Nsmf (NMDA receptor synaptonuclear signaling and neuronal migration factor) - Rat Genome Database
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Gene: Nsmf (NMDA receptor synaptonuclear signaling and neuronal migration factor) Rattus norvegicus
Analyze
Symbol: Nsmf
Name: NMDA receptor synaptonuclear signaling and neuronal migration factor
RGD ID: 619819
Description: Exhibits calcium-dependent protein binding activity. Involved in several processes, including cellular response to electrical stimulus; postsynapse to nucleus signaling pathway; and regulation of dendrite morphogenesis. Localizes to several cellular components, including dendrite; nucleus; and perikaryon. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 7 with or without anosmia and hypogonadotropic hypogonadism 9 with or without anosmia. Orthologous to human NSMF (NMDA receptor synaptonuclear signaling and neuronal migration factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 3,3',5-triiodo-L-thyronine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Jac; Jacob; juxtasynaptic attractor of caldendrin on dendritic boutons protein; MGC105348; nasal embryonic LHRH factor; nasal embryonic luteinizing hormone-releasing hormone factor; Nelf
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.032,262,173 - 2,270,996 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,262,253 - 2,270,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,243,484 - 2,252,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,201,581 - 5,210,256 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.135,201,580 - 5,210,256 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:19014935   PMID:19654008   PMID:20025934   PMID:23539133   PMID:25248434   PMID:26514267   PMID:29476059  


Genomics

Comparative Map Data
Nsmf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.032,262,173 - 2,270,996 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,262,253 - 2,270,995 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,243,484 - 2,252,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,201,581 - 5,210,256 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.135,201,580 - 5,210,256 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBICelera
Cytogenetic Map3p13NCBI
NSMF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9137,447,573 - 137,459,334 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl9137,447,570 - 137,459,334 (-)EnsemblGRCh38hg38GRCh38
GRCh389137,447,570 - 137,459,334 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379140,342,022 - 140,353,808 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,462,498 - 139,473,575 (-)NCBINCBI36hg18NCBI36
Build 349137,618,513 - 137,629,591NCBI
Celera9110,868,305 - 110,878,574 (-)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9109,806,039 - 109,817,921 (-)NCBIHuRef
CHM1_19140,490,446 - 140,501,310 (-)NCBICHM1_1
Nsmf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39224,944,370 - 24,952,893 (+)NCBIGRCm39mm39
GRCm38225,054,361 - 25,062,881 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,054,355 - 25,062,881 (+)EnsemblGRCm38mm10GRCm38
MGSCv37224,909,899 - 24,918,401 (+)NCBIGRCm37mm9NCBIm37
MGSCv36224,876,388 - 24,884,890 (+)NCBImm8
Celera224,781,465 - 24,789,967 (+)NCBICelera
Cytogenetic Map2A3NCBI
Nsmf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,369,218 - 5,375,670 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,368,384 - 5,376,480 (-)NCBIChiLan1.0ChiLan1.0
NSMF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19137,482,420 - 137,495,951 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,482,420 - 137,495,990 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09108,518,698 - 108,531,316 (-)NCBIMhudiblu_PPA_v0panPan3
NSMF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl948,287,014 - 48,294,780 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1948,287,019 - 48,295,540 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nsmf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936669606,392 - 614,748 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NSMF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21313,980,663 - 313,982,378 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NSMF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112734,863 - 744,214 (+)NCBI
ChlSab1.1 Ensembl12735,127 - 744,659 (+)Ensembl
Nsmf
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624760575,805 - 583,410 (+)NCBI

Position Markers
RH132853  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.032,264,445 - 2,264,646NCBIRnor6.0
Rnor_5.032,245,693 - 2,245,894UniSTSRnor5.0
RGSC_v3.435,203,705 - 5,203,906UniSTSRGSC3.4
Celera32,693,289 - 2,693,490UniSTS
Cytogenetic Map3p13UniSTS
RH132502  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.032,261,624 - 2,261,833NCBIRnor6.0
Rnor_5.032,242,872 - 2,243,081UniSTSRnor5.0
RGSC_v3.435,200,884 - 5,201,093UniSTSRGSC3.4
Celera32,690,468 - 2,690,677UniSTS
Cytogenetic Map3p13UniSTS
RH 3.4 Map1845.3UniSTS
UniSTS:224573  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.032,270,801 - 2,270,956NCBIRnor6.0
Rnor_5.032,252,049 - 2,252,204UniSTSRnor5.0
RGSC_v3.435,210,061 - 5,210,216UniSTSRGSC3.4
Celera32,699,645 - 2,699,800UniSTS
Cytogenetic Map3p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:897
Count of miRNA genes:199
Interacting mature miRNAs:251
Transcripts:ENSRNOT00000012129, ENSRNOT00000042100, ENSRNOT00000048137, ENSRNOT00000048353, ENSRNOT00000061303
Prediction methods:Microtar, 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


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 2 28 10 10 2 10 74 20 33 9
Low 1 15 47 31 17 31 8 11 15 8 2 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_057190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_073057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07051238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01020445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ293697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ293698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ293699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ534640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ534641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ534642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000012129   ⟹   ENSRNOP00000012129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,262,454 - 2,269,902 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042100   ⟹   ENSRNOP00000044714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,262,253 - 2,270,995 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000048137   ⟹   ENSRNOP00000045393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,262,454 - 2,269,902 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000048353   ⟹   ENSRNOP00000040572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,262,454 - 2,269,902 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000061303   ⟹   ENSRNOP00000058016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,262,321 - 2,270,743 (+)Ensembl
RefSeq Acc Id: NM_001270626   ⟹   NP_001257555
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,253 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270627   ⟹   NP_001257556
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,253 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270628   ⟹   NP_001257557
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,253 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBI
Sequence:
RefSeq Acc Id: NM_057190   ⟹   NP_476538
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,253 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
RGSC_v3.435,201,581 - 5,210,256 (+)RGD
Celera32,691,097 - 2,699,840 (+)NCBI
Sequence:
RefSeq Acc Id: NR_073057
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,253 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
Celera32,691,097 - 2,699,840 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233554   ⟹   XP_006233616
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,173 - 2,270,996 (+)NCBI
Rnor_5.032,243,484 - 2,252,244 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_476538   ⟸   NM_057190
- Peptide Label: isoform 1
- UniProtKB: Q9EPI6 (UniProtKB/Swiss-Prot),   D4AAJ2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257555   ⟸   NM_001270626
- Peptide Label: isoform 2
- UniProtKB: Q9EPI6 (UniProtKB/Swiss-Prot),   D4A9M2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257556   ⟸   NM_001270627
- Peptide Label: isoform 3
- UniProtKB: Q9EPI6 (UniProtKB/Swiss-Prot),   F1LLY3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257557   ⟸   NM_001270628
- Peptide Label: isoform 4
- UniProtKB: Q9EPI6 (UniProtKB/Swiss-Prot),   D3ZVR5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233616   ⟸   XM_006233554
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000045393   ⟸   ENSRNOT00000048137
RefSeq Acc Id: ENSRNOP00000012129   ⟸   ENSRNOT00000012129
RefSeq Acc Id: ENSRNOP00000058016   ⟸   ENSRNOT00000061303
RefSeq Acc Id: ENSRNOP00000040572   ⟸   ENSRNOT00000048353
RefSeq Acc Id: ENSRNOP00000044714   ⟸   ENSRNOT00000042100

Transcriptome

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

Promoters
RGD ID:13691857
Promoter ID:EPDNEW_R2381
Type:multiple initiation site
Name:Nsmf_1
Description:NMDA receptor synaptonuclear signaling and neuronal migrationfactor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,262,259 - 2,262,319EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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
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/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 (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)
Visual CSV TAB Printer
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)
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)
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
FHH/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)
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)
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)
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
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/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
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 (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
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
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 (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
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
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 (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 (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
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 (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 (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/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 (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
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 5208458 5208459 A G snv SHRSP/Gcrc (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619819 AgrOrtholog
Ensembl Genes ENSRNOG00000008810 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012129 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000040572 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000044714 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000045393 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000058016 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012129 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000042100 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000048137 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000048353 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000061303 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7318793 IMAGE-MGC_LOAD
InterPro NSMF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:117536 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105348 IMAGE-MGC_LOAD
NCBI Gene 117536 ENTREZGENE
PANTHER PTHR32061 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nsmf PhenoGen
UniGene Rn.7504 ENTREZGENE
UniProt A0A140TAI4_RAT UniProtKB/TrEMBL
  D3ZVR5 ENTREZGENE, UniProtKB/TrEMBL
  D4A9M2 ENTREZGENE, UniProtKB/TrEMBL
  D4AAJ2 ENTREZGENE, UniProtKB/TrEMBL
  F1LLY3 ENTREZGENE, UniProtKB/TrEMBL
  NSMF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5PPF6 UniProtKB/Swiss-Prot
  Q7TSC6 UniProtKB/Swiss-Prot
  Q7TSC8 UniProtKB/Swiss-Prot
  Q9EPI4 UniProtKB/Swiss-Prot
  Q9EPI5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-06 Nsmf  NMDA receptor synaptonuclear signaling and neuronal migration factor  Nelf  nasal embryonic LHRH factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Nelf  nasal embryonic LHRH factor      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Nelf  nasal embryonic LHRH factor      Symbol and Name status set to provisional 70820 PROVISIONAL