Fmr1 (FMRP translational regulator 1) - Rat Genome Database

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Gene: Fmr1 (FMRP translational regulator 1) Rattus norvegicus
Analyze
Symbol: Fmr1
Name: FMRP translational regulator 1
RGD ID: 2623
Description: Enables several functions, including RNA binding activity; enzyme binding activity; and translation regulator activity. Involved in several processes, including modulation of chemical synaptic transmission; negative regulation of transport; and regulation of cellular protein metabolic process. Located in several cellular components, including dendrite; distal axon; and endoplasmic reticulum. Part of polysome. Is active in glutamatergic synapse and postsynaptic cytosol. Used to study autism spectrum disorder and fragile X syndrome. Biomarker of childhood onset epileptic encephalopathy; transient cerebral ischemia; and withdrawal disorder. Human ortholog(s) of this gene implicated in fragile X syndrome; fragile X-associated tremor/ataxia syndrome; and primary ovarian insufficiency 1. Orthologous to human FMR1 (FMRP translational regulator 1); INTERACTS WITH (S)-3,5-dihydroxyphenylglycine; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: FMRP; fragile X mental retardation 1; fragile X mental retardation protein 1 homolog; fragile X mental retardation syndrome 1 homolog; fragile X mental retardation-1 protein; protein FMR-1; ragile X mental retardation protein; synaptic functional regulator FMR1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Fmr1em2Mcwi   Fmr1em4Mcwi   Fmr1em1Sage   Fmr1em1Mzhe  
Genetic Models: SD-Fmr1em1Mzhe LE-Fmr1em2Mcwi SD-Fmr1em1Sage LE-Fmr1em4Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X147,240,239 - 147,278,057 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX147,240,301 - 147,278,050 (+)Ensembl
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX154,684,935 - 154,722,314 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,408,220 - 150,445,658 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X154,756,031 - 154,793,782 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X154,829,463 - 154,867,215 (+)NCBI
Celera1134,092,390 - 134,130,141 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-3,5-dihydroxyphenylglycine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-arachidonoylglycerol  (ISO)
2-methyl-6-(phenylethynyl)pyridine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
acamprosate  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aminomalonic acid  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
chrysene  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
D-glucitol  (ISO)
D-threitol  (ISO)
DDE  (EXP)
dibutyl phthalate  (EXP)
dimethyl sulfoxide  (ISO)
ebselen  (ISO)
epoxiconazole  (EXP)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
hydroxyl  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
linuron  (EXP)
menadione  (ISO)
methoxychlor  (ISO)
minocycline  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel sulfate  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenytoin  (EXP)
poly(I:C)  (ISO)
potassium chloride  (EXP)
potassium chromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
quercetin  (ISO)
resveratrol  (EXP)
rimonabant  (ISO)
superoxide  (ISO)
suramin  (ISO)
tamoxifen  (ISO)
tetrahydropalmatine  (ISO)
tetraphene  (ISO)
threitol  (ISO)
threonic acid  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
urethane  (ISO)
vigabatrin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterograde axonal transport  (ISO)
cellular response to DNA damage stimulus  (IEA,ISO,ISS)
cellular response to hydroxyurea  (ISO,ISS)
cellular response to monosodium glutamate  (IEP)
cellular response to potassium ion  (IEP)
cellular response to UV  (ISO,ISS)
cellular response to virus  (IEA,ISO)
central nervous system development  (ISO)
dendritic spine development  (ISO)
detection of mechanical stimulus involved in sensory perception  (IEP)
excitatory chemical synaptic transmission  (ISO)
gene silencing by RNA  (IEA)
glutamate receptor signaling pathway  (IDA,ISO)
inhibitory chemical synaptic transmission  (ISO)
modulation by host of viral RNA genome replication  (IEA,ISO)
mRNA processing  (IEA)
mRNA transport  (ISO,ISS)
negative regulation of cytoplasmic translation  (ISO,ISS)
negative regulation of gene expression  (IMP,ISO,ISS)
negative regulation of long-term synaptic depression  (ISO,ISS)
negative regulation of mRNA catabolic process  (IEA,ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of neuron differentiation  (IMP)
negative regulation of protein processing  (IMP)
negative regulation of receptor internalization  (IMP)
negative regulation of synaptic vesicle exocytosis  (IMP)
negative regulation of translation  (IBA,IEA,ISO,ISS)
negative regulation of translational initiation  (ISO,ISS)
negative regulation of voltage-gated calcium channel activity  (IMP)
nervous system development  (IEA)
ovarian follicle development  (IEP)
positive regulation of dendritic spine development  (ISO,ISS)
positive regulation of filopodium assembly  (ISO,ISS)
positive regulation of gene expression  (IMP)
positive regulation of gene silencing by miRNA  (IEA,ISO,ISS)
positive regulation of histone phosphorylation  (IEA,ISO,ISS)
positive regulation of intracellular transport of viral material  (IEA,ISO)
positive regulation of long-term neuronal synaptic plasticity  (IMP)
positive regulation of long-term synaptic depression  (IMP)
positive regulation of long-term synaptic potentiation  (IMP)
positive regulation of mRNA binding  (IEA,ISO,ISS)
positive regulation of proteasomal protein catabolic process  (ISO,ISS)
positive regulation of protein phosphorylation  (IBA,IMP)
positive regulation of receptor internalization  (IEA,ISO,ISS)
positive regulation of response to DNA damage stimulus  (IBA,IEA,ISO,ISS)
positive regulation of synaptic transmission  (IMP)
positive regulation of translation  (IBA,IEA,ISO,ISS)
regulation of alternative mRNA splicing, via spliceosome  (IBA,IEA,ISO,ISS)
regulation of dendritic spine development  (IEA,ISO,ISS)
regulation of filopodium assembly  (IBA,IEA,ISO,ISS)
regulation of gene silencing by miRNA  (ISO,ISS)
regulation of modification of synaptic structure  (ISO)
regulation of mRNA stability  (IBA,ISO,ISS)
regulation of neuronal action potential  (IEA,IMP,ISO,ISS)
regulation of neurotransmitter secretion  (IMP)
regulation of translation  (TAS)
regulation of translation at postsynapse, modulating synaptic transmission  (ISO)
regulation of translation at presynapse, modulating synaptic transmission  (IDA,IMP)
response to activity  (IEP)
response to cocaine  (IEP)
response to electrical stimulus  (IEP)
response to gonadotropin  (IEP)
response to interleukin-1  (IEP)
response to interleukin-17  (ISO)
response to light stimulus  (IEP)
RNA splicing  (IEA)
skeletal muscle organ development  (ISS)
social behavior  (ISO)

Cellular Component
axon  (IBA,IDA,ISO)
axon cytoplasm  (IEA)
axon terminus  (IDA)
Cajal body  (ISO)
cell body  (IDA)
cell projection  (ISO)
chromocenter  (ISO,ISS)
chromosome  (ISO,ISS)
chromosome, centromeric region  (IEA)
cytoplasm  (ISO)
cytoplasmic ribonucleoprotein granule  (IBA,IDA,ISO)
cytoplasmic stress granule  (IDA,IEA,ISO)
cytosol  (IDA,IEA,ISO)
dendrite  (IDA,ISO)
dendritic filopodium  (IBA,IDA,ISO)
dendritic spine  (IBA,IDA,IEA,ISO)
dendritic spine head  (IDA)
dendritic spine neck  (IBA,IDA)
extrinsic component of plasma membrane  (ISO,ISS)
filopodium tip  (IEA,ISO,ISS)
glial cell projection  (IDA)
glutamatergic synapse  (IDA,IMP,ISO)
growth cone  (IBA,IDA,IEA,ISO,ISS)
growth cone filopodium  (ISO,ISS)
hippocampal mossy fiber to CA3 synapse  (ISO)
membrane  (IBA)
messenger ribonucleoprotein complex  (IEA,ISO)
microtubule cytoskeleton  (IDA)
mRNA cap binding complex  (ISO,ISS)
neuron projection  (IDA,ISO)
neuronal cell body  (IBA,IDA)
neuronal ribonucleoprotein granule  (IDA,ISO)
nucleolus  (IEA,ISO,ISS)
nucleoplasm  (IDA,IEA,ISO,ISS)
nucleus  (IBA,IDA,ISO)
perikaryon  (IDA,IEA,ISO)
perinuclear region of cytoplasm  (IDA,IEA,ISO,ISS)
polysome  (IBA,IDA,IEA,ISO)
postsynapse  (ISO)
postsynaptic cytosol  (IDA)
postsynaptic density  (IBA,IDA)
presynapse  (IBA,ISO,ISS)
presynaptic cytosol  (ISO)
presynaptic membrane  (IEA)
proximal dendrite  (IDA)
ribonucleoprotein complex  (ISO)
rough endoplasmic reticulum  (IDA)
Schaffer collateral - CA1 synapse  (IDA,ISO)
SMN complex  (IEA,ISO,ISS)
smooth endoplasmic reticulum  (IDA)
spine apparatus  (IDA)
synapse  (ISO)
terminal bouton  (IDA)

References

References - curated
1. Antar LN, etal., Genes Brain Behav. 2005 Aug;4(6):350-9.
2. Antar LN, etal., J Neurosci 2004 Mar 17;24(11):2648-55.
3. Bernard PB, etal., Neurobiol Dis. 2013 Nov;59:1-17. doi: 10.1016/j.nbd.2013.06.013. Epub 2013 Jul 2.
4. Berzhanskaya J, etal., Sci Rep. 2016 Jul 28;6:30769. doi: 10.1038/srep30769.
5. Caffino L, etal., Neurotox Res. 2014 Oct;26(3):299-306. doi: 10.1007/s12640-014-9472-1. Epub 2014 May 9.
6. Davidovic L, etal., Hum Mol Genet. 2006 May 1;15(9):1525-38. Epub 2006 Mar 28.
7. Davidovic L, etal., Hum Mol Genet. 2007 Dec 15;16(24):3047-58. Epub 2007 Sep 19.
8. De Diego Otero Y, etal., Mol Cell Biol 2002 Dec;22(23):8332-41.
9. Dolzhanskaya N, etal., Brain Res. 2006 Sep 27;1112(1):56-64. Epub 2006 Aug 17.
10. Engineer CT, etal., Brain Res. 2014 May 20;1564:72-84. doi: 10.1016/j.brainres.2014.03.049. Epub 2014 Apr 5.
11. Feng Y, etal., J Neurosci. 1997 Mar 1;17(5):1539-47.
12. Ferder I, etal., Reproduction. 2013 Apr 15;145(4):335-43. doi: 10.1530/REP-12-0305. Print 2013 Apr.
13. Ferron L, etal., Nat Commun. 2014 Apr 7;5:3628. doi: 10.1038/ncomms4628.
14. Gabel LA, etal., J Neurosci. 2004 Nov 24;24(47):10579-83.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. GOA data from the GO Consortium
17. Golden CEM, etal., Cereb Cortex. 2019 May 1;29(5):2228-2244. doi: 10.1093/cercor/bhz029.
18. Hamilton SM, etal., Behav Neurosci. 2014 Apr;128(2):103-9. doi: 10.1037/a0035988.
19. Hmadcha A, etal., J Exp Med. 1999 Dec 6;190(11):1595-604.
20. Hoffman GE, etal., J Histochem Cytochem. 2012 Jun;60(6):439-56. doi: 10.1369/0022155412441002. Epub 2012 Apr 2.
21. Huber KM, etal., Proc Natl Acad Sci U S A. 2002 May 28;99(11):7746-50.
22. Irwin SA, etal., Neurobiol Learn Mem. 2000 Jul;74(1):87-93.
23. Jeon SJ, etal., Cell Mol Neurobiol. 2014 Mar;34(2):297-305. doi: 10.1007/s10571-013-0014-9. Epub 2013 Dec 12.
24. Jeon SJ, etal., J Neurochem. 2012 Oct;123(2):226-38. doi: 10.1111/j.1471-4159.2012.07886.x. Epub 2012 Aug 22.
25. Kaufmann WE, etal., Microsc Res Tech. 2002 May 1;57(3):135-44.
26. Kim SH, etal., J Neurosci. 2006 Mar 1;26(9):2413-8.
27. Kremer EJ, etal., Science. 1991 Jun 21;252(5013):1711-4.
28. MGD data from the GO Consortium
29. Milochau A, etal., FEBS Lett. 2014 Jun 27;588(14):2217-22. doi: 10.1016/j.febslet.2014.05.031. Epub 2014 May 29.
30. Nakamoto M, etal., Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15537-42. Epub 2007 Sep 19.
31. NCBI rat LocusLink and RefSeq merged data July 26, 2002
32. OMIM Disease Annotation Pipeline
33. Online Mendelian Inheritance in Man, OMIM (TM).
34. Panja D, etal., Cell Rep. 2014 Nov 20;9(4):1430-45. doi: 10.1016/j.celrep.2014.10.016. Epub 2014 Nov 6.
35. Price TJ, etal., Neuroscience. 2006 Sep 15;141(4):2107-16. Epub 2006 Jun 30.
36. RGD automated data pipeline
37. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
38. RGD automated import pipeline for gene-chemical interactions
39. Tian Y, etal., Front Mol Neurosci. 2017 Aug 28;10:269. doi: 10.3389/fnmol.2017.00269. eCollection 2017.
40. Todd PK, etal., Brain Res Mol Brain Res. 2003 Feb 20;110(2):267-78.
41. Valentine G, etal., Brain Res Mol Brain Res. 2000 Feb 22;75(2):337-41.
42. Van Dam D, etal., Behav Brain Res. 2005 Jul 30;162(2):233-9.
43. Wang H, etal., Hum Mol Genet. 2004 Jan 1;13(1):79-89. Epub 2003 Nov 12.
44. Weiler IJ, etal., Proc Natl Acad Sci U S A. 1997 May 13;94(10):5395-400.
Additional References at PubMed
PMID:7489725   PMID:7688265   PMID:8156595   PMID:9659908   PMID:10496225   PMID:11157796   PMID:11376146   PMID:11438589   PMID:12700164   PMID:12927206   PMID:15121898   PMID:15380484  
PMID:15381419   PMID:15805463   PMID:16055059   PMID:16631377   PMID:16790844   PMID:17057366   PMID:17254795   PMID:17417632   PMID:17850748   PMID:18093976   PMID:18539120   PMID:18614030  
PMID:18653529   PMID:18805096   PMID:18936162   PMID:19097999   PMID:19166269   PMID:19193898   PMID:19946888   PMID:20159450   PMID:21446998   PMID:21933836   PMID:22022532   PMID:22357842  
PMID:22658674   PMID:22681889   PMID:23235829   PMID:23509247   PMID:24204304   PMID:24349419   PMID:24514761   PMID:24658146   PMID:24813610   PMID:25225333   PMID:25464849   PMID:25561520  
PMID:26037301   PMID:26166728   PMID:26586091   PMID:26627310   PMID:27666021   PMID:30053369   PMID:30361391   PMID:30969437   PMID:31291981   PMID:31413325   PMID:32452512   PMID:32788572  
PMID:33139785  


Genomics

Comparative Map Data
Fmr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X147,240,239 - 147,278,057 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX147,240,301 - 147,278,050 (+)Ensembl
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX154,684,935 - 154,722,314 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,408,220 - 150,445,658 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X154,756,031 - 154,793,782 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X154,829,463 - 154,867,215 (+)NCBI
Celera1134,092,390 - 134,130,141 (-)NCBICelera
Cytogenetic MapXq37NCBI
FMR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX147,911,919 - 147,951,125 (+)EnsemblGRCh38hg38GRCh38
GRCh38X147,911,919 - 147,951,125 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X146,993,437 - 147,032,645 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X146,801,201 - 146,840,303 (+)NCBINCBI36hg18NCBI36
Build 34X146,699,054 - 146,738,157NCBI
CeleraX147,345,446 - 147,384,585 (+)NCBI
Cytogenetic MapXq27.3NCBI
HuRefX135,963,879 - 135,993,282 (+)NCBIHuRef
CHM1_1X146,904,323 - 146,943,501 (+)NCBICHM1_1
Fmr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X67,722,142 - 67,761,569 (+)NCBIGRCm39mm39
GRCm39 EnsemblX67,722,147 - 67,761,569 (+)Ensembl
GRCm38X68,678,536 - 68,717,963 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX68,678,541 - 68,717,963 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X65,931,730 - 65,971,138 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X51,835,932 - 51,875,340 (+)NCBImm8
MGSCv36X64,939,220 - 64,978,628 (+)NCBImm8
Cytogenetic MapXA7.1NCBI
cM MapX34.83NCBI
Fmr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955498566,688 - 595,360 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955498566,741 - 594,837 (+)NCBIChiLan1.0ChiLan1.0
FMR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X147,366,713 - 147,405,327 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX147,365,748 - 147,405,321 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X136,937,889 - 136,976,828 (+)NCBIMhudiblu_PPA_v0panPan3
FMR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X116,249,079 - 116,287,008 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX116,249,142 - 116,321,439 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX102,141,952 - 102,179,858 (+)NCBI
ROS_Cfam_1.0X118,308,237 - 118,346,144 (+)NCBI
UMICH_Zoey_3.1X115,421,122 - 115,459,027 (+)NCBI
UNSW_CanFamBas_1.0X117,632,687 - 117,670,590 (+)NCBI
UU_Cfam_GSD_1.0X117,359,050 - 117,396,958 (+)NCBI
Fmr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X114,286,773 - 114,324,847 (+)NCBI
SpeTri2.0NW_0049365131,290,038 - 1,327,850 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FMR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX120,361,229 - 120,399,835 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X120,361,232 - 120,400,282 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X137,792,642 - 137,831,753 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FMR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X122,635,383 - 122,674,298 (+)NCBI
ChlSab1.1X122,635,383 - 122,674,298 (+)NCBI
ChlSab1.1X122,635,383 - 122,674,298 (+)NCBI
ChlSab1.1X122,635,383 - 122,674,298 (+)NCBI
ChlSab1.1 EnsemblX122,635,439 - 122,674,355 (+)Ensembl
Vero_WHO_p1.0NW_02366606560,266,278 - 60,318,872 (+)NCBI
Fmr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624883645,524 - 681,705 (+)NCBI

Position Markers
L23971  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X147,276,203 - 147,276,383 (-)MAPPERmRatBN7.2
Rnor_6.0X154,686,598 - 154,686,777NCBIRnor6.0
Rnor_6.0X154,498,788 - 154,498,967NCBIRnor6.0
Rnor_5.01150,221,481 - 150,221,660UniSTSRnor5.0
Rnor_5.01150,409,894 - 150,410,073UniSTSRnor5.0
RGSC_v3.4X154,791,934 - 154,792,113UniSTSRGSC3.4
Celera1134,094,059 - 134,094,238UniSTS
Cytogenetic MapXq37UniSTS
GDB:342159  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X147,240,416 - 147,240,512 (-)MAPPERmRatBN7.2
Rnor_6.0X154,722,103 - 154,722,198NCBIRnor6.0
Rnor_5.01150,445,399 - 150,445,494UniSTSRnor5.0
RGSC_v3.4X154,756,147 - 154,756,242UniSTSRGSC3.4
Celera1134,129,930 - 134,130,025UniSTS
Cytogenetic MapXq37UniSTS
GDB:370773  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X147,258,915 - 147,259,237 (-)MAPPERmRatBN7.2
Rnor_6.0X154,703,378 - 154,703,699NCBIRnor6.0
Rnor_5.01150,426,674 - 150,426,995UniSTSRnor5.0
RGSC_v3.4X154,774,646 - 154,774,967UniSTSRGSC3.4
Celera1134,111,205 - 134,111,526UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat


Genetic Models
This gene Fmr1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:728
Count of miRNA genes:298
Interacting mature miRNAs:385
Transcripts:ENSRNOT00000016228
Prediction methods:Microtar, Miranda, 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


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 55 39 19 39 6 6 74 34 36 11 6
Low 9 2 2 2 2 5 1 5 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_052804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF435434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY224680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY240947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY630337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JX901083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MZ044289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U60145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000087893   ⟹   ENSRNOP00000074033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX147,240,301 - 147,278,046 (+)Ensembl
Rnor_6.0 EnsemblX154,684,935 - 154,722,314 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089743   ⟹   ENSRNOP00000071204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX147,240,408 - 147,278,050 (+)Ensembl
Rnor_6.0 EnsemblX154,684,938 - 154,722,220 (-)Ensembl
RefSeq Acc Id: NM_052804   ⟹   NP_434691
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,301 - 147,278,052 (+)NCBI
Rnor_6.0X154,684,929 - 154,722,314 (-)NCBI
Rnor_5.01150,408,220 - 150,445,658 (-)NCBI
RGSC_v3.4X154,756,031 - 154,793,782 (+)RGD
Celera1134,092,390 - 134,130,141 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229530   ⟹   XP_006229592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,240 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBI
Rnor_5.01150,408,220 - 150,445,658 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229531   ⟹   XP_006229593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,240 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBI
Rnor_5.01150,408,220 - 150,445,658 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229532   ⟹   XP_006229594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,241 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBI
Rnor_5.01150,408,220 - 150,445,658 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601917   ⟹   XP_017457406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,240 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601918   ⟹   XP_017457407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,241 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,368 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601919   ⟹   XP_017457408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,240 - 147,278,057 (+)NCBI
Rnor_6.0X154,684,924 - 154,722,369 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099491   ⟹   XP_038955419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X147,240,239 - 147,270,583 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_434691   ⟸   NM_052804
- UniProtKB: Q80WE1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006229593   ⟸   XM_006229531
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006229592   ⟸   XM_006229530
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229594   ⟸   XM_006229532
- Peptide Label: isoform X3
- UniProtKB: Q80WE1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017457406   ⟸   XM_017601917
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457408   ⟸   XM_017601919
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457407   ⟸   XM_017601918
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000074033   ⟸   ENSRNOT00000087893
RefSeq Acc Id: ENSRNOP00000071204   ⟸   ENSRNOT00000089743
RefSeq Acc Id: XP_038955419   ⟸   XM_039099491
- Peptide Label: isoform X7
Protein Domains
Agenet-like   FXMR_C2   FXMRP1_C_core   KH   Tudor_FRX1

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13702059
Promoter ID:EPDNEW_R12558
Type:multiple initiation site
Name:Fmr1_2
Description:fragile X mental retardation 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12559  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X154,722,256 - 154,722,316EPDNEW
RGD ID:13702037
Promoter ID:EPDNEW_R12559
Type:multiple initiation site
Name:Fmr1_1
Description:fragile X mental retardation 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12558  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X154,722,359 - 154,722,419EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2623 AgrOrtholog
Ensembl Genes ENSRNOG00000057464 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071204 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074033 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000087893 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000089743 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1370.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Agenet-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FMR1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FMRP_KH0 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FXMR_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FXMRP1_C_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom_type_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_dom_type_1_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tudor_FRX1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24948 UniProtKB/Swiss-Prot
NCBI Gene 24948 ENTREZGENE
PANTHER PTHR10603 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Agenet UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FXMR_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FXMRP1_C_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tudor_FRX1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fmr1 PhenoGen
PROSITE AGENET_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KH_TYPE_1 UniProtKB/Swiss-Prot
SMART SM00322 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54791 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A067XMK2_RAT UniProtKB/TrEMBL
  A0A067XMN7_RAT UniProtKB/TrEMBL
  A0A067XMS9_RAT UniProtKB/TrEMBL
  A0A067XMV0_RAT UniProtKB/TrEMBL
  A0A067XMV1_RAT UniProtKB/TrEMBL
  A0A067XNH0_RAT UniProtKB/TrEMBL
  A0A0G2JZV8 ENTREZGENE, UniProtKB/TrEMBL
  FMR1_RAT UniProtKB/Swiss-Prot
  Q6GWE1_RAT UniProtKB/TrEMBL
  Q80WE1 ENTREZGENE
UniProt Secondary P70568 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-29 Fmr1  fragile X mental retardation 1  Fmr1  fragile X mental retardation syndrome 1 homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Fmr1  Fragile X mental retardation 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog causes the fragile X mental retardation syndrome 628492
gene_domains contains RNA-binding motifs, two KH domains and an RGG box 628492
gene_expression ubiquitous; abundant in neurons and spermatogonia (testis) 628492
gene_function an RNA binding protein 628492
gene_physical_interaction associates with ribosomes and interacts with kinesin heavy chain and FXR1P 628492
gene_process plays a role in translation and trafficking of mRNAs 628492