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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
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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

Gene LinkOut

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