA synthesis is interrupted. Rapidly dividing cells involved in erythropoiesis are particularly affected.
SIMILARITY: Contains 27 CUB domains.
SIMILARITY: Contains 7 EGF-like domains.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CUBN";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CUBN
Diseases sorted by gene-association score: megaloblastic anemia-1, finnish type* (1672), megaloblastic anemia (79), dent disease (18), fanconi-like syndrome (11), fanconi syndrome (11), chylomicron retention disease (10), congenital intrinsic factor deficiency (9), cystinosis (9), 3-methylglutaconic aciduria, type i (8), vitamin metabolic disorder (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.51 RPKM in Kidney - Cortex
Total median expression: 44.38 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.8046-0.387 Picture PostScript Text
3' UTR -283.401009-0.281 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000859 - CUB
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR024731 - EGF_dom_MSP1-like
IPR009030 - Growth_fac_rcpt

Pfam Domains:
PF00008 - EGF-like domain
PF00431 - CUB domain
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF
PF12947 - EGF domain

SCOP Domains:
49854 - Spermadhesin, CUB domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3KQ4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O60494
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008144 drug binding
GO:0031419 cobalamin binding
GO:0038023 signaling receptor activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0001894 tissue homeostasis
GO:0006629 lipid metabolic process
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0007165 signal transduction
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0009235 cobalamin metabolic process
GO:0015031 protein transport
GO:0015889 cobalamin transport
GO:0034384 high-density lipoprotein particle clearance
GO:0042359 vitamin D metabolic process
GO:0042953 lipoprotein transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005903 brush border
GO:0005905 clathrin-coated pit
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030139 endocytic vesicle
GO:0031232 extrinsic component of external side of plasma membrane
GO:0031526 brush border membrane
GO:0043202 lysosomal lumen
GO:0045177 apical part of cell
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF034611 - Homo sapiens intrinsic factor-B12 receptor precursor, mRNA, complete cds.
AB209880 - Homo sapiens mRNA for cubilin variant protein.
AK075228 - Homo sapiens cDNA FLJ90747 fis, clone PLACE1011708, highly similar to Cubilin precursor.
AK309623 - Homo sapiens cDNA, FLJ99664.
AK310404 - Homo sapiens cDNA, FLJ17446.
AF086456 - Homo sapiens full length insert cDNA clone ZD83H02.
JD557511 - Sequence 538535 from Patent EP1572962.
AK074536 - Homo sapiens cDNA FLJ90055 fis, clone HEMBA1003047, highly similar to Cubilin precursor.
JD366554 - Sequence 347578 from Patent EP1572962.
JD504733 - Sequence 485757 from Patent EP1572962.
JD517726 - Sequence 498750 from Patent EP1572962.
JD364447 - Sequence 345471 from Patent EP1572962.
JD050797 - Sequence 31821 from Patent EP1572962.
JD097396 - Sequence 78420 from Patent EP1572962.
JD512478 - Sequence 493502 from Patent EP1572962.
JD350929 - Sequence 331953 from Patent EP1572962.
JD182466 - Sequence 163490 from Patent EP1572962.
JD331738 - Sequence 312762 from Patent EP1572962.
JD444065 - Sequence 425089 from Patent EP1572962.
JD444064 - Sequence 425088 from Patent EP1572962.
JD447168 - Sequence 428192 from Patent EP1572962.
JD447169 - Sequence 428193 from Patent EP1572962.
JD503987 - Sequence 485011 from Patent EP1572962.
JD554125 - Sequence 535149 from Patent EP1572962.
JD220287 - Sequence 201311 from Patent EP1572962.
JD279195 - Sequence 260219 from Patent EP1572962.
JD399468 - Sequence 380492 from Patent EP1572962.
JD564539 - Sequence 545563 from Patent EP1572962.
JD127943 - Sequence 108967 from Patent EP1572962.
JD453721 - Sequence 434745 from Patent EP1572962.
JD179735 - Sequence 160759 from Patent EP1572962.
JD293927 - Sequence 274951 from Patent EP1572962.
JD481401 - Sequence 462425 from Patent EP1572962.
JD392954 - Sequence 373978 from Patent EP1572962.
AK308290 - Homo sapiens cDNA, FLJ98238.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O60494 (Reactome details) participates in the following event(s):

R-HSA-350186 CUBN binds GC:25(OH)D
R-HSA-8963864 CUBN dissociates from 25(OH)D
R-HSA-264848 apoA-I binds to CUBN:AMN
R-HSA-3000103 CUBN:AMN binds GIF:Cbl
R-HSA-350168 LRP2 transports CUBN:GC:25(OH)D from extracellular region to cytosol
R-HSA-209760 CUBN:GC:25(OH)D translocates from cytosol to lysosomal lumen
R-HSA-3000137 CUBN:AMN transports extracellular GIF:Cbl to endosome
R-HSA-196791 Vitamin D (calciferol) metabolism
R-HSA-8964011 HDL clearance
R-HSA-196741 Cobalamin (Cbl, vitamin B12) transport and metabolism
R-HSA-3359462 Defective AMN causes hereditary megaloblastic anemia 1
R-HSA-209943 Steroid hormones
R-HSA-8957322 Metabolism of steroids
R-HSA-3359463 Defective CUBN causes hereditary megaloblastic anemia 1
R-HSA-8964043 Plasma lipoprotein clearance
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-3296469 Defects in cobalamin (B12) metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-3296482 Defects in vitamin and cofactor metabolism
R-HSA-1430728 Metabolism
R-HSA-382551 Transport of small molecules
R-HSA-5668914 Diseases of metabolism
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B0YIZ4, CUBN_HUMAN, ENST00000377833.1, ENST00000377833.2, ENST00000377833.3, ENST00000377833.4, ENST00000377833.5, ENST00000377833.6, ENST00000377833.7, ENST00000377833.8, ENST00000377833.9, IFCR, NM_001081, O60494, Q5VTA6, Q96RU9, uc318nwl.1, uc318nwl.2
UCSC ID: ENST00000377833.10_7
RefSeq Accession: NM_001081.4
Protein: O60494 (aka CUBN_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.