RGMA Gene (Protein Coding)

Repulsive Guidance Molecule BMP Co-Receptor A

GC15M093035
GIFtS:
41
This gene encodes a member of the repulsive guidance molecule family. The encoded protein is a glycosylphosphatidylinositol-anchored glycoprotein that functions as an axon guidance protein in the developing and adult central nervous system. This protein may also function as a tumor suppressor in some cancers. Alternate splicing results in multiple transcript variants. [provided... See more...

Aliases for RGMA Gene

Aliases for RGMA Gene

  • Repulsive Guidance Molecule BMP Co-Receptor A 2 3 5
  • RGM 2 3 4
  • Repulsive Guidance Molecule Family Member A 2 3
  • Repulsive Guidance Molecule A 3 4
  • RGM Domain Family, Member A 2 3
  • RGM Domain Family Member A 4
  • RGMA 5

External Ids for RGMA Gene

Previous GeneCards Identifiers for RGMA Gene

  • GC15M091173
  • GC15M091316
  • GC15M091387
  • GC15M093586
  • GC15M069723

Summaries for RGMA Gene

Entrez Gene Summary for RGMA Gene

  • This gene encodes a member of the repulsive guidance molecule family. The encoded protein is a glycosylphosphatidylinositol-anchored glycoprotein that functions as an axon guidance protein in the developing and adult central nervous system. This protein may also function as a tumor suppressor in some cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

GeneCards Summary for RGMA Gene

RGMA (Repulsive Guidance Molecule BMP Co-Receptor A) is a Protein Coding gene. Diseases associated with RGMA include Hemochromatosis Type 2 and Amusia. Among its related pathways are Netrin-1 signaling and Signaling by BMP. Gene Ontology (GO) annotations related to this gene include coreceptor activity. An important paralog of this gene is RGMB.

UniProtKB/Swiss-Prot Summary for RGMA Gene

  • Member of the repulsive guidance molecule (RGM) family that performs several functions in the developing and adult nervous system. Regulates cephalic neural tube closure, inhibits neurite outgrowth and cortical neuron branching, and the formation of mature synapses. Binding to its receptor NEO1/neogenin induces activation of RHOA-ROCK1/Rho-kinase signaling pathway through UNC5B-ARHGEF12/LARG-PTK2/FAK1 cascade, leading to collapse of the neuronal growth cone and neurite outgrowth inhibition. Furthermore, RGMA binding to NEO1/neogenin leads to HRAS inactivation by influencing HRAS-PTK2/FAK1-AKT1 pathway. It also functions as a bone morphogenetic protein (BMP) coreceptor that may signal through SMAD1, SMAD5, and SMAD8.

Gene Wiki entry for RGMA Gene

Additional gene information for RGMA Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RGMA Gene

Genomics for RGMA Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RGMA 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
GH15J093069 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.4 +17.4 17365 5.3 PRDM10 ZNF629 ZNF692 PRDM1 ZIC2 PATZ1 POLR2A ZNF341 ZNF561 ZBTB44 lnc-FAM174B-7 RGMA CHD2 ASB9P1 ENSG00000260361 HMGN1P38 YBX2P2
GH15J093085 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 603.7 +1.0 1003 4.5 CTCF TEAD4 PRDM10 ZNF692 TARDBP FOXA1 ZNF143 POLR2A PATZ1 REST RGMA LOC101927025 lnc-CHD2-2 lnc-FAM174B-7 CHD2
GH15J093068 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 10.6 +20.4 20432 0.2 ZNF629 PRDM1 ZIC2 PATZ1 POLR2A ZNF600 SCRT2 ZNF639 CTBP1 TSHZ1 RGMA YBX2P2 lnc-FAM174B-7 CHD2
GH15J092816 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 3.8 +269.0 269025 6.9 SP1 CREB1 PRDM10 REST TFE3 RFX1 LEF1 IKZF1 KDM1A ZNF692 ENSG00000272888 CHD2 ENSG00000258922 RGMA ST8SIA2 FAM174B piR-61945-166 ENSG00000279765
GH15J093188 Enhancer 0.4 Ensembl CraniofacialAtlas 10.7 -100.2 -100190 1.2 KDM1A piR-36075-001 RGMA ENSG00000285663 LOC105370980 ENSG00000258888 lnc-CHD2-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RGMA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RGMA

Top Transcription factor binding sites by QIAGEN in the RGMA gene promoter:
  • AML1a
  • GR
  • GR-alpha
  • GR-beta
  • Ik-2
  • Nkx2-5
  • p53
  • STAT1
  • STAT1alpha
  • STAT1beta

Genomic Locations for RGMA Gene

Genomic Locations for RGMA Gene
chr15:93,035,271-93,089,211
(GRCh38/hg38)
Size:
53,941 bases
Orientation:
Minus strand
chr15:93,586,636-93,632,443
(GRCh37/hg19)
Size:
45,808 bases
Orientation:
Minus strand

Genomic View for RGMA Gene

Genes around RGMA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RGMA Gene

Proteins for RGMA Gene

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  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q96B86-RGMA_HUMAN
    Recommended name:
    Repulsive guidance molecule A
    Protein Accession:
    Q96B86
    Secondary Accessions:
    • B2RTW1
    • B7Z5S8
    • F5GXQ7
    • F5GZU6
    • G3V518
    • Q0JV97
    • Q8NC80
    • Q9H0E6
    • Q9NPM3

    Protein attributes for RGMA Gene

    Size:
    450 amino acids
    Molecular mass:
    49347 Da
    Quaternary structure:
    • Interacts with NEO1, BMP2 and BMP4.
    SequenceCaution:
    • Sequence=AAH15886.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=CAB98207.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RGMA Gene

    Alternative splice isoforms for RGMA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RGMA Gene

Protein Expression for RGMA Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RGMA Gene

  • Autocatalytically cleaved at low pH; the two chains remain linked via two disulfide bonds.
  • Glycosylation at Asn114, Asn159, and Asn389
  • Modification sites at PhosphoSitePlus

Other Protein References for RGMA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RGMA Gene

Domains & Families for RGMA Gene

Gene Families for RGMA Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for RGMA Gene

InterPro:
Blocks:
  • Repulsive guidance molecule, C-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for RGMA Gene

GenScript: Design optimal peptide antigens:
  • RGMA protein (A1L187_HUMAN)
  • Repulsive guidance molecule A (C6G485_HUMAN)
  • RGM domain family member A (RGMA_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96B86

UniProtKB/Swiss-Prot:

RGMA_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 RGMA: view

Function for RGMA Gene

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  2. CRISPR
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Molecular function for RGMA Gene

UniProtKB/Swiss-Prot Function:
Member of the repulsive guidance molecule (RGM) family that performs several functions in the developing and adult nervous system. Regulates cephalic neural tube closure, inhibits neurite outgrowth and cortical neuron branching, and the formation of mature synapses. Binding to its receptor NEO1/neogenin induces activation of RHOA-ROCK1/Rho-kinase signaling pathway through UNC5B-ARHGEF12/LARG-PTK2/FAK1 cascade, leading to collapse of the neuronal growth cone and neurite outgrowth inhibition. Furthermore, RGMA binding to NEO1/neogenin leads to HRAS inactivation by influencing HRAS-PTK2/FAK1-AKT1 pathway. It also functions as a bone morphogenetic protein (BMP) coreceptor that may signal through SMAD1, SMAD5, and SMAD8.

Phenotypes From GWAS Catalog for RGMA Gene

Gene Ontology (GO) - Molecular Function for RGMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IEA --
GO:0005515 protein binding IPI 21044950
GO:0015026 coreceptor activity IBA 21873635
GO:1990459 transferrin receptor binding IPI 22728873
genes like me logo Genes that share ontologies with RGMA: view
genes like me logo Genes that share phenotypes with RGMA: view

Animal Models for RGMA Gene

MGI Knock Outs for RGMA:
  • Rgma Rgma<tm1Arbr>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGMA

Clone Products

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

Localization for RGMA Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGMA Gene

Cell membrane. Lipid-anchor, GPI-anchor.

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 RGMA gene
Compartment Confidence
plasma membrane 4
endoplasmic reticulum 4
cytoskeleton 3
nucleus 3
cytosol 3
extracellular 2
mitochondrion 2
endosome 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RGMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA --
GO:0005886 plasma membrane IBA 21873635
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with RGMA: view

Pathways & Interactions for RGMA Gene

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

Pathways by source for RGMA Gene

3 Reactome pathways for RGMA Gene
2 KEGG pathways for RGMA Gene

Gene Ontology (GO) - Biological Process for RGMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001843 neural tube closure IEA --
GO:0010975 regulation of neuron projection development IEA --
GO:0010976 positive regulation of neuron projection development IEA --
GO:0010977 negative regulation of neuron projection development IEA --
GO:0030509 BMP signaling pathway IBA 21873635
genes like me logo Genes that share ontologies with RGMA: view

No data available for SIGNOR curated interactions for RGMA Gene

Drugs & Compounds for RGMA Gene

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  1. Drug
No Compound Related Data Available

Transcripts for RGMA Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RGMA Gene

6 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGMA

Clone Products

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

ExUns: 1 ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e · 7f ^ 8
SP1: - - - -
SP2: - - - - - - - -
SP3: - - - - - - - -
SP4: - - - - -
SP5: - - - -
SP6: - - -
SP7: - - -
SP8: - -

Relevant External Links for RGMA Gene

GeneLoc Exon Structure for
RGMA

Expression for RGMA Gene

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

mRNA expression in normal human tissues for RGMA Gene
mRNA expression by BioGPS for RGMA GenemRNA expression by GTEx for RGMA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Muscle - Skeletal (x5.7) and Esophagus - Muscularis (x4.7).

Protein differential expression in normal tissues from HIPED for RGMA Gene

This gene is overexpressed in Fetal Brain (19.4), Testis (14.7), Frontal cortex (14.7), and Spinal cord (12.7).

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



Protein tissue co-expression partners for RGMA Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RGMA

SOURCE GeneReport for Unigene cluster for RGMA Gene:

Hs.271277

Evidence on tissue expression from TISSUES for RGMA Gene

  • Nervous system(4.9)
  • Eye(4.4)
  • Muscle(2.7)
  • Stomach(2.5)
  • Bone marrow(2.5)
  • Spleen(2.4)
  • Blood(2.4)
  • Heart(2.3)
  • Lymph node(2.3)
  • Intestine(2.3)
  • Skin(2.2)
  • Lung(2)
genes like me logo Genes that share expression patterns with RGMA: view

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

Orthologs for RGMA Gene

This gene was present in the common ancestor of animals.

Orthologs for RGMA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RGMA 30 31
  • 99.63 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RGMA 30 31
  • 91.93 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RGMA 30 31
  • 91.73 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rgma 30
  • 89.53 (n)
Mouse
(Mus musculus)
 Mammalia Rgma 30 17 31
  • 89.1 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RGMA 31
  • 83 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RGMA 31
  • 81 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RGMA 30 31
  • 82.22 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RGMA 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rgma 30
  • 75.64 (n)
African clawed frog
(Xenopus laevis)
 Amphibia rgma-prov 30
Zebrafish
(Danio rerio)
 Actinopterygii rgma 30 31
  • 68.71 (n)
 OneToOne
wufb36g11 30
Worm
(Caenorhabditis elegans)
 Secernentea drag-1 31
  • 25 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 44 (a)
 OneToMany
Species where no ortholog for RGMA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 Vase (Ciona intestinalis)
  • 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 RGMA Gene

ENSEMBL:
Gene Tree for RGMA (if available)
TreeFam:
Gene Tree for RGMA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RGMA: view image

Paralogs for RGMA Gene

Paralogs for RGMA Gene

(3) SIMAP similar genes for RGMA Gene using alignment to 10 proteins:

  • RGMA_HUMAN
  • A1L187_HUMAN
  • C6G485_HUMAN
  • F5GZU6_HUMAN
  • F5H7G2_HUMAN
  • G3V3Z3_HUMAN
  • G3V4C2_HUMAN
  • G3V518_HUMAN
  • G3V545_HUMAN
  • H3BQ68_HUMAN
genes like me logo Genes that share paralogs with RGMA: view

Variants for RGMA Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RGMA Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
709915 Benign: not provided 93,073,717(-) A/G SPLICE_DONOR_VARIANT,INTRON_VARIANT
712174 Benign: not provided 93,045,427(-) G/A SYNONYMOUS_VARIANT
rs4238485 - p.Asp415Glu
rs4778078 - p.Ala431Val

Additional dbSNP identifiers (rs#s) for RGMA Gene

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

Variant ID Type Subtype PubMed ID
dgv157n21 CNV loss 19592680
nsv1045427 CNV gain 25217958
nsv1052724 CNV gain 25217958
nsv473934 CNV novel sequence insertion 20440878
nsv523617 CNV loss 19592680
nsv833096 CNV loss 17160897
nsv976965 CNV duplication 23825009

Variation tolerance for RGMA Gene

Residual Variation Intolerance Score: 44.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.53; 72.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RGMA Gene

Human Gene Mutation Database (HGMD)
RGMA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGMA

SNP Genotyping and Copy Number Assay Products

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

Disorders for RGMA Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
hemochromatosis type 2
  • hfe2
amusia
  • receptive amusia
- elite association - COSMIC cancer census association via MalaCards
Search RGMA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RGMA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RGMA: view

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

Publications for RGMA Gene

  1. RGMA and IL21R show association with experimental inflammation and multiple sclerosis. (PMID: 20072140) Nohra R … Olsson T (Genes and immunity 2010) 3 41
  2. Unc5B associates with LARG to mediate the action of repulsive guidance molecule. (PMID: 19273616) Hata K … Yamashita T (The Journal of cell biology 2009) 3 4
  3. Inactivation of Ras by p120GAP via focal adhesion kinase dephosphorylation mediates RGMa-induced growth cone collapse. (PMID: 19458235) Endo M … Yamashita T (The Journal of neuroscience : the official journal of the Society for Neuroscience 2009) 3 4
  4. Emerging roles for neogenin and its ligands in CNS development. (PMID: 18485097) De Vries M … Cooper HM (Journal of neurochemistry 2008) 3 23
  5. Linkage disequilibrium mapping of a chromosome 15q25-26 major depression linkage region and sequencing of NTRK3. (PMID: 18367154) Verma R … Levinson DF (Biological psychiatry 2008) 3 41

ExternalLinks

View latest publications for RGMA gene in Mastermind

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