Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RGMB Gene

Aliases for RGMB Gene

  • Repulsive Guidance Molecule Family Member B 2 3 5
  • DRG11-Responsive Axonal Guidance And Outgrowth Of Neurite 3 4
  • RGM Domain Family, Member B 2 3
  • DRAGON 3 4
  • Repulsive Guidance Molecule B 3
  • RGM Domain Family Member B 3

External Ids for RGMB Gene

Previous GeneCards Identifiers for RGMB Gene

  • GC05P098181
  • GC05P098132
  • GC05P093292

Summaries for RGMB Gene

Entrez Gene Summary for RGMB Gene

  • 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]

GeneCards Summary for RGMB Gene

RGMB (Repulsive Guidance Molecule Family Member B) is a Protein Coding gene. Diseases associated with RGMB include Basilar Artery Occlusion. Among its related pathways are Developmental Biology and Netrin-1 signaling. GO annotations related to this gene include identical protein binding and coreceptor activity. An important paralog of this gene is RGMA.

UniProtKB/Swiss-Prot for RGMB Gene

  • Member of the repulsive guidance molecule (RGM) family that contributes to the patterning of the developing nervous system (By similarity). Acts as a bone morphogenetic protein (BMP) coreceptor that potentiates BMP signaling (By similarity). Promotes neuronal adhesion (By similarity). May inhibit neurite outgrowth.

Gene Wiki entry for RGMB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RGMB Gene

Genomics for RGMB Gene

Regulatory Elements for RGMB Gene

Enhancers for RGMB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G098796 1.3 Ensembl ENCODE dbSUPER 11.7 +27.8 27818 0.9 CTCF TEAD4 SIN3A CHD7 ZNF2 RAD21 TEAD3 ZNF664 GATA3 POLR2A RGMB-AS1 RGMB ENSG00000279232 CSNK1A1P3
GH05G099019 1.3 Ensembl ENCODE 10.1 +252.3 252261 3.3 PKNOX1 ATF1 FEZF1 ZNF2 FOS YY2 REST TSHZ1 PPARG ZNF518A RGMB-AS1 CHD1 LINC02062 RGMB PIR38453 GC05P099011 PIR33197
GH05G099032 1.2 Ensembl ENCODE 10.1 +264.7 264715 2.5 FOXA2 CBX3 RB1 TBL1XR1 ARNT WRNIP1 RAD21 RARA RFX5 YY1 RGMB-AS1 CHD1 LINC02062 RGMB GC05P099011 PIR38453 PIR33197
GH05G098413 1.1 FANTOM5 ENCODE dbSUPER 8.3 -353.2 -353174 4.3 JUND FOS MAFK ATF2 RGMB RGMB-AS1 MTCO1P24 CTBP2P4
GH05G098839 0.8 FANTOM5 Ensembl 11.2 +71.1 71051 0.6 CTCF MTA2 TCF7 JUNB TBX21 RAD21 RGMB-AS1 RGMB LOC105379099 CSNK1A1P3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RGMB on UCSC Golden Path with GeneCards custom track

Promoters for RGMB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000184536 1550 4001 PKNOX1 FOXA2 FEZF1 ZNF2 ZBTB7B ZNF143 ZNF263 SP3 REST TBX21

Transcription factor binding sites by QIAGEN in the RGMB gene promoter:

Genomic Location for RGMB Gene

Chromosome:
5
Start:
98,768,650 bp from pter
End:
98,798,643 bp from pter
Size:
29,994 bases
Orientation:
Plus strand

Genomic View for RGMB Gene

Genes around RGMB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGMB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGMB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGMB Gene

Proteins for RGMB Gene

  • Protein details for RGMB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6NW40-RGMB_HUMAN
    Recommended name:
    RGM domain family member B
    Protein Accession:
    Q6NW40
    Secondary Accessions:
    • D6R9A0
    • Q8NC92

    Protein attributes for RGMB Gene

    Size:
    437 amino acids
    Molecular mass:
    47547 Da
    Quaternary structure:
    • Homooligomer (By similarity). Interacts with DRGX (By similarity). Interacts with BMP2 and BMP4 (By similarity). Interacts with the BMP type I receptors ACVR1, BMPR1A and BMPR1B and with the BMP type II receptor ACVR2B (By similarity). The functional complex with its receptor NEO1/neogenin appears to be a heterotetramer with a 2:2 stoichiometry, RGM molecules acting as staples that brings two NEO1 receptors together without interacting themselves, this arrangement leads to activation of downstream signaling via RhoA.
    SequenceCaution:
    • Sequence=AAH67736.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAC11268.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RGMB Gene

neXtProt entry for RGMB Gene

Post-translational modifications for RGMB Gene

  • Autocatalytically cleaved at low pH; the two chains remain linked via two disulfide bonds.
  • GPI-anchored.
  • Glycosylation at Asn120, Thr127, Thr135, and Asn383
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RGMB Gene

Domains & Families for RGMB Gene

Protein Domains for RGMB Gene

Suggested Antigen Peptide Sequences for RGMB Gene

Graphical View of Domain Structure for InterPro Entry

Q6NW40

UniProtKB/Swiss-Prot:

RGMB_HUMAN :
  • Belongs to the repulsive guidance molecule (RGM) family.
Family:
  • Belongs to the repulsive guidance molecule (RGM) family.
genes like me logo Genes that share domains with RGMB: view

No data available for Gene Families for RGMB Gene

Function for RGMB Gene

Molecular function for RGMB Gene

UniProtKB/Swiss-Prot Function:
Member of the repulsive guidance molecule (RGM) family that contributes to the patterning of the developing nervous system (By similarity). Acts as a bone morphogenetic protein (BMP) coreceptor that potentiates BMP signaling (By similarity). Promotes neuronal adhesion (By similarity). May inhibit neurite outgrowth.

Gene Ontology (GO) - Molecular Function for RGMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015026 coreceptor activity IBA --
GO:0042802 identical protein binding ISS --
genes like me logo Genes that share ontologies with RGMB: view
genes like me logo Genes that share phenotypes with RGMB: view

Animal Models for RGMB Gene

MGI Knock Outs for RGMB:

Animal Model Products

  • Taconic Biosciences Mouse Models for RGMB

CRISPR Products

miRNA for RGMB Gene

miRTarBase miRNAs that target RGMB

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RGMB Gene

Localization for RGMB Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGMB Gene

Cell membrane; Lipid-anchor, GPI-anchor. Membrane raft.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RGMB gene
Compartment Confidence
plasma membrane 5
nucleus 3
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for RGMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment ISS --
GO:0005886 plasma membrane IBA,IEA --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
GO:0045121 membrane raft IEA --
genes like me logo Genes that share ontologies with RGMB: view

Pathways & Interactions for RGMB Gene

genes like me logo Genes that share pathways with RGMB: view

Pathways by source for RGMB Gene

1 BioSystems pathway for RGMB Gene
3 Reactome pathways for RGMB Gene

Gene Ontology (GO) - Biological Process for RGMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion ISS --
GO:0007165 signal transduction ISS --
GO:0030509 BMP signaling pathway ISS,IBA --
GO:0045893 positive regulation of transcription, DNA-templated ISS --
genes like me logo Genes that share ontologies with RGMB: view

No data available for SIGNOR curated interactions for RGMB Gene

Drugs & Compounds for RGMB Gene

No Compound Related Data Available

Transcripts for RGMB Gene

Unigene Clusters for RGMB Gene

RGM domain family, member B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RGMB Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4
SP1: - -
SP2: -
SP3:

Relevant External Links for RGMB Gene

GeneLoc Exon Structure for
RGMB
ECgene alternative splicing isoforms for
RGMB

Expression for RGMB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RGMB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RGMB Gene

This gene is overexpressed in Esophagus - Muscularis (x5.1) and Esophagus - Gastroesophageal Junction (x4.0).

Protein differential expression in normal tissues from HIPED for RGMB Gene

This gene is overexpressed in Cerebrospinal fluid (61.5) and Fetal Brain (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RGMB Gene



Protein tissue co-expression partners for RGMB Gene

NURSA nuclear receptor signaling pathways regulating expression of RGMB Gene:

RGMB

SOURCE GeneReport for Unigene cluster for RGMB Gene:

Hs.526902

Evidence on tissue expression from TISSUES for RGMB Gene

  • Skin(2.1)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with RGMB: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGMB Gene

Orthologs for RGMB Gene

This gene was present in the common ancestor of animals.

Orthologs for RGMB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RGMB 34 35
  • 99.51 (n)
mouse
(Mus musculus)
Mammalia Rgmb 34 16 35
  • 87.95 (n)
cow
(Bos Taurus)
Mammalia RGMB 34 35
  • 87.24 (n)
rat
(Rattus norvegicus)
Mammalia Rgmb 34
  • 86.29 (n)
oppossum
(Monodelphis domestica)
Mammalia RGMB 35
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RGMB 35
  • 76 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RGMB 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves RGMB 34 35
  • 76 (n)
lizard
(Anolis carolinensis)
Reptilia RGMB 35
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rgmb 34
  • 71.99 (n)
MGC75814 34
zebrafish
(Danio rerio)
Actinopterygii rgmb 34 35 35
  • 69.41 (n)
rgmd 35
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea drag-1 34 35
  • 44 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 46 (a)
OneToMany
Species where no ortholog for RGMB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RGMB Gene

ENSEMBL:
Gene Tree for RGMB (if available)
TreeFam:
Gene Tree for RGMB (if available)

Paralogs for RGMB Gene

Paralogs for RGMB Gene

(2) SIMAP similar genes for RGMB Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RGMB: view

Variants for RGMB Gene

Sequence variations from dbSNP and Humsavar for RGMB Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000068120 -- 98,774,802(+) GGGAA(A/G)AGCTC intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000120841 -- 98,796,645(+) CTATA(G/T)CATTA downstream-variant-500B
rs1000264907 -- 98,776,683(+) CCATC(A/C)TCTCT intron-variant
rs1000303188 -- 98,787,158(+) ATTTC(A/G)GTTAA intron-variant
rs1000369323 -- 98,769,700(+) CCGGG(A/G)CTGTT intron-variant, nc-transcript-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RGMB Gene

Variant ID Type Subtype PubMed ID
dgv1627e212 CNV loss 25503493

Variation tolerance for RGMB Gene

Residual Variation Intolerance Score: 54.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.61; 56.43% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RGMB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGMB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RGMB Gene

Disorders for RGMB Gene

MalaCards: The human disease database

(1) MalaCards diseases for RGMB Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
basilar artery occlusion
- elite association - COSMIC cancer census association via MalaCards
Search RGMB in MalaCards View complete list of genes associated with diseases

Relevant External Links for RGMB

Human Genome Epidemiology (HuGE) Navigator
RGMB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RGMB
genes like me logo Genes that share disorders with RGMB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RGMB Gene

Publications for RGMB Gene

  1. Repulsive guidance molecule b inhibits neurite growth and is increased after spinal cord injury. (PMID: 19324014) Liu X. … Yamashita T. (Biochem. Biophys. Res. Commun. 2009) 2 3 4 64
  2. Structure of the repulsive guidance molecule (RGM)-neogenin signaling hub. (PMID: 23744777) Bell C.H. … Siebold C. (Science 2013) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Dragon (repulsive guidance molecule b, RGMb) is a novel gene that promotes colorectal cancer growth. (PMID: 26029998) Shi Y. … Guleng B. (Oncotarget 2015) 3 64

Products for RGMB Gene

Sources for RGMB Gene

Content
Loading form....