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

    Gene ID: 56963, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001166283.2NP_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:234419
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:56229
      RGM_N; Repulsive guidance molecule (RGM) N-terminus
    2. NM_001166286.2NP_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:210395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus
    3. NM_001166287.2NP_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:210395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus
    4. NM_001166288.2NP_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:210395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus
    5. NM_001166289.2NP_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:210395
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:32205
      RGM_N; Repulsive guidance molecule (RGM) N-terminus
    6. NM_020211.3NP_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:226411
      RGM_C; Repulsive guidance molecule (RGM) C-terminus
      pfam06535
      Location:48221
      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)