Human Gene CANX (uc003mkl.3) Description and Page Index
  Description: Homo sapiens calnexin (CANX), transcript variant 2, mRNA.
RefSeq Summary (NM_001024649): This gene encodes a member of the calnexin family of molecular chaperones. The encoded protein is a calcium-binding, endoplasmic reticulum (ER)-associated protein that interacts transiently with newly synthesized N-linked glycoproteins, facilitating protein folding and assembly. It may also play a central role in the quality control of protein folding by retaining incorrectly folded protein subunits within the ER for degradation. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2018]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC042843.1, SRR1660809.10008.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr5:179,125,930-179,158,639 Size: 32,710 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr5:179,132,683-179,155,645 Size: 22,963 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:179,125,930-179,158,639)mRNA (may differ from genome)Protein (592 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Calnexin; AltName: Full=IP90; AltName: Full=Major histocompatibility complex class I antigen-binding protein p88; AltName: Full=p90; Flags: Precursor;
FUNCTION: Calcium-binding protein that interacts with newly synthesized glycoproteins in the endoplasmic reticulum. It may act in assisting protein assembly and/or in the retention within the ER of unassembled protein subunits. It seems to play a major role in the quality control apparatus of the ER by the retention of incorrectly folded proteins. Associated with partial T-cell antigen receptor complexes that escape the ER of immature thymocytes, it may function as a signaling complex regulating thymocyte maturation. Additionally it may play a role in receptor- mediated endocytosis at the synapse.
SUBUNIT: Interacts with MAPK3/ERK1. Interacts with KCNH2. Associates with ribosomes. Interacts with SGIP1; involved in negative regulation of endocytosis (By similarity). The palmitoylated form interacts with the ribosome-translocon complex component SSR1, promoting efficient folding of glycoproteins.
INTERACTION: Q92597:NDRG1; NbExp=2; IntAct=EBI-355947, EBI-716486;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. The palmitoylated form preferentially localizes to the perinuclear rough ER.
PTM: Phosphorylated at Ser-564 by MAPK3/ERK1. phosphorylation by MAPK3/ERK1 increases its association with ribosomes (By similarity).
PTM: Palmitoylation by DHHC6 leads to the preferential localization to the perinuclear rough ER. It mediates the association of calnexin with the ribosome-translocon complex (RTC) which is required for efficient folding of glycosylated proteins.
SIMILARITY: Belongs to the calreticulin family.
WEB RESOURCE: Name=Wikipedia; Note=Calnexin entry; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CANX
CDC HuGE Published Literature: CANX
Positive Disease Associations: nephrogenic diabetes insipidus
Related Studies:
  1. nephrogenic diabetes insipidus
    Morello JP et al. 2001, Association of calnexin with wild type and mutant AVPR2 that causes nephrogenic diabetes insipidus., Biochemistry. 2001 Jun;40(23):6766-75. [PubMed 11389590]

-  MalaCards Disease Associations
  MalaCards Gene Search: CANX
Diseases sorted by gene-association score: orbital melanoma (17), frey syndrome (15), maxillary sinus squamous cell carcinoma (13), myeloperoxidase deficiency (10), lateral medullary syndrome (9), suppurative cholangitis (7), glossopharyngeal neuralgia (6), glossopharyngeal nerve disease (5), long qt syndrome 2 (4), muscular dystrophy-dystroglycanopathy , type b, 5 (4), cystic fibrosis (3), long qt syndrome (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 118.82 RPKM in Cells - Transformed fibroblasts
Total median expression: 3549.10 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 -58.30124-0.470 Picture PostScript Text
3' UTR -763.382994-0.255 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
IPR001580 - Calret/calnex
IPR018124 - Calret/calnex_CS
IPR009033 - Calreticulin/calnexin_P
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp

Pfam Domains:
PF00262 - Calreticulin family

SCOP Domains:
63887 - P-domain of calnexin/calreticulin
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on P27824
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0030246 carbohydrate binding
GO:0034185 apolipoprotein binding
GO:0035255 ionotropic glutamate receptor binding
GO:0046872 metal ion binding
GO:0051082 unfolded protein binding

Biological Process:
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0006457 protein folding
GO:0007568 aging
GO:0009306 protein secretion
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0034975 protein folding in endoplasmic reticulum
GO:0048488 synaptic vesicle endocytosis
GO:0061077 chaperone-mediated protein folding
GO:0070106 interleukin-27-mediated signaling pathway
GO:0070757 interleukin-35-mediated signaling pathway
GO:0072583 clathrin-dependent endocytosis

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005789 endoplasmic reticulum membrane
GO:0005790 smooth endoplasmic reticulum
GO:0005791 rough endoplasmic reticulum
GO:0005840 ribosome
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030424 axon
GO:0032839 dendrite cytoplasm
GO:0032991 macromolecular complex
GO:0042470 melanosome
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0043209 myelin sheath
GO:0044233 ER-mitochondrion membrane contact site
GO:0044322 endoplasmic reticulum quality control compartment
GO:0070062 extracellular exosome
GO:0071556 integral component of lumenal side of endoplasmic reticulum membrane

-  Descriptions from all associated GenBank mRNAs
  AK294702 - Homo sapiens cDNA FLJ55574 complete cds, highly similar to Calnexin precursor.
LF384720 - JP 2014500723-A/192223: Polycomb-Associated Non-Coding RNAs.
AK129990 - Homo sapiens cDNA FLJ26480 fis, clone KDN05071, highly similar to Calnexin precursor.
AK304420 - Homo sapiens cDNA FLJ54242 complete cds, highly similar to Calnexin precursor.
BC003552 - Homo sapiens calnexin, mRNA (cDNA clone MGC:1196 IMAGE:3546389), complete cds.
BC042843 - Homo sapiens calnexin, mRNA (cDNA clone MGC:17014 IMAGE:4342723), complete cds.
M94859 - Human calnexin mRNA, complete cds.
L18887 - Human calnexin mRNA, complete cds.
L10284 - Homo sapiens integral membrane protein, calnexin, (IP90) mRNA, complete cds.
AK312334 - Homo sapiens cDNA, FLJ92651, Homo sapiens calnexin (CANX), mRNA.
JD060154 - Sequence 41178 from Patent EP1572962.
JD423230 - Sequence 404254 from Patent EP1572962.
JD487569 - Sequence 468593 from Patent EP1572962.
AJ271880 - Homo sapiens mRNA for calnexin (CANX gene).
JD332057 - Sequence 313081 from Patent EP1572962.
BC050534 - Homo sapiens cDNA clone IMAGE:6061363, containing frame-shift errors.
CU678492 - Synthetic construct Homo sapiens gateway clone IMAGE:100017724 5' read CANX mRNA.
DQ890627 - Synthetic construct clone IMAGE:100003257; FLH164466.01X; RZPDo839G07162D calnexin (CANX) gene, encodes complete protein.
DQ893794 - Synthetic construct Homo sapiens clone IMAGE:100008254; FLH164462.01L; RZPDo839G07161D calnexin (CANX) gene, encodes complete protein.
AB527263 - Synthetic construct DNA, clone: pF1KB3649, Homo sapiens CANX gene for calnexin, without stop codon, in Flexi system.
LF325636 - JP 2014500723-A/133139: Polycomb-Associated Non-Coding RNAs.
GQ891329 - Homo sapiens clone HEL-S-100d epididymis secretory sperm binding protein mRNA, partial cds.
S67659 - calnexin [human, melanoma cells, SK MEL 23, mRNA Partial, 816 nt].
LF325635 - JP 2014500723-A/133138: Polycomb-Associated Non-Coding RNAs.
LF325634 - JP 2014500723-A/133137: Polycomb-Associated Non-Coding RNAs.
LF325631 - JP 2014500723-A/133134: Polycomb-Associated Non-Coding RNAs.
LF325630 - JP 2014500723-A/133133: Polycomb-Associated Non-Coding RNAs.
LF325627 - JP 2014500723-A/133130: Polycomb-Associated Non-Coding RNAs.
LF325624 - JP 2014500723-A/133127: Polycomb-Associated Non-Coding RNAs.
LF325623 - JP 2014500723-A/133126: Polycomb-Associated Non-Coding RNAs.
M98452 - Human calnexin mRNA, complete cds.
LF325619 - JP 2014500723-A/133122: Polycomb-Associated Non-Coding RNAs.
LF325617 - JP 2014500723-A/133120: Polycomb-Associated Non-Coding RNAs.
LF325614 - JP 2014500723-A/133117: Polycomb-Associated Non-Coding RNAs.
LF325613 - JP 2014500723-A/133116: Polycomb-Associated Non-Coding RNAs.
LF325610 - JP 2014500723-A/133113: Polycomb-Associated Non-Coding RNAs.
LF325608 - JP 2014500723-A/133111: Polycomb-Associated Non-Coding RNAs.
AK130080 - Homo sapiens cDNA FLJ26570 fis, clone LNF05710.
LF325604 - JP 2014500723-A/133107: Polycomb-Associated Non-Coding RNAs.
LF325603 - JP 2014500723-A/133106: Polycomb-Associated Non-Coding RNAs.
LF325601 - JP 2014500723-A/133104: Polycomb-Associated Non-Coding RNAs.
JD189587 - Sequence 170611 from Patent EP1572962.
LF325600 - JP 2014500723-A/133103: Polycomb-Associated Non-Coding RNAs.
JD328050 - Sequence 309074 from Patent EP1572962.
JD084557 - Sequence 65581 from Patent EP1572962.
LF325599 - JP 2014500723-A/133102: Polycomb-Associated Non-Coding RNAs.
JD327999 - Sequence 309023 from Patent EP1572962.
JD301713 - Sequence 282737 from Patent EP1572962.
JD171838 - Sequence 152862 from Patent EP1572962.
LF325598 - JP 2014500723-A/133101: Polycomb-Associated Non-Coding RNAs.
LF325597 - JP 2014500723-A/133100: Polycomb-Associated Non-Coding RNAs.
LF325596 - JP 2014500723-A/133099: Polycomb-Associated Non-Coding RNAs.
AF070646 - Homo sapiens clone 24797 mRNA sequence.
LF325595 - JP 2014500723-A/133098: Polycomb-Associated Non-Coding RNAs.
JD429209 - Sequence 410233 from Patent EP1572962.
JD321426 - Sequence 302450 from Patent EP1572962.
JD237089 - Sequence 218113 from Patent EP1572962.
LF325593 - JP 2014500723-A/133096: Polycomb-Associated Non-Coding RNAs.
JD166800 - Sequence 147824 from Patent EP1572962.
JD083626 - Sequence 64650 from Patent EP1572962.
LF325592 - JP 2014500723-A/133095: Polycomb-Associated Non-Coding RNAs.
JD220339 - Sequence 201363 from Patent EP1572962.
JD224483 - Sequence 205507 from Patent EP1572962.
JD239924 - Sequence 220948 from Patent EP1572962.
LF325591 - JP 2014500723-A/133094: Polycomb-Associated Non-Coding RNAs.
JD559560 - Sequence 540584 from Patent EP1572962.
LF325590 - JP 2014500723-A/133093: Polycomb-Associated Non-Coding RNAs.
JD459849 - Sequence 440873 from Patent EP1572962.
JD220883 - Sequence 201907 from Patent EP1572962.
JD516012 - Sequence 497036 from Patent EP1572962.
JD285005 - Sequence 266029 from Patent EP1572962.
JD270354 - Sequence 251378 from Patent EP1572962.
JD429688 - Sequence 410712 from Patent EP1572962.
LF209059 - JP 2014500723-A/16562: Polycomb-Associated Non-Coding RNAs.
MA620297 - JP 2018138019-A/192223: Polycomb-Associated Non-Coding RNAs.
MA561213 - JP 2018138019-A/133139: Polycomb-Associated Non-Coding RNAs.
MA561212 - JP 2018138019-A/133138: Polycomb-Associated Non-Coding RNAs.
MA561211 - JP 2018138019-A/133137: Polycomb-Associated Non-Coding RNAs.
MA561208 - JP 2018138019-A/133134: Polycomb-Associated Non-Coding RNAs.
MA561207 - JP 2018138019-A/133133: Polycomb-Associated Non-Coding RNAs.
MA561204 - JP 2018138019-A/133130: Polycomb-Associated Non-Coding RNAs.
MA561201 - JP 2018138019-A/133127: Polycomb-Associated Non-Coding RNAs.
MA561200 - JP 2018138019-A/133126: Polycomb-Associated Non-Coding RNAs.
MA561196 - JP 2018138019-A/133122: Polycomb-Associated Non-Coding RNAs.
MA561194 - JP 2018138019-A/133120: Polycomb-Associated Non-Coding RNAs.
MA561191 - JP 2018138019-A/133117: Polycomb-Associated Non-Coding RNAs.
MA561190 - JP 2018138019-A/133116: Polycomb-Associated Non-Coding RNAs.
MA561187 - JP 2018138019-A/133113: Polycomb-Associated Non-Coding RNAs.
MA561185 - JP 2018138019-A/133111: Polycomb-Associated Non-Coding RNAs.
MA561181 - JP 2018138019-A/133107: Polycomb-Associated Non-Coding RNAs.
MA561180 - JP 2018138019-A/133106: Polycomb-Associated Non-Coding RNAs.
MA561178 - JP 2018138019-A/133104: Polycomb-Associated Non-Coding RNAs.
MA561177 - JP 2018138019-A/133103: Polycomb-Associated Non-Coding RNAs.
MA561176 - JP 2018138019-A/133102: Polycomb-Associated Non-Coding RNAs.
MA561175 - JP 2018138019-A/133101: Polycomb-Associated Non-Coding RNAs.
MA561174 - JP 2018138019-A/133100: Polycomb-Associated Non-Coding RNAs.
MA561173 - JP 2018138019-A/133099: Polycomb-Associated Non-Coding RNAs.
MA561172 - JP 2018138019-A/133098: Polycomb-Associated Non-Coding RNAs.
MA561170 - JP 2018138019-A/133096: Polycomb-Associated Non-Coding RNAs.
MA561169 - JP 2018138019-A/133095: Polycomb-Associated Non-Coding RNAs.
MA561168 - JP 2018138019-A/133094: Polycomb-Associated Non-Coding RNAs.
MA561167 - JP 2018138019-A/133093: Polycomb-Associated Non-Coding RNAs.
MA444636 - JP 2018138019-A/16562: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04612 - Antigen processing and presentation

BioCarta from NCI Cancer Genome Anatomy Project
h_eradPathway - ER┐associated degradation (ERAD) Pathway

Reactome (by CSHL, EBI, and GO)

Protein P27824 (Reactome details) participates in the following event(s):

R-HSA-2130478 Interaction of invariant chain trimer and MHC II alpha beta dimer
R-HSA-8950387 CANX binds EBI3
R-HSA-8951500 Dissociation of CANX from nonameric complex
R-HSA-548890 Removal of the third glucose by glucosidase II and release from the chaperone
R-HSA-2213241 Formation of nonameric complex
R-HSA-535717 Binding of calnexin/calreticulin to the unfolded protein
R-HSA-983145 Binding of newly synthesized MHC class I heavy chain (HC) with calnexin
R-HSA-983146 Interaction of beta-2-microglobulin (B2M) chain with class I HC
R-HSA-901047 Binding of ERp57
R-HSA-983148 Interaction of Erp57 with MHC class I HC
R-HSA-2132295 MHC class II antigen presentation
R-HSA-9020956 Interleukin-27 signaling
R-HSA-8984722 Interleukin-35 Signalling
R-HSA-901042 Calnexin/calreticulin cycle
R-HSA-1280218 Adaptive Immune System
R-HSA-447115 Interleukin-12 family signaling
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC
R-HSA-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-HSA-168256 Immune System
R-HSA-449147 Signaling by Interleukins
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5V8, CALX_HUMAN, D3DWQ3, NM_001024649, NP_001737, P27824
UCSC ID: uc003mkl.3
RefSeq Accession: NM_001024649
Protein: P27824 (aka CALX_HUMAN)
CCDS: CCDS4447.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001024649.1
exon count: 15CDS single in 3' UTR: no RNA size: 4900
ORF size: 1779CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3758.00frame shift in genome: no % Coverage: 99.94
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.