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RGMA Gene(Protein Coding)

Repulsive Guidance Molecule Family Member A

GCID:
GC15M093035
GIFtS:
59
Genes Participants
UDN Logo

Aliases for RGMA Gene

Aliases for RGMA Gene

  • Repulsive Guidance Molecule Family Member A 2 3 5
  • RGM Domain Family, Member A 2 3
  • RGM 3 4
  • Repulsive Guidance Molecule A 3
  • RGM Domain Family Member A 4

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 Family Member A) is a Protein Coding gene. Diseases associated with RGMA include Leukemia, Acute Myeloid. Among its related pathways are Developmental Biology and Spinal Cord Injury. GO annotations related to this gene include coreceptor activity. An important paralog of this gene is RGMB.

UniProtKB/Swiss-Prot 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

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

Genomics for RGMA Gene

Products:

  1. Regulatory Element

Regulatory Elements for RGMA Gene

Enhancers for RGMA 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
GH15F093068 1.1 FANTOM5 ENCODE 10.5 +20.4 20435 0.2 PKNOX1 INSM2 FEZF1 ZIC2 ZNF121 POLR2A PATZ1 SCRT2 ZNF600 EGR2 RGMA LOC100124334
GH15F092816 1.5 FANTOM5 ENCODE 3.8 +269.0 269028 6.9 PKNOX1 SIN3A YBX1 FEZF1 DMAP1 ZNF2 YY1 FOS DEK ZHX2 CHD2 ASB9P1 HMGN1P38 ENSG00000258922 RGMA ST8SIA2 ENSG00000275175 GC15P095281
GH15F093122 0.4 ENCODE 11.1 -33.4 -33423 0.8 RFX1 RGMA LOC101927025 LOC105370980
GH15F093089 1.1 FANTOM5 Ensembl ENCODE 3.8 -0.8 -751 1.0 KLF1 RNF2 SUZ12 POLR2A CBX2 KLF8 NR2F2 EZH2 RGMA LOC101927025 LOC105370980
GH15F093027 1.4 FANTOM5 Ensembl ENCODE 2 +60.0 59980 4.1 ZNF2 RAD21 YY1 GLIS2 SCRT2 ZNF143 FOS ZNF654 REST HDAC8 CHD2 RGMA LOC105370979 MIR3175
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RGMA on UCSC Golden Path with GeneCards custom track

Promoters for RGMA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000413732 514 2201 KLF17 ZNF2 RAD21 ZNF143 ZNF280D ZNF654 REST ZFP69B ZBTB26 WT1

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

Genomic Location for RGMA Gene

Chromosome:
15
Start:
93,035,273 bp from pter
End:
93,089,214 bp from pter
Size:
53,942 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

Products:

  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=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAB98207.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; 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 Asn 114, Asn 159, and Asn 389
  • Modification sites at PhosphoSitePlus

Other Protein References for RGMA Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for RGMA

No data available for DME Specific Peptides for RGMA Gene

Domains & Families for RGMA Gene

Protein Domains for RGMA Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for RGMA Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for RGMA Gene

Function for RGMA Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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.

Gene Ontology (GO) - Molecular Function for RGMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001948 glycoprotein binding IPI 22728873
GO:0005515 protein binding IPI 21044950
GO:0015026 coreceptor activity IBA --
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:

Animal Model Products

Flow Cytometry 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
extracellular 5
endoplasmic reticulum 5
plasma membrane 4
nucleus 3
cytosol 3
cytoskeleton 2
mitochondrion 2
peroxisome 1
lysosome 1

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 IEA,IBA --
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

2 BioSystems pathways for RGMA Gene
3 Reactome pathways for RGMA Gene

Gene Ontology (GO) - Biological Process for RGMA Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0030510 regulation of BMP signaling pathway IEA --
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RGMA Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for RGMA Gene

(6) REFSEQ mRNAs :
(14) Additional mRNA sequences :
(113) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RGMA Gene

RGM domain family, member A:
Representative Sequences:

Flow Cytometry 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
ECgene alternative splicing isoforms for
RGMA

Expression for RGMA Gene

Products:

  1. Primer

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, PaxDb, and MOPED for RGMA Gene



Protein tissue co-expression partners for RGMA Gene

NURSA nuclear receptor signaling pathways regulating expression of RGMA Gene:

RGMA

SOURCE GeneReport for Unigene cluster for RGMA Gene:

Hs.271277
genes like me logo Genes that share expression patterns with RGMA: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.63 (n)
dog
(Canis familiaris)
 Mammalia RGMA 34 35
  • 91.93 (n)
cow
(Bos Taurus)
 Mammalia RGMA 34 35
  • 91.73 (n)
rat
(Rattus norvegicus)
 Mammalia Rgma 34
  • 89.53 (n)
mouse
(Mus musculus)
 Mammalia Rgma 34 16 35
  • 89.1 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia RGMA 35
  • 83 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia RGMA 35
  • 81 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves RGMA 34 35
  • 82.22 (n)
lizard
(Anolis carolinensis)
 Reptilia RGMA 35
  • 71 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia rgma 34
  • 75.64 (n)
African clawed frog
(Xenopus laevis)
 Amphibia rgma-prov 34
zebrafish
(Danio rerio)
 Actinopterygii rgma 34 35
  • 68.71 (n)
wufb36g11 34
worm
(Caenorhabditis elegans)
 Secernentea drag-1 35
  • 25 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 44 (a)
 OneToMany
Species where no ortholog for RGMA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for RGMA Gene

Paralogs for RGMA Gene

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

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

Variants for RGMA Gene

Sequence variations from dbSNP and Humsavar for RGMA Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1012200 -- 93,082,239(+) GTATG(A/T)ACAGG intron-variant
rs10153038 -- 93,074,766(+) TCACC(A/G)AACGG intron-variant, upstream-variant-2KB
rs10630191 -- 93,059,022(+) CTGCC(-/CT)GATTA intron-variant
rs10646785 -- 93,046,905(+) GGCAC(-/TG)TGTTC intron-variant
rs10852187 -- 93,061,430(+) CCGGC(A/G)TGAGC intron-variant

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

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

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)

Relevant External Links for RGMA Gene

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

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

Disorders for RGMA Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
leukemia, acute myeloid
  • leukemia, acute myeloid, somatic
- elite association - COSMIC cancer census association via MalaCards
Search RGMA in MalaCards View complete list of genes associated with diseases

Relevant External Links for RGMA

Genetic Association Database (GAD)
RGMA
Human Genome Epidemiology (HuGE) Navigator
RGMA
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RGMA
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 Immun. 2010) 3 46 64
  2. Unc5B associates with LARG to mediate the action of repulsive guidance molecule. (PMID: 19273616) Hata K. … Yamashita T. (J. Cell Biol. 2009) 3 4 64
  3. Inactivation of Ras by p120GAP via focal adhesion kinase dephosphorylation mediates RGMa-induced growth cone collapse. (PMID: 19458235) Endo M. … Yamashita T. (J. Neurosci. 2009) 3 4 64
  4. Linkage disequilibrium mapping of a chromosome 15q25-26 major depression linkage region and sequencing of NTRK3. (PMID: 18367154) Verma R. … Levinson D.F. (Biol. Psychiatry 2008) 3 46 64
  5. Emerging roles for neogenin and its ligands in CNS development. (PMID: 18485097) De Vries M. … Cooper H.M. (J. Neurochem. 2008) 3 22 64

Products for RGMA Gene

Sources for RGMA Gene

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