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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 and Miller-Dieker Lissencephaly Syndrome. Among its related pathways are Developmental Biology and Signaling by BMP. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for RGMB Gene

Promoters and enhancers for RGMB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I098767 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 555.5 +3.9 3892 10.3 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 RGMB-AS1 RGMB CHD1
GH05I098796 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.7 +27.8 27818 0.9 CTCF TEAD4 MZF1 ZNF2 RAD21 TEAD3 ZNF664 GATA3 ZNF366 SMC3 ENSG00000279232 RGMB-AS1 RGMB CSNK1A1P3
GH05I099019 Enhancer 1.2 Ensembl ENCODE 10.1 +252.3 252260 3.3 PKNOX1 ATF1 FEZF1 ZNF2 ZNF213 ATF7 FOS KLF13 YY2 REST RGMB-AS1 CHD1 LINC02062 RGMB GC05P099011 PIR38453 PIR33197
GH05I099032 Enhancer 1.1 Ensembl ENCODE 10.1 +264.7 264714 2.5 RB1 ARNT RAD21 ZBTB40 RARA RFX5 YY1 EGR1 ARID2 SCRT2 RGMB-AS1 CHD1 LINC02062 RGMB PIR38453 GC05P099011 PIR33197
GH05I098413 Enhancer 1 FANTOM5 ENCODE dbSUPER 8.3 -353.2 -353174 4.3 JUND ATF7 FOS ATF2 RGMB RGMB-AS1 MTCO1P24 CTBP2P4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RGMB on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for RGMB Gene

Genomic Locations for RGMB Gene
chr5:98,768,650-98,798,643
(GRCh38/hg38)
Size:
29,994 bases
Orientation:
Plus strand
chr5:98,104,354-98,134,347
(GRCh37/hg19)

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 isoforms=120, isoforms=127, Thr135, and isoforms=383

No data available for DME Specific Peptides for RGMB Gene

Domains & Families for RGMB Gene

Gene Families for RGMB Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins

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

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.

Phenotypes From GWAS Catalog for RGMB Gene

Gene Ontology (GO) - Molecular Function for RGMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25938661
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

miRNA for RGMB Gene

miRTarBase miRNAs that target RGMB

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

Subcellular locations from the

Human Protein Atlas (HPA)

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 --
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 --
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:

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

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 33 34
  • 99.51 (n)
mouse
(Mus musculus)
Mammalia Rgmb 33 16 34
  • 87.95 (n)
cow
(Bos Taurus)
Mammalia RGMB 33 34
  • 87.24 (n)
rat
(Rattus norvegicus)
Mammalia Rgmb 33
  • 86.29 (n)
oppossum
(Monodelphis domestica)
Mammalia RGMB 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RGMB 34
  • 76 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RGMB 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves RGMB 33 34
  • 76 (n)
lizard
(Anolis carolinensis)
Reptilia RGMB 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rgmb 33
  • 71.99 (n)
MGC75814 33
zebrafish
(Danio rerio)
Actinopterygii rgmb 33 34 34
  • 69.41 (n)
rgmd 34
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea drag-1 33 34
  • 44 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs1000068120 -- 98,774,802(+) A/G 5_prime_UTR_variant, intron_variant
rs1000120841 -- 98,796,645(+) G/T downstream_transcript_variant
rs1000264907 -- 98,776,683(+) A/C/G intron_variant
rs1000303188 -- 98,787,158(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000369323 -- 98,769,700(+) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

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)

Additional Variant Information 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

(2) MalaCards diseases for RGMB Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search RGMB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 (Biochemical and biophysical research communications 2009) 2 3 4 58
  2. Structure of the repulsive guidance molecule (RGM)-neogenin signaling hub. (PMID: 23744777) Bell CH … Siebold C (Science (New York, N.Y.) 2013) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Repulsive guidance molecule B inhibits metastasis and is associated with decreased mortality in non-small cell lung cancer. (PMID: 26910889) Li J … He J (Oncotarget 2016) 3 58

Products for RGMB Gene

Sources for RGMB Gene

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