Human Gene RGMB (uc003knc.3) Description and Page Index
  Description: Homo sapiens RGM domain family, member B (RGMB), mRNA.
RefSeq Summary (NM_001012761): RGMB is a glycosylphosphatidylinositol (GPI)-anchored member of the repulsive guidance molecule family (see RGMA, MIM 607362) and contributes to the patterning of the developing nervous system (Samad et al., 2005 [PubMed 15671031]).[supplied by OMIM, Apr 2009]. 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 :: SRR1803615.109671.1, SRR1660805.153107.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968189, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr5:98,104,999-98,132,198 Size: 27,200 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr5:98,106,373-98,129,457 Size: 23,085 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:98,104,999-98,132,198)mRNA (may differ from genome)Protein (478 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: J3KNF6_HUMAN
DESCRIPTION: SubName: Full=RGM domain family member B;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  MalaCards Disease Associations
  MalaCards Gene Search: RGMB
Diseases sorted by gene-association score: basilar artery occlusion (2), miller-dieker lissencephaly syndrome (1)

-  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: 39.20 RPKM in Esophagus - Muscularis
Total median expression: 402.45 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -204.70402-0.509 Picture PostScript Text
3' UTR -749.792741-0.274 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
IPR009496 - RGM_C
IPR010536 - RGM_N

Pfam Domains:
PF06534 - Repulsive guidance molecule (RGM) C-terminus
PF06535 - Repulsive guidance molecule (RGM) N-terminus

ModBase Predicted Comparative 3D Structure on J3KNF6
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 orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042802 identical protein binding

Biological Process:
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0030509 BMP signaling pathway
GO:0045893 positive regulation of transcription, DNA-templated

Cellular Component:
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0046658 anchored component of plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BC067736 - Homo sapiens RGM domain family, member B, mRNA (cDNA clone MGC:86970 IMAGE:30340500), complete cds.
JD300658 - Sequence 281682 from Patent EP1572962.
AK074887 - Homo sapiens cDNA FLJ90406 fis, clone NT2RP2006134.
JD174687 - Sequence 155711 from Patent EP1572962.
JD539398 - Sequence 520422 from Patent EP1572962.
JD426297 - Sequence 407321 from Patent EP1572962.
JD103028 - Sequence 84052 from Patent EP1572962.
KJ900590 - Synthetic construct Homo sapiens clone ccsbBroadEn_09984 RGMB gene, encodes complete protein.
JD100636 - Sequence 81660 from Patent EP1572962.
JD157959 - Sequence 138983 from Patent EP1572962.
JD082649 - Sequence 63673 from Patent EP1572962.
JD379303 - Sequence 360327 from Patent EP1572962.
JD268735 - Sequence 249759 from Patent EP1572962.
AK125284 - Homo sapiens cDNA FLJ43294 fis, clone MESTC1000042.
JD355408 - Sequence 336432 from Patent EP1572962.
JD380560 - Sequence 361584 from Patent EP1572962.
AK054622 - Homo sapiens cDNA FLJ30060 fis, clone ADRGL2000097.
JD299588 - Sequence 280612 from Patent EP1572962.
JD402410 - Sequence 383434 from Patent EP1572962.
JD147017 - Sequence 128041 from Patent EP1572962.
BC020513 - Homo sapiens RGM domain family, member B, mRNA (cDNA clone IMAGE:3852164).
JD419111 - Sequence 400135 from Patent EP1572962.
BC044231 - Homo sapiens RGM domain family, member B, mRNA (cDNA clone IMAGE:5557971).
JD082105 - Sequence 63129 from Patent EP1572962.
JD493238 - Sequence 474262 from Patent EP1572962.
JD365001 - Sequence 346025 from Patent EP1572962.
JD549367 - Sequence 530391 from Patent EP1572962.
JD200849 - Sequence 181873 from Patent EP1572962.
JD291926 - Sequence 272950 from Patent EP1572962.
JD044093 - Sequence 25117 from Patent EP1572962.
JD508910 - Sequence 489934 from Patent EP1572962.
JD112703 - Sequence 93727 from Patent EP1572962.
JD071535 - Sequence 52559 from Patent EP1572962.
JD349262 - Sequence 330286 from Patent EP1572962.
JD403999 - Sequence 385023 from Patent EP1572962.
JD503325 - Sequence 484349 from Patent EP1572962.
JD393861 - Sequence 374885 from Patent EP1572962.
JD286211 - Sequence 267235 from Patent EP1572962.
JD272696 - Sequence 253720 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: J3KNF6, J3KNF6_HUMAN, NM_001012761, NP_001012779
UCSC ID: uc003knc.3
RefSeq Accession: NM_001012761
Protein: J3KNF6 CCDS: CCDS47251.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001012761.2
exon count: 5CDS single in 3' UTR: no RNA size: 4601
ORF size: 1437CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2975.00frame shift in genome: no % Coverage: 99.54
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.