Human Gene DMBT1 (uc001lgk.1) Description and Page Index
  Description: Homo sapiens deleted in malignant brain tumors 1 (DMBT1), transcript variant 2, mRNA.
RefSeq Summary (NM_007329): Loss of sequences from human chromosome 10q has been associated with the progression of human cancers. This gene was originally isolated based on its deletion in a medulloblastoma cell line. This gene is expressed with transcripts of 6.0, 7.5, and 8.0 kb in fetal lung and with one transcript of 8.0 kb in adult lung, although the 7.5 kb transcript has not been characterized. The encoded protein precursor is a glycoprotein containing multiple scavenger receptor cysteine-rich (SRCR) domains separated by SRCR-interspersed domains (SID). Transcript variant 2 (8.0 kb) has been shown to bind surfactant protein D independently of carbohydrate recognition. This indicates that DMBT1 may not be a classical tumor suppressor gene, but rather play a role in the interaction of tumor cells and the immune system. [provided by RefSeq, Mar 2016]. 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 :: AF159456.1, AJ297935.1 [ECO:0000332] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr10:124,320,181-124,403,252 Size: 83,072 Total Exon Count: 53 Strand: +
Coding Region
   Position: hg19 chr10:124,320,287-124,402,914 Size: 82,628 Coding Exon Count: 53 

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 (chr10:124,320,181-124,403,252)mRNA (may differ from genome)Protein (2413 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DMBT1_HUMAN
DESCRIPTION: RecName: Full=Deleted in malignant brain tumors 1 protein; AltName: Full=Glycoprotein 340; Short=Gp-340; AltName: Full=Hensin; AltName: Full=Salivary agglutinin; Short=SAG; AltName: Full=Surfactant pulmonary-associated D-binding protein; Flags: Precursor;
FUNCTION: May be considered as a candidate tumor suppressor gene for brain, lung, esophageal, gastric, and colorectal cancers. May play roles in mucosal defense system, cellular immune defense and epithelial differentiation. May play a role as an opsonin receptor for SFTPD and SPAR in macrophage tissues throughout the body, including epithelial cells lining the gastrointestinal tract. May play a role in liver regeneration. May be an important factor in fate decision and differentiation of transit-amplifying ductular (oval) cells within the hepatic lineage. Required for terminal differentiation of columnar epithelial cells during early embryogenesis. May function as a binding protein in saliva for the regulation of taste sensation. Binds to HIV-1 envelope protein and has been shown to both inhibit and facilitate viral transmission. Displays a broad calcium-dependent binding spectrum against both Gram-positive and Gram-negative bacteria, suggesting a role in defense against bacterial pathogens. Binds to a range of poly- sulfated and poly-phosphorylated ligands which may explain its broad bacterial-binding specificity. Inhibits cytoinvasion of S.enterica. Associates with the actin cytoskeleton and is involved in its remodeling during regulated exocytosis. Interacts with pancreatic zymogens in a pH-dependent manner and may act as a Golgi cargo receptor in the regulated secretory pathway of the pancreatic acinar cell.
SUBUNIT: Interacts with LGALS3 (By similarity). Binds SFTPD and SPAR in a calcium-dependent manner. Binds to HIV-1 glycoprotein 120.
SUBCELLULAR LOCATION: Secreted (By similarity). Note=Some isoforms may be membrane-bound. Localized to the lumenal aspect of crypt cells in the small intestine. In the colon, seen in the lumenal aspect of surface epithelial cells. Formed in the ducts of von Ebner gland, and released into the fluid bathing the taste buds contained in the taste papillae (By similarity).
TISSUE SPECIFICITY: Highly expressed in alveolar and macrophage tissues. In some macrophages, expression is seen on the membrane, and in other macrophages, strongly expressed in the phagosome/phagolysosome compartments. Expressed in lung, trachea, salivary gland, small intestine and stomach. In pancreas, expressed in certain cells of the islets of Langerhans. In digestive tract, confined to tissues with large epithelial surfaces. In intestinal tissue, moderately expressed in epithelial cells of the midcrypts and the crypt base. Expression is significantly elevated in intestinal tissue from patients with inflammatory bowel disease (IBD), particularly in surface epithelial and Paneth cells, but not in IBD patients with mutant NOD2. Present in crypt bases of the duodenum, in crypt tops of the colon, and in collecting ducts of the cortical kidney. Expressed in stratified squamous epithelium of vagina and in outer luminar surface and basilar region of columnar epithelial cells in cervix (at protein level). Isoform 1 is secreted to the lumen of the respiratory tract.
DEVELOPMENTAL STAGE: Expressed in fetal lung, intestine and skin. Secreted to the extracellular matrix (ECM) in certain fetal epithelia.
INDUCTION: Up-regulated in intestinal epithelial cells in response to proinflammatory stimuli including TNF and bacterial lipopolysaccharides (LPS).
DOMAIN: The SRCR domains mediate binding to bacteria. The minimal bacterial-binding site is an 11-residue repeat of GRVEVLYRGSW where VEVL and W are critical residues.
PTM: Highly N- and O-glycosylated. The O-glycans are heavily sulfated (By similarity).
POLYMORPHISM: The number of SRCR and SRCR-interspersed domains is polymorphic in a variety of tumors and may represent the major site of alterations in cancer.
DISEASE: Defects in DMBT1 are involved in the development of glioma (GLM) [MIM:137800]. Gliomas are central nervous system neoplasms derived from glial cells and comprise astrocytomas, glioblastoma multiforme, oligodendrogliomas, and ependymomas. Note=Homozygous deletions may be the predominant mechanism of DMBT1 inactivation playing a role in carcinogenesis. DMBT1 is deleted in medulloblastoma and glioblastoma cell lines; point mutations have also been reported in patients with glioma. A loss or reduction of DMBT1 expression has been seen in esophageal, gastric, lung and colorectal carcinomas as well.
SIMILARITY: Belongs to the DMBT1 family.
SIMILARITY: Contains 2 CUB domains.
SIMILARITY: Contains 14 SRCR domains.
SIMILARITY: Contains 1 ZP domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/DMBT1ID309ch10q26.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DMBT1
CDC HuGE Published Literature: DMBT1

-  MalaCards Disease Associations
  MalaCards Gene Search: DMBT1
Diseases sorted by gene-association score: glioblastoma (16), medulloblastoma (16), glioma (15), glioblastoma multiforme (15), astrocytoma (7), cholangitis, primary sclerosing (7), brain cancer (7), grade iii astrocytoma (7), appendicitis (5), malignant glioma (4)

-  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: 52.25 RPKM in Small Intestine - Terminal Ileum
Total median expression: 116.36 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 -17.40106-0.164 Picture PostScript Text
3' UTR -108.39338-0.321 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
IPR001190 - Srcr_rcpt
IPR017448 - Srcr_rcpt-rel
IPR001507 - ZP_dom
IPR017977 - ZP_dom_CS

Pfam Domains:
PF00100 - Zona pellucida-like domain
PF00431 - CUB domain
PF00530 - Scavenger receptor cysteine-rich domain

SCOP Domains:
49854 - Spermadhesin, CUB domain
56487 - SRCR-like

ModBase Predicted Comparative 3D Structure on Q9UGM3
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
  Molecular Function:
GO:0001530 lipopolysaccharide binding
GO:0003677 DNA binding
GO:0005044 scavenger receptor activity
GO:0005515 protein binding
GO:0008329 signaling pattern recognition receptor activity
GO:0035375 zymogen binding
GO:0038187 pattern recognition receptor activity
GO:0048306 calcium-dependent protein binding
GO:0070891 lipoteichoic acid binding
GO:1904399 heparan sulfate binding

Biological Process:
GO:0002221 pattern recognition receptor signaling pathway
GO:0006898 receptor-mediated endocytosis
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0015031 protein transport
GO:0016032 viral process
GO:0030154 cell differentiation
GO:0030855 epithelial cell differentiation
GO:0043152 induction of bacterial agglutination
GO:0044267 cellular protein metabolic process
GO:0045087 innate immune response
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0051607 defense response to virus

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0030670 phagocytic vesicle membrane
GO:0042589 zymogen granule membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF159456 - Homo sapiens gp-340 variant protein (DMBT1) mRNA, complete cds.
AJ000342 - Homo sapiens mRNA for DMBT1 6 kb transcript variant 1 (DMBT1 gene).
AJ243212 - Homo sapiens mRNA for DMBT1 protein 8kb transcript variant 2 (DMBT1/8kb.2).
AJ243224 - Homo sapiens mRNA for DMBT1 protein 8kb transcript variant 1 (DMBT1/8kb.1).
BC153299 - Homo sapiens deleted in malignant brain tumors 1, mRNA (cDNA clone MGC:164738 IMAGE:40147087), complete cds.
AJ297935 - Homo sapiens mRNA for DMBT1 8 kb transcript variant 2 (DMBT1 gene).
AK304149 - Homo sapiens cDNA FLJ61619 complete cds, highly similar to Deleted in malignant brain tumors 1 protein precursor.
AK304128 - Homo sapiens cDNA FLJ61058 complete cds, highly similar to Deleted in malignant brain tumors 1 protein precursor.
KJ905191 - Synthetic construct Homo sapiens clone ccsbBroadEn_14617 DMBT1 gene, encodes complete protein.
BX640988 - Homo sapiens mRNA; cDNA DKFZp686E03231 (from clone DKFZp686E03231).
AB209691 - Homo sapiens mRNA for deleted in malignant brain tumors 1 isoform b precursor variant protein.
FJ234410 - Homo sapiens cell-line 76NTERT deleted in malignant brain tumors 1 (DMBT1) mRNA, partial cds.
JD545955 - Sequence 526979 from Patent EP1572962.
JD148446 - Sequence 129470 from Patent EP1572962.
JD164600 - Sequence 145624 from Patent EP1572962.
JD285637 - Sequence 266661 from Patent EP1572962.

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

Protein Q9UGM3 (Reactome details) participates in the following event(s):

R-HSA-5687284 DMBT1 binds SFTPD 12mer, SFTPAs
R-HSA-5683826 Surfactant metabolism
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDG4, A6NDJ5, A8E4R5, B1ARE7, B1ARE8, B1ARE9, B1ARF0, DMBT1_HUMAN, GP340, NM_007329, NP_015568, Q59EX0, Q5JR26, Q6MZN4, Q96DU4, Q9UGM2, Q9UGM3, Q9UJ57, Q9UKJ4, Q9Y211, Q9Y4V9
UCSC ID: uc001lgk.1
RefSeq Accession: NM_007329
Protein: Q9UGM3 (aka DMBT1_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007329.2
exon count: 53CDS single in 3' UTR: no RNA size: 7686
ORF size: 7242CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10451.50frame shift in genome: no % Coverage: 100.00
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.