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    RGMA repulsive guidance molecule BMP co-receptor a [ Homo sapiens (human) ]

    Gene ID: 56963, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RGMAprovided by HGNC
    Official Full Name
    repulsive guidance molecule BMP co-receptor aprovided by HGNC
    Primary source
    HGNC:HGNC:30308
    See related
    Ensembl:ENSG00000182175 MIM:607362; AllianceGenome:HGNC:30308
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RGM
    Summary
    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]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Biased expression in brain (RPKM 32.8), endometrium (RPKM 14.6) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RGMA in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (93035271..93089211, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90797572..90851558, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (93578501..93632440, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93425915-93426556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10129 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93447162-93448361 Neighboring gene CHD2 adjacent suppressive regulatory RNA Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93460529-93461365 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93464712-93465911 Neighboring gene microRNA 3175 Neighboring gene chromodomain helicase DNA binding protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:93488387-93488611 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93492919-93494118 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93523977-93525176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93571676-93572182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93575221-93575725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93595001-93595610 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93605093-93605890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93606687-93607483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93608443-93609406 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:93616734-93616872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93617029-93617786 Neighboring gene uncharacterized LOC101927025 Neighboring gene YBX2 pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93648672-93649381 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93678957-93679495 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93679496-93680033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93723165-93723703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93723704-93724241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93725793-93726360 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:93726361-93726927 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:93732455-93732986 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:93732987-93733516 Neighboring gene putative uncharacterized protein UNQ9370/PRO34162

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Repulsive guidance molecule A suppresses angiogenesis. Harada K, et al. Biochem Biophys Res Commun, 2016 Jan 22. PMID 26721439
    2. Decreased expression of repulsive guidance molecule member A by DNA methylation in colorectal cancer is related to tumor progression. Zhao ZW, et al. Oncol Rep, 2012 May. PMID 22367090
    3. Molecular biology, genetics and biochemistry of the repulsive guidance molecule family. Severyn CJ, et al. Biochem J, 2009 Aug 27. PMID 19698085, Free PMC Article
    4. Inactivation of Ras by p120GAP via focal adhesion kinase dephosphorylation mediates RGMa-induced growth cone collapse. Endo M, et al. J Neurosci, 2009 May 20. PMID 19458235, Free PMC Article
    5. Frequent inactivation of axon guidance molecule RGMA in human colon cancer through genetic and epigenetic mechanisms. Li VS, et al. Gastroenterology, 2009 Jul. PMID 19303019

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circular RNA circHIPK2 inhibits colon cancer cells through miR-373-3p/RGMA axis.
      Title: Circular RNA circHIPK2 inhibits colon cancer cells through miR-373-3p/RGMA axis.
    2. Decreased DNA Methylation of RGMA is Associated with Intracranial Hypertension After Severe Traumatic Brain Injury: An Exploratory Epigenome-Wide Association Study.
      Title: Decreased DNA Methylation of RGMA is Associated with Intracranial Hypertension After Severe Traumatic Brain Injury: An Exploratory Epigenome-Wide Association Study.
    3. Repulsive Guidance Molecule-a and Central Nervous System Diseases.
      Title: Repulsive Guidance Molecule-a and Central Nervous System Diseases.
    4. MicroRNA-4472 Promotes Tumor Proliferation and Aggressiveness in Breast Cancer by Targeting RGMA and Inducing EMT.
      Title: MicroRNA-4472 Promotes Tumor Proliferation and Aggressiveness in Breast Cancer by Targeting RGMA and Inducing EMT.
    5. a regulatory variant of RGMA is associated with opioid dependence in European Americans
      Title: Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans.
    6. RGMA is regulated by the HIF1A/miR-210 axis and inhibits oral squamous cell carcinoma.
      Title: Downregulation of RGMA by HIF-1A/miR-210-3p axis promotes cell proliferation in oral squamous cell carcinoma.
    7. Dysregulation of RGMa plays an important role in the pathology of Parkinson's disease.
      Title: Repulsive Guidance Molecule a (RGMa) Induces Neuropathological and Behavioral Changes That Closely Resemble Parkinson's Disease.
    8. Thus, we conclude that RGMa inhibits angiogenesis in vitro and in vivo suggesting that its manipulation would be an efficient therapeutic strategy for pro-angiogenic conditions.
      Title: Repulsive guidance molecule A suppresses angiogenesis.
    9. RGMa expression and promoter methylation status are closely related to colorectal cancer genesis and progression.
      Title: Decreased expression of repulsive guidance molecule member A by DNA methylation in colorectal cancer is related to tumor progression.
    10. identification of neogenin-binding site on the repulsive guidance molecule A
      Title: Identification of the neogenin-binding site on the repulsive guidance molecule A.
    Submit: New GeneRIF Correction See all GeneRIFs (20)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker.
    EBI GWAS Catalog
    New susceptibility loci associated with kidney disease in type 1 diabetes.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables coreceptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transferrin receptor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in membrane protein ectodomain proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of axon regeneration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of collateral sprouting IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural tube closure IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of membrane protein ectodomain proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    repulsive guidance molecule A
    Names
    RGM domain family, member A
    repulsive guidance molecule family member a

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001166283.2 → NP_001159755.1  repulsive guidance molecule A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform 1.
      Source sequence(s)
      AC013394, AC087641, KF456122
      Consensus CDS
      CCDS53974.1
      UniProtKB/TrEMBL
      A0A0A0MTQ4, C6G485
      Related
      ENSP00000452126.1, ENST00000557301.2
      Conserved Domains (2) summary
      pfam06534
      Location:234 → 419
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:56 → 229
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    2. NM_001166286.2 → NP_001159758.1  repulsive guidance molecule A isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159758.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2, 3, 5 and 6 encode the same isoform (2).
      Source sequence(s)
      AC013394, AC087641, BC015886, DA453869, KF456122
      Consensus CDS
      CCDS53973.1
      UniProtKB/TrEMBL
      C6G485
      Related
      ENSP00000440025.2, ENST00000542321.6
      Conserved Domains (2) summary
      pfam06534
      Location:210 → 395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32 → 205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    3. NM_001166287.2 → NP_001159759.1  repulsive guidance molecule A isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159759.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2, 3, 5 and 6 encode the same isoform (2).
      Source sequence(s)
      AC013394, AC087641, AL136826, DA183348, KF456122
      Consensus CDS
      CCDS53973.1
      UniProtKB/TrEMBL
      C6G485
      Related
      ENSP00000442498.1, ENST00000543599.5
      Conserved Domains (2) summary
      pfam06534
      Location:210 → 395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32 → 205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    4. NM_001166288.2 → NP_001159760.1  repulsive guidance molecule A isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159760.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2, 3, 5 and 6 encode the same isoform (2).
      Source sequence(s)
      AC013394, AC087641, BC140838, DA512691
      Consensus CDS
      CCDS53973.1
      UniProtKB/TrEMBL
      C6G485
      Conserved Domains (2) summary
      pfam06534
      Location:210 → 395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32 → 205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    5. NM_001166289.2 → NP_001159761.1  repulsive guidance molecule A isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159761.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Variants 2, 3, 5 and 6 encode the same isoform (2).
      Source sequence(s)
      AC013394, AC087641, KF456122
      Consensus CDS
      CCDS53973.1
      UniProtKB/TrEMBL
      C6G485
      Related
      ENSP00000404442.2, ENST00000425933.6
      Conserved Domains (2) summary
      pfam06534
      Location:210 → 395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32 → 205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    6. NM_020211.3 → NP_064596.2  repulsive guidance molecule A isoform 3 precursor

      See identical proteins and their annotated locations for NP_064596.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC013394, AC087641, AL136826, DA805034
      Consensus CDS
      CCDS45357.1
      UniProtKB/Swiss-Prot
      B2RTW1, B7Z5S8, F5GXQ7, F5GZU6, G3V518, Q0JV97, Q8NC80, Q96B86, Q9H0E6, Q9NPM3
      UniProtKB/TrEMBL
      C6G485
      Related
      ENSP00000330005.7, ENST00000329082.12
      Conserved Domains (2) summary
      pfam06534
      Location:226 → 411
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:48 → 221
      RGM_N; Repulsive guidance molecule (RGM) N-terminus

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      93035271..93089211 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      90797572..90851558 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96B86.4 GenPept UniProtKB/Swiss-Prot:Q96B86

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