Human Gene HLA-DMB (uc003ocj.2) Description and Page Index
  Description: Homo sapiens major histocompatibility complex, class II, DM beta (HLA-DMB), mRNA.
RefSeq Summary (NM_002118): HLA-DMB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta (DMB) chain, both anchored in the membrane. It is located in intracellular vesicles. DM plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP (class II-associated invariant chain peptide) molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and its gene contains 6 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. [provided by RefSeq, Jul 2008]. 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 :: U15085.1, AY645722.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA2145313 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000418107.3/ ENSP00000398890.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr6:32,902,410-32,908,847 Size: 6,438 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr6:32,906,366-32,908,584 Size: 2,219 Coding Exon Count: 2 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:32,902,410-32,908,847)mRNA (may differ from genome)Protein (143 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
UniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HLA-DMB
CDC HuGE Published Literature: HLA-DMB
Positive Disease Associations: Multiple Sclerosis , psoriasis
Related Studies:
  1. Multiple Sclerosis
    David A Hafler et al. The New England journal of medicine 2007, Risk alleles for multiple sclerosis identified by a genomewide study., The New England journal of medicine. [PubMed 17660530]
    Alleles of IL2RA and IL7RA and those in the HLA locus are identified as heritable risk factors for multiple sclerosis.
  2. psoriasis
    Pyo CW 2003, Association of TAP and HLA-DM genes with psoriasis in Koreans., The Journal of investigative dermatology. 2003 Apr;120(4):616-22. [PubMed 12648225]
    In conclusion, our data suggest that the TAP and HLA-DM alleles could lead to genetic susceptibility toward psoriasis in Koreans.

-  MalaCards Disease Associations
  MalaCards Gene Search: HLA-DMB
Diseases sorted by gene-association score: nodular medulloblastoma (11), red-green color blindness (8), red color blindness (7), acromesomelic dysplasia (5), rheumatoid arthritis (4), systemic lupus erythematosus (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: 131.31 RPKM in Spleen
Total median expression: 855.95 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 -99.50263-0.378 Picture PostScript Text
3' UTR -1384.543956-0.350 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
IPR011162 - MHC_I/II-like_Ag-recog
IPR014745 - MHC_II_a/b_N
IPR000353 - MHC_II_b_N

Pfam Domains:
PF00969 - Class II histocompatibility antigen, beta domain

SCOP Domains:
54452 - MHC antigen-recognition domain

ModBase Predicted Comparative 3D Structure on Q59F83
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:0006955 immune response
GO:0019882 antigen processing and presentation

Cellular Component:
GO:0016020 membrane
GO:0042613 MHC class II protein complex


-  Descriptions from all associated GenBank mRNAs
  BC017508 - Homo sapiens major histocompatibility complex, class II, DM beta, mRNA (cDNA clone IMAGE:4852869), with apparent retained intron.
BC035650 - Homo sapiens major histocompatibility complex, class II, DM beta, mRNA (cDNA clone IMAGE:5576676), with apparent retained intron.
AB209577 - Homo sapiens mRNA for major histocompatibility complex, class II, DM beta precursor variant protein.
BC027175 - Homo sapiens major histocompatibility complex, class II, DM beta, mRNA (cDNA clone MGC:17194 IMAGE:4341639), complete cds.
U15085 - Human HLA-DMB mRNA, complete cds.
Z23139 - H.sapiens RING7 mRNA for HLA class II alpha chain-like product.
AY645722 - Homo sapiens MHC class II antigen (HLA-DMB) mRNA, complete cds.
JD065505 - Sequence 46529 from Patent EP1572962.
JD073921 - Sequence 54945 from Patent EP1572962.
JD485309 - Sequence 466333 from Patent EP1572962.
JD279787 - Sequence 260811 from Patent EP1572962.
JD449477 - Sequence 430501 from Patent EP1572962.
AB362554 - Homo sapiens HLA-DMB mRNA for MHC class II antigen, partial cds, splicing variant 1.
AB362555 - Homo sapiens HLA-DMB mRNA for MHC class II antigen, partial cds, splicing variant 2.
AB362556 - Homo sapiens HLA-DMB mRNA for MHC class II antigen, partial cds, splicing variant 3.
DQ891141 - Synthetic construct clone IMAGE:100003771; FLH169680.01X; RZPDo839E1296D major histocompatibility complex, class II, DM beta (HLA-DMB) gene, encodes complete protein.
KJ896976 - Synthetic construct Homo sapiens clone ccsbBroadEn_06370 HLA-DMB gene, encodes complete protein.
DQ894320 - Synthetic construct Homo sapiens clone IMAGE:100008780; FLH169676.01L; RZPDo839E1295D major histocompatibility complex, class II, DM beta (HLA-DMB) gene, encodes complete protein.
CU693252 - Synthetic construct Homo sapiens gateway clone IMAGE:100016921 5' read HLA-DMB mRNA.
CR407606 - Homo sapiens full open reading frame cDNA clone RZPDo834A052D for gene HLA-DMB, major histocompatibility complex, class II, DM beta complete cds, without stopcodon.
AB590298 - Synthetic construct DNA, clone: pFN21AE2234, Homo sapiens HLA-DMB gene for major histocompatibility complex, class II, DM beta, without stop codon, in Flexi system.
AK315979 - Homo sapiens cDNA, FLJ78878 complete cds, highly similar to HLA class II histocompatibility antigen, DMbeta chain precursor.
AK301017 - Homo sapiens cDNA FLJ51332 complete cds, highly similar to HLA class II histocompatibility antigen, DMbeta chain precursor.
HZ482250 - JP 2015535430-A/2756: TERMINALLY MODIFIED RNA.
HZ482268 - JP 2015535430-A/2774: TERMINALLY MODIFIED RNA.
HZ792181 - JP 2016504050-A/3926: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
HZ792199 - JP 2016504050-A/3944: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC514913 - Sequence 5166 from Patent WO2014113089.
JC514931 - Sequence 5184 from Patent WO2014113089.
LF160330 - JP 2016513950-A/396: Oligomers with improved off-target profile.
LF161817 - JP 2016513950-A/1883: Oligomers with improved off-target profile.
LQ072501 - Sequence 2825 from Patent EP2964234.
LQ072519 - Sequence 2843 from Patent EP2964234.
MS890098 - Sequence 1 from Patent WO2017005773.
HZ483253 - JP 2015535430-A/3759: TERMINALLY MODIFIED RNA.
HZ793184 - JP 2016504050-A/4929: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC515916 - Sequence 6169 from Patent WO2014113089.
LQ073504 - Sequence 3828 from Patent EP2964234.
HZ483238 - JP 2015535430-A/3744: TERMINALLY MODIFIED RNA.
HZ483264 - JP 2015535430-A/3770: TERMINALLY MODIFIED RNA.
HZ483280 - JP 2015535430-A/3786: TERMINALLY MODIFIED RNA.
HZ793169 - JP 2016504050-A/4914: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
HZ793195 - JP 2016504050-A/4940: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
HZ793211 - JP 2016504050-A/4956: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC515901 - Sequence 6154 from Patent WO2014113089.
JC515927 - Sequence 6180 from Patent WO2014113089.
JC515943 - Sequence 6196 from Patent WO2014113089.
LQ073489 - Sequence 3813 from Patent EP2964234.
LQ073515 - Sequence 3839 from Patent EP2964234.
LQ073531 - Sequence 3855 from Patent EP2964234.
HZ482226 - JP 2015535430-A/2732: TERMINALLY MODIFIED RNA.
HZ792157 - JP 2016504050-A/3902: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC505996 - Sequence 15 from Patent EP2733219.
JC506180 - Sequence 199 from Patent EP2733219.
JC514889 - Sequence 5142 from Patent WO2014113089.
JC737420 - Sequence 15 from Patent WO2014075911.
JC737604 - Sequence 199 from Patent WO2014075911.
LF161329 - JP 2016513950-A/1395: Oligomers with improved off-target profile.
LQ072477 - Sequence 2801 from Patent EP2964234.
HZ483244 - JP 2015535430-A/3750: TERMINALLY MODIFIED RNA.
HZ793175 - JP 2016504050-A/4920: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC515907 - Sequence 6160 from Patent WO2014113089.
LQ073495 - Sequence 3819 from Patent EP2964234.
HZ482199 - JP 2015535430-A/2705: TERMINALLY MODIFIED RNA.
HZ482213 - JP 2015535430-A/2719: TERMINALLY MODIFIED RNA.
HZ482249 - JP 2015535430-A/2755: TERMINALLY MODIFIED RNA.
HZ792130 - JP 2016504050-A/3875: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
HZ792144 - JP 2016504050-A/3889: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
HZ792180 - JP 2016504050-A/3925: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC505995 - Sequence 14 from Patent EP2733219.
JC505997 - Sequence 16 from Patent EP2733219.
JC505998 - Sequence 17 from Patent EP2733219.
JC506179 - Sequence 198 from Patent EP2733219.
JC506181 - Sequence 200 from Patent EP2733219.
JC506182 - Sequence 201 from Patent EP2733219.
JC514862 - Sequence 5115 from Patent WO2014113089.
JC514876 - Sequence 5129 from Patent WO2014113089.
JC514912 - Sequence 5165 from Patent WO2014113089.
JC737419 - Sequence 14 from Patent WO2014075911.
JC737421 - Sequence 16 from Patent WO2014075911.
JC737422 - Sequence 17 from Patent WO2014075911.
JC737603 - Sequence 198 from Patent WO2014075911.
JC737605 - Sequence 200 from Patent WO2014075911.
JC737606 - Sequence 201 from Patent WO2014075911.
LF161172 - JP 2016513950-A/1238: Oligomers with improved off-target profile.
LF161281 - JP 2016513950-A/1347: Oligomers with improved off-target profile.
LF161930 - JP 2016513950-A/1996: Oligomers with improved off-target profile.
LQ072450 - Sequence 2774 from Patent EP2964234.
LQ072464 - Sequence 2788 from Patent EP2964234.
LQ072500 - Sequence 2824 from Patent EP2964234.
JD168154 - Sequence 149178 from Patent EP1572962.
AK295872 - Homo sapiens cDNA FLJ56696 complete cds, highly similar to HLA class II histocompatibility antigen, DMbeta chain precursor.
JD325013 - Sequence 306037 from Patent EP1572962.
JD444627 - Sequence 425651 from Patent EP1572962.
JD376538 - Sequence 357562 from Patent EP1572962.
JD203960 - Sequence 184984 from Patent EP1572962.
MA646002 - JP 2017113010-A/3926: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA646020 - JP 2017113010-A/3944: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA733886 - JP 2017140048-A/2756: TERMINALLY MODIFIED RNA.
MA733904 - JP 2017140048-A/2774: TERMINALLY MODIFIED RNA.
MA647005 - JP 2017113010-A/4929: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA734889 - JP 2017140048-A/3759: TERMINALLY MODIFIED RNA.
MA646990 - JP 2017113010-A/4914: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA647016 - JP 2017113010-A/4940: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA647032 - JP 2017113010-A/4956: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA734874 - JP 2017140048-A/3744: TERMINALLY MODIFIED RNA.
MA734900 - JP 2017140048-A/3770: TERMINALLY MODIFIED RNA.
MA734916 - JP 2017140048-A/3786: TERMINALLY MODIFIED RNA.
MA645978 - JP 2017113010-A/3902: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA733862 - JP 2017140048-A/2732: TERMINALLY MODIFIED RNA.
MA646996 - JP 2017113010-A/4920: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA734880 - JP 2017140048-A/3750: TERMINALLY MODIFIED RNA.
MA645951 - JP 2017113010-A/3875: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA645965 - JP 2017113010-A/3889: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA646001 - JP 2017113010-A/3925: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA733835 - JP 2017140048-A/2705: TERMINALLY MODIFIED RNA.
MA733849 - JP 2017140048-A/2719: TERMINALLY MODIFIED RNA.
MA733885 - JP 2017140048-A/2755: TERMINALLY MODIFIED RNA.
MP014950 - Sequence 153 from Patent WO2019016252.
MA803055 - JP 2018183181-A/3926: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA803073 - JP 2018183181-A/3944: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA804058 - JP 2018183181-A/4929: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA804043 - JP 2018183181-A/4914: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA804069 - JP 2018183181-A/4940: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA804085 - JP 2018183181-A/4956: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA803031 - JP 2018183181-A/3902: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA804049 - JP 2018183181-A/4920: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA803004 - JP 2018183181-A/3875: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA803018 - JP 2018183181-A/3889: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA803054 - JP 2018183181-A/3925: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04612 - Antigen processing and presentation
hsa04672 - Intestinal immune network for IgA production
hsa04940 - Type I diabetes mellitus
hsa05140 - Leishmaniasis
hsa05310 - Asthma
hsa05320 - Autoimmune thyroid disease
hsa05322 - Systemic lupus erythematosus
hsa05330 - Allograft rejection
hsa05332 - Graft-versus-host disease
hsa05416 - Viral myocarditis

-  Other Names for This Gene
  Alternate Gene Symbols: AB209577, Q59F83, Q59F83_HUMAN
UCSC ID: uc003ocj.2
RefSeq Accession: NM_002118
Protein: Q59F83

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB209577.1
exon count: 2CDS single in 3' UTR: no RNA size: 4565
ORF size: 432CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 1064.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 8
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 4051# 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.