Human Gene MUC4 (uc021xjp.1)
  Description: Homo sapiens mucin 4, cell surface associated (MUC4), transcript variant 1, mRNA.
RefSeq Summary (NM_018406): The major constituents of mucus, the viscous secretion that covers epithelial surfaces such as those in the trachea, colon, and cervix, are highly glycosylated proteins called mucins. These glycoproteins play important roles in the protection of the epithelial cells and have been implicated in epithelial renewal and differentiation. This gene encodes an integral membrane glycoprotein found on the cell surface, although secreted isoforms may exist. At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues. This gene contains a region in the coding sequence which has a variable number (>100) of 48 nt tandem repeats. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr3:195,473,638-195,538,844 Size: 65,207 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr3:195,474,047-195,538,688 Size: 64,642 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:195,473,638-195,538,844)mRNA (may differ from genome)Protein (5412 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PDY6_HUMAN
DESCRIPTION: SubName: Full=Mucin-4;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MUC4
CDC HuGE Published Literature: MUC4

-  MalaCards Disease Associations
  MalaCards Gene Search: MUC4
Diseases sorted by gene-association score: intrahepatic cholangiocarcinoma (32), filamentary keratitis (23), ovarian epithelial cancer (18), bile duct mucoepidermoid carcinoma (15), adenosquamous carcinoma (13), mucoepidermoid carcinoma (13), pancreatic cancer (13), biliary tract neoplasm (12), adenomyoma (11), mucinous tubular and spindle renal cell carcinoma (10), colorectal cancer 1 (9), breast secretory carcinoma (9), chronic ethmoiditis (9), cap polyposis (9), bile duct carcinoma (7), limbal stem cell deficiency (7), pancreatic ductal adenocarcinoma (7), dry eye syndrome (7), cystadenoma (6), kidney fibrosarcoma (6), ethmoid sinusitis (6), adenocarcinoma (6), cholangiocarcinoma, susceptibility to (5), pancreatitis (5), arrhythmogenic right ventricular dysplasia 1 (5), pancreas adenocarcinoma (5), pancreatitis, hereditary (4), fibrosarcoma of bone (3), lung cancer (2), esophageal cancer (2), colorectal cancer (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: 25.40 RPKM in Colon - Transverse
Total median expression: 49.69 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 -67.10156-0.430 Picture PostScript Text
3' UTR -116.36409-0.284 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
IPR005533 - AMOP
IPR000742 - EG-like_dom
IPR003886 - Nidogen_extracell_dom
IPR001846 - VWF_type-D

Pfam Domains:
PF00094 - von Willebrand factor type D domain
PF06119 - Nidogen-like

SCOP Domains:
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on E9PDY6
FrontTopSide
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007160 cell-matrix adhesion

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AJ010901 - Homo sapiens MUC4 gene, 3' flanking region.
AJ242541 - Homo sapiens partial mRNA for sv1-MUC4 apomucin.
AJ242542 - Homo sapiens partial mRNA for sv2-MUC4 apomucin.
AJ242543 - Homo sapiens partial mRNA for sv3-MUC4 apomucin.
AJ242544 - Homo sapiens partial mRNA for sv4-MUC4 apomucin.
AJ242545 - Homo sapiens partial mRNA for sv5-MUC4 apomucin.
AJ242546 - Homo sapiens partial mRNA for sv6-MUC4 apomucin.
AJ242547 - Homo sapiens partial mRNA for sv7-MUC4 apomucin.
AJ242548 - Homo sapiens partial mRNA for sv8-MUC4 apomucin.
AJ242549 - Homo sapiens mRNA for MUC4/Y apomucin.
AJ242550 - Homo sapiens mRNA for MUC4/X apomucin.
JD347848 - Sequence 328872 from Patent EP1572962.
JD097720 - Sequence 78744 from Patent EP1572962.
AJ276359 - Homo sapiens mRNA for mucin 4 (MUC4 gene).
AJ277412 - Homo sapiens mRNA for mucin 4, variant V3 (MUC4 gene).
AJ277505 - Homo sapiens mRNA for MUC4 splice variant sv11 (MUC4 gene).
AJ400633 - Homo sapiens mRNA for MUC4 protein variant VI1.
AJ400849 - Homo sapiens mRNA for MUC4 protein splice variant sv12 (MUC4 gene).
AJ400850 - Homo sapiens mRNA for MUC4 protein splice variant sv13 (MUC4 gene).
AJ400851 - Homo sapiens mRNA for MUC4 protein splice variant sv14 (MUC4 gene).
AJ400852 - Homo sapiens mRNA for MUC4 protein splice variant sv15 (MUC4 gene).
AJ400853 - Homo sapiens mRNA for MUC4 protein splice variant sv16 (MUC4 gene).
AJ400854 - Homo sapiens mRNA for MUC4 protein splice variant sv17 (MUC4 gene).
AJ400855 - Homo sapiens mRNA for MUC4 protein splice variant sv18 (MUC4 gene).
AJ400856 - Homo sapiens mRNA for MUC4 protein splice variant sv19 (MUC4 gene).
AJ400857 - Homo sapiens mRNA for MUC4 protein splice variant sv20 (MUC4 gene).
AJ400858 - Homo sapiens mRNA for MUC4 protein splice variant sv21 (MUC4 gene).
JD538908 - Sequence 519932 from Patent EP1572962.
JD559797 - Sequence 540821 from Patent EP1572962.
JD537628 - Sequence 518652 from Patent EP1572962.
JD371762 - Sequence 352786 from Patent EP1572962.
JD435310 - Sequence 416334 from Patent EP1572962.
JD201174 - Sequence 182198 from Patent EP1572962.
JD549021 - Sequence 530045 from Patent EP1572962.
JD191264 - Sequence 172288 from Patent EP1572962.
JD376179 - Sequence 357203 from Patent EP1572962.
JD471900 - Sequence 452924 from Patent EP1572962.
JD540856 - Sequence 521880 from Patent EP1572962.
JD485006 - Sequence 466030 from Patent EP1572962.
JD232486 - Sequence 213510 from Patent EP1572962.
AK074437 - Homo sapiens cDNA FLJ23857 fis, clone LNG07164.
JD173752 - Sequence 154776 from Patent EP1572962.
JD274218 - Sequence 255242 from Patent EP1572962.
JD504857 - Sequence 485881 from Patent EP1572962.
JD043962 - Sequence 24986 from Patent EP1572962.
JD428948 - Sequence 409972 from Patent EP1572962.
JD162817 - Sequence 143841 from Patent EP1572962.
JD492383 - Sequence 473407 from Patent EP1572962.
JD492382 - Sequence 473406 from Patent EP1572962.
JD158231 - Sequence 139255 from Patent EP1572962.
JD150404 - Sequence 131428 from Patent EP1572962.
JD475643 - Sequence 456667 from Patent EP1572962.
JD560477 - Sequence 541501 from Patent EP1572962.
JD432269 - Sequence 413293 from Patent EP1572962.
JD213904 - Sequence 194928 from Patent EP1572962.
JD276565 - Sequence 257589 from Patent EP1572962.
JD561137 - Sequence 542161 from Patent EP1572962.
JD066742 - Sequence 47766 from Patent EP1572962.
JD409864 - Sequence 390888 from Patent EP1572962.
JD438172 - Sequence 419196 from Patent EP1572962.
JD411109 - Sequence 392133 from Patent EP1572962.
JD408038 - Sequence 389062 from Patent EP1572962.
JD057795 - Sequence 38819 from Patent EP1572962.
JD114488 - Sequence 95512 from Patent EP1572962.
JD522196 - Sequence 503220 from Patent EP1572962.
JD254116 - Sequence 235140 from Patent EP1572962.
JD162132 - Sequence 143156 from Patent EP1572962.
JD465950 - Sequence 446974 from Patent EP1572962.
JD424157 - Sequence 405181 from Patent EP1572962.
JD478409 - Sequence 459433 from Patent EP1572962.
JD407704 - Sequence 388728 from Patent EP1572962.
JD213500 - Sequence 194524 from Patent EP1572962.
JD128682 - Sequence 109706 from Patent EP1572962.
JD458207 - Sequence 439231 from Patent EP1572962.
JD120850 - Sequence 101874 from Patent EP1572962.
JD287094 - Sequence 268118 from Patent EP1572962.
EF091824 - Homo sapiens mucin 4 mRNA, complete cds.
JD400749 - Sequence 381773 from Patent EP1572962.
JD457070 - Sequence 438094 from Patent EP1572962.
JD210017 - Sequence 191041 from Patent EP1572962.
JD271201 - Sequence 252225 from Patent EP1572962.
JD466582 - Sequence 447606 from Patent EP1572962.
JD376126 - Sequence 357150 from Patent EP1572962.
JD151686 - Sequence 132710 from Patent EP1572962.
AF058804 - Homo sapiens clone G4-10-3 mucin 4 (MUC4) mRNA, partial cds.
AF177925 - Homo sapiens mucin 4 (MUC4) mRNA, partial cds.
AJ000281 - Homo sapiens mRNA for mucin protein, MUC4.
AF177925 - Homo sapiens mucin 4 (MUC4) mRNA, partial cds.
AF058803 - Homo sapiens clone G4-5-10 mucin 4 (MUC4) mRNA, partial cds.
AK307054 - Homo sapiens cDNA, FLJ97002.
JD423640 - Sequence 404664 from Patent EP1572962.
JD191229 - Sequence 172253 from Patent EP1572962.
JD128882 - Sequence 109906 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PDY6, E9PDY6_HUMAN, NM_018406, NP_060876
UCSC ID: uc021xjp.1
RefSeq Accession: NM_018406
Protein: E9PDY6 CCDS: CCDS54700.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018406.6
exon count: 25CDS single in 3' UTR: no RNA size: 16819
ORF size: 16239CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 16686.00frame shift in genome: no % Coverage: 99.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.