Rgma (repulsive guidance molecule family member A) - Rat Genome Database

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Gene: Rgma (repulsive guidance molecule family member A) Mus musculus
Analyze
Symbol: Rgma
Name: repulsive guidance molecule family member A
RGD ID: 1323725
MGI Page MGI
Description: Enables coreceptor activity and signaling receptor binding activity. Acts upstream of or within several processes, including nervous system development; positive regulation of GTPase activity; and positive regulation of membrane protein ectodomain proteolysis. Located in cell surface. Is expressed in several structures, including future brain; gut; nervous system; sensory organ; and trunk somite. Human ortholog(s) of this gene implicated in multiple sclerosis. Orthologous to human RGMA (repulsive guidance molecule BMP co-receptor a); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BC059072; C230063O06; MGC38550; MGC69915; repulsive guidance molecule A; RGM domain family, member A
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39773,025,268 - 73,069,647 (+)NCBIGRCm39mm39
GRCm39 Ensembl773,025,257 - 73,069,647 (+)Ensembl
GRCm38773,375,520 - 73,419,899 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl773,375,509 - 73,419,899 (+)EnsemblGRCm38mm10GRCm38
MGSCv37780,520,406 - 80,564,785 (+)NCBIGRCm37mm9NCBIm37
MGSCv36773,249,020 - 73,293,410 (+)NCBImm8
Celera770,823,178 - 70,867,680 (+)NCBICelera
Cytogenetic Map7D1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:14610273   PMID:14678836   PMID:14749425   PMID:14985445   PMID:15053976   PMID:15084667   PMID:15258590   PMID:15489334  
PMID:15975920   PMID:16032658   PMID:16141072   PMID:16141073   PMID:16782087   PMID:17389603   PMID:17472960   PMID:17942375   PMID:18519029   PMID:18799693   PMID:21059867   PMID:21187450  
PMID:21267068   PMID:21423182   PMID:21467223   PMID:21873635   PMID:21957482   PMID:22183806   PMID:22396795   PMID:22568948   PMID:23457482   PMID:24123853   PMID:24312340   PMID:25456136  
PMID:26073538   PMID:26611327   PMID:26633881   PMID:26651291   PMID:26896667   PMID:26930384   PMID:27143755   PMID:27545491   PMID:29478698   PMID:30333477   PMID:30733433   PMID:31541165  
PMID:32243839   PMID:33740419  


Genomics

Comparative Map Data
Rgma
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39773,025,268 - 73,069,647 (+)NCBIGRCm39mm39
GRCm39 Ensembl773,025,257 - 73,069,647 (+)Ensembl
GRCm38773,375,520 - 73,419,899 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl773,375,509 - 73,419,899 (+)EnsemblGRCm38mm10GRCm38
MGSCv37780,520,406 - 80,564,785 (+)NCBIGRCm37mm9NCBIm37
MGSCv36773,249,020 - 73,293,410 (+)NCBImm8
Celera770,823,178 - 70,867,680 (+)NCBICelera
Cytogenetic Map7D1NCBI
RGMA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1593,035,273 - 93,089,204 (-)EnsemblGRCh38hg38GRCh38
GRCh381593,035,271 - 93,089,211 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371593,578,501 - 93,632,440 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361591,387,641 - 91,433,437 (-)NCBINCBI36hg18NCBI36
Build 341591,387,640 - 91,433,437NCBI
Celera1569,998,187 - 70,044,004 (-)NCBI
Cytogenetic Map15q26.1NCBI
HuRef1569,723,091 - 69,768,218 (-)NCBIHuRef
CHM1_11593,427,333 - 93,473,451 (-)NCBICHM1_1
Rgma
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21127,128,934 - 127,172,918 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1127,128,934 - 127,172,918 (+)Ensembl
Rnor_6.01134,699,053 - 134,742,512 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1134,699,299 - 134,742,514 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01135,725,212 - 135,768,409 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41128,547,399 - 128,591,304 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11128,641,975 - 128,668,760 (+)NCBI
Celera1119,260,496 - 119,304,476 (+)NCBICelera
Cytogenetic Map1q31NCBI
Rgma
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541621,221,023 - 21,261,831 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541621,221,023 - 21,261,831 (-)NCBIChiLan1.0ChiLan1.0
RGMA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11590,922,199 - 90,951,704 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1590,922,199 - 90,956,179 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01571,728,669 - 71,774,447 (-)NCBIMhudiblu_PPA_v0panPan3
RGMA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1347,044,342 - 47,089,923 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl347,061,910 - 47,089,294 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha349,744,736 - 49,788,688 (+)NCBI
ROS_Cfam_1.0347,453,705 - 47,497,710 (+)NCBI
UMICH_Zoey_3.1346,971,723 - 47,015,658 (+)NCBI
UNSW_CanFamBas_1.0347,203,068 - 47,247,025 (+)NCBI
UU_Cfam_GSD_1.0347,534,393 - 47,578,334 (+)NCBI
Rgma
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640136,541,660 - 136,581,389 (-)NCBI
SpeTri2.0NW_0049364839,753,112 - 9,792,817 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RGMA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl785,921,586 - 85,968,888 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1785,921,524 - 85,968,887 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2791,815,011 - 91,862,487 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RGMA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12911,592,929 - 11,638,955 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2911,592,604 - 11,638,860 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605935,022,501 - 35,068,477 (+)NCBIVero_WHO_p1.0
Rgma
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476810,739,674 - 10,778,036 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Rgma  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7D1UniSTS
cM Map7 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7346321287493512Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76500000133900000Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718994869119886157Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719413473142366067Mouse
4141805Sle19_msystematic lupus erythematosus susceptibility 19 (mouse)Not determined3033306081485905Mouse
26884404Huml1_mhumerus length 1, 5 week (mouse)730500000109400000Mouse
1301514Rigs1_mradiation induced gastroschisis 1 (mouse)Not determined73658059092745138Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736580590116817642Mouse
25314303Vmm4_mvariable multisystem mineralization 4, kidney (mouse)73760000087400000Mouse
1300791Abbp3_mA/J and C57BL/6 blood pressure 3 (mouse)Not determined740024463103860803Mouse
4141929Chlq18_mcirculating hormone level QTL 18 (mouse)Not determined74149907275499217Mouse
11252140Fdr1_mfat response to dietary restriction 1 (mouse)74149907275499217Mouse
10043926Bw1n_mbody weight 1 in NSY (mouse)Not determined745512542119094307Mouse
12880417V125Dq5_mvitamin D active form serum level QTL 5 (mouse)74560000079600000Mouse
25314302Vmm2_mvariable multisystem mineralization 2, heart (mouse)74750000074500000Mouse
1302141Fcsa6_mfemoral cross-sectional area 6 (mouse)Not determined74873471382734859Mouse
11532741Tbrs5_mtuberculosis resistance 5 (mouse)74950947983586207Mouse
1357752Tabw_mtally ho asscoiated body weight (mouse)Not determined74954353083543642Mouse
10054064Bwq11_mbody weight QTL 11 (mouse)Not determined75147520685475345Mouse
10053685Eae43_mexperimental allergic encephalomyelitis susceptibility 43 (mouse)Not determined75147520685475345Mouse
13208555Lgth10_mbody length 10 (mouse)752000000126000000Mouse
12880418V125Dq6_mvitamin D active form serum level QTL 6 (mouse)75250000086500000Mouse
27226751Femd5_mfemur midshaft diameter 5, 10 week (mouse)753600000143600000Mouse
25823170Hrsq7_mhost response to SARS QTL 7, log titer (mouse)755169841117223580Mouse
11565101Tsve1_mvariable short tail (Tsv) enhancer 1 (mouse)75623976087493512Mouse
27226778Femd11_mfemur midshaft diameter 11, 16 week (mouse)757300000134400000Mouse
1300952Hcs1_mhepatocarcinogenesis susceptibility 1 (mouse)Not determined75767637391676604Mouse
1301465Egrm3_mearly growth rate (mouse)Not determined75767637391676604Mouse
1301663Skull9_mskull morphology 9 (mouse)Not determined75767637391676604Mouse
26884408Bzwq13_mbi-zygomatic width QTL 13, 16 week (mouse)762100000121800000Mouse
27095916Scvln15_msacral vertebrae length 2, 16 week (mouse)762100000124100000Mouse
25314305Vmm6_mvariable multisystem mineralization 6, eye (mouse)762200000103100000Mouse
1301383Aem2_manti-erythrocyte autoantibody modifier 2 (mouse)Not determined76448567698485905Mouse
26884381Bzwq2_mbi-zygomatic width QTL 2, 5 week (mouse)76560000097300000Mouse
26884440Sklq4_mskull length QTL 4, 5 week (mouse)765600000126900000Mouse
13506750Tbthq2_mtrabecular bone thickness QTL 2 (mouse)76601000077900000Mouse
11553865Stmm1c_mskin tumor modifier of MSM 1c (mouse)766139778100139778Mouse
11553866Stmm1d_mskin tumor modifier of MSM 1d (mouse)766139778100139778Mouse
27095937Ulnl7_mulna length 7, 10 week (mouse)76680000098700000Mouse
12801463Rta1_mretinal aging 1 (mouse)76751827989440781Mouse
1301784Ses2_msalmonella enteritidis susceptibility 2 (mouse)Not determined767640886101641032Mouse
1301826Pgia3_mproteoglycan induced arthritis 3 (mouse)Not determined767640886101641032Mouse
1300620Pgia21_mproteoglycan induced arthritis 21 (mouse)Not determined767640886101641032Mouse
26884418Bzwq7_mbi-zygomatic width QTL 7, 10 week (mouse)768200000105800000Mouse
27226715Metcl3_mmetatarsal-calcaneal length 3, 5 week (mouse)768200000119900000Mouse
26884444Sklq8_mskull length QTL 8, 10 week (mouse)768200000124600000Mouse
26884451Sklq14_mskull length QTL 14, 16 week (mouse)768200000125400000Mouse
1300654Bomd1_mbone mineral density 1 (mouse)Not determined768716387102716494Mouse
27095907Scvln4_msacral vertebrae length 2, 5 week (mouse)770300000120900000Mouse
1301155Bpq7_mblood pressure QTL 7 (mouse)Not determined770493929104494171Mouse
10043973Obq29_mobesity QTL 29 (mouse)Not determined772614164106614164Mouse
4142319Powg_mpost-ovarectomy weight gain (mouse)Not determined7320735792932955Mouse
27095910Pglq13_mpelvic girdle length QTL 13, 16 week (mouse)773400000126100000Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2483
Count of miRNA genes:645
Interacting mature miRNAs:809
Transcripts:ENSMUST00000094312, ENSMUST00000119206, ENSMUST00000128471, ENSMUST00000139780
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000094312   ⟹   ENSMUSP00000091870
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl773,025,268 - 73,069,647 (+)Ensembl
GRCm38.p6 Ensembl773,375,520 - 73,419,899 (+)Ensembl
RefSeq Acc Id: ENSMUST00000119206   ⟹   ENSMUSP00000112599
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl773,025,257 - 73,069,647 (+)Ensembl
GRCm38.p6 Ensembl773,375,509 - 73,419,899 (+)Ensembl
RefSeq Acc Id: ENSMUST00000128471   ⟹   ENSMUSP00000116552
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl773,040,908 - 73,059,199 (+)Ensembl
GRCm38.p6 Ensembl773,391,160 - 73,409,451 (+)Ensembl
RefSeq Acc Id: ENSMUST00000139780   ⟹   ENSMUSP00000145758
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl773,040,975 - 73,069,647 (+)Ensembl
GRCm38.p6 Ensembl773,391,227 - 73,419,899 (+)Ensembl
RefSeq Acc Id: ENSMUST00000206253
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl773,041,024 - 73,042,995 (+)Ensembl
GRCm38.p6 Ensembl773,391,276 - 73,393,247 (+)Ensembl
RefSeq Acc Id: NM_177740   ⟹   NP_808408
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39773,025,268 - 73,069,647 (+)NCBI
GRCm38773,375,520 - 73,419,899 (+)ENTREZGENE
MGSCv37780,520,406 - 80,564,785 (+)RGD
Celera770,823,178 - 70,867,680 (+)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006540902   ⟹   XP_006540965
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39773,040,642 - 73,069,647 (+)NCBI
GRCm38773,390,894 - 73,419,899 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_808408   ⟸   NM_177740
- Peptide Label: precursor
- UniProtKB: Q6PCX7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006540965   ⟸   XM_006540902
- Peptide Label: isoform X1
- UniProtKB: Q6PCX7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000145758   ⟸   ENSMUST00000139780
RefSeq Acc Id: ENSMUSP00000112599   ⟸   ENSMUST00000119206
RefSeq Acc Id: ENSMUSP00000091870   ⟸   ENSMUST00000094312
RefSeq Acc Id: ENSMUSP00000116552   ⟸   ENSMUST00000128471
Protein Domains
RGM_C   RGM_N

Promoters
RGD ID:8664427
Promoter ID:EPDNEW_M10244
Type:initiation region
Name:Rgma_1
Description:Mus musculus repulsive guidance molecule family member A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M10246  EPDNEW_M10247  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38773,375,509 - 73,375,569EPDNEW
RGD ID:8664431
Promoter ID:EPDNEW_M10246
Type:single initiation site
Name:Rgma_3
Description:Mus musculus repulsive guidance molecule family member A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M10244  EPDNEW_M10247  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38773,389,456 - 73,389,516EPDNEW
RGD ID:8664433
Promoter ID:EPDNEW_M10247
Type:initiation region
Name:Rgma_2
Description:Mus musculus repulsive guidance molecule family member A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M10244  EPDNEW_M10246  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38773,391,277 - 73,391,337EPDNEW
RGD ID:6841916
Promoter ID:MM_KWN:51112
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   ES_Cell,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000077778,   OTTMUST00000077779
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36780,535,789 - 80,536,289 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2679262 AgrOrtholog
Ensembl Genes ENSMUSG00000070509 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000091870 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000112599 UniProtKB/TrEMBL
  ENSMUSP00000116552 UniProtKB/TrEMBL
  ENSMUSP00000145758 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000094312 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000119206 UniProtKB/TrEMBL
  ENSMUST00000128471 UniProtKB/TrEMBL
  ENSMUST00000139780 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro RGM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RGM_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RGM_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RGMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:244058 UniProtKB/Swiss-Prot
MGD MGI:2679262 ENTREZGENE
NCBI Gene 244058 ENTREZGENE
PANTHER PTHR31428 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR31428:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RGM_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RGM_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rgma PhenoGen
UniProt D3Z4W0_MOUSE UniProtKB/TrEMBL
  Q6PCX7 ENTREZGENE
  Q8C4C4_MOUSE UniProtKB/TrEMBL
  RGMA_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q7TQ34 UniProtKB/Swiss-Prot
  Q8CIH6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-12-03 Rgma  repulsive guidance molecule family member A    RGM domain family, member A  Symbol and/or name change 5135510 APPROVED