Sema3f (semaphorin 3F) - Rat Genome Database

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Gene: Sema3f (semaphorin 3F) Rattus norvegicus
Analyze
Symbol: Sema3f
Name: semaphorin 3F
RGD ID: 1308514
Description: Predicted to have chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; regulation of postsynapse organization; and ventral trunk neural crest cell migration. Predicted to localize to extracellular space; glutamatergic synapse; and integral component of plasma membrane. Orthologous to human SEMA3F (semaphorin 3F); INTERACTS WITH (+)-schisandrin B; benzo[a]pyrene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F; SemaIV; semaphorin IV; semaphorin-3F
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
mRatBN7.28108,357,629 - 108,387,083 (-)NCBI
Rnor_6.0 Ensembl8116,437,696 - 116,469,915 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08116,439,996 - 116,469,915 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08115,795,106 - 115,824,684 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,932,112 - 112,962,333 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18112,951,566 - 112,982,883 (-)NCBI
Celera8107,663,870 - 107,693,466 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:9753685   PMID:11683995   PMID:12435358   PMID:15814794   PMID:15967098   PMID:16258027   PMID:16319111   PMID:17395160   PMID:18041777   PMID:18804103   PMID:19386662   PMID:20010807  
PMID:20298787   PMID:21724473   PMID:22790009   PMID:22977659   PMID:23063687   PMID:24006456   PMID:25143608   PMID:27309587  


Genomics

Comparative Map Data
Sema3f
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28108,357,629 - 108,387,083 (-)NCBI
Rnor_6.0 Ensembl8116,437,696 - 116,469,915 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08116,439,996 - 116,469,915 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08115,795,106 - 115,824,684 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48112,932,112 - 112,962,333 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18112,951,566 - 112,982,883 (-)NCBI
Celera8107,663,870 - 107,693,466 (-)NCBICelera
Cytogenetic Map8q32NCBI
SEMA3F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl350,155,045 - 50,189,075 (+)EnsemblGRCh38hg38GRCh38
GRCh38350,155,058 - 50,189,075 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37350,192,491 - 50,226,508 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36350,167,852 - 50,201,512 (+)NCBINCBI36hg18NCBI36
Build 34350,167,851 - 50,201,511NCBI
Celera350,165,676 - 50,199,339 (+)NCBI
Cytogenetic Map3p21.31NCBI
HuRef350,248,557 - 50,282,194 (+)NCBIHuRef
CHM1_1350,144,748 - 50,178,783 (+)NCBICHM1_1
Sema3f
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399107,558,698 - 107,587,674 (-)NCBIGRCm39mm39
GRCm39 Ensembl9107,558,699 - 107,587,674 (-)Ensembl
GRCm389107,681,499 - 107,710,475 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9107,681,500 - 107,710,475 (-)EnsemblGRCm38mm10GRCm38
MGSCv379107,583,833 - 107,612,806 (-)NCBIGRCm37mm9NCBIm37
MGSCv369107,539,603 - 107,568,576 (-)NCBImm8
Celera9107,287,142 - 107,316,223 (-)NCBICelera
Cytogenetic Map9F1NCBI
Sema3f
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555321,988,486 - 2,017,170 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555321,992,417 - 2,015,879 (+)NCBIChiLan1.0ChiLan1.0
SEMA3F
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1351,318,089 - 51,351,958 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl351,318,089 - 51,351,958 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0350,083,733 - 50,117,518 (+)NCBIMhudiblu_PPA_v0panPan3
SEMA3F
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12039,135,580 - 39,165,381 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2039,136,523 - 39,161,325 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2039,056,637 - 39,085,160 (-)NCBI
ROS_Cfam_1.02039,491,876 - 39,521,715 (-)NCBI
UMICH_Zoey_3.12038,859,427 - 38,889,253 (-)NCBI
UNSW_CanFamBas_1.02039,263,538 - 39,293,588 (-)NCBI
UU_Cfam_GSD_1.02039,543,271 - 39,573,112 (-)NCBI
Sema3f
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560264,944,032 - 64,972,968 (+)NCBI
SpeTri2.0NW_0049365291,704,523 - 1,733,465 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA3F
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1332,641,423 - 32,671,223 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11332,641,376 - 32,671,231 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21335,820,323 - 35,849,831 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA3F
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12211,540,958 - 11,574,888 (+)NCBI
ChlSab1.1 Ensembl2211,545,455 - 11,575,006 (+)Ensembl
Sema3f
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247304,035,909 - 4,064,796 (+)NCBI

Position Markers
RH133726  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,365,267 - 108,365,451 (+)MAPPER
Rnor_6.08116,447,635 - 116,447,818NCBIRnor6.0
Rnor_5.08115,802,745 - 115,802,928UniSTSRnor5.0
RGSC_v3.48112,939,750 - 112,939,933UniSTSRGSC3.4
Celera8107,671,615 - 107,671,798UniSTS
RH 3.4 Map81118.6UniSTS
Cytogenetic Map8q32UniSTS
D3S4520  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,360,547 - 108,360,820 (+)MAPPER
Rnor_6.08116,442,915 - 116,443,187NCBIRnor6.0
Rnor_5.08115,798,025 - 115,798,297UniSTSRnor5.0
RGSC_v3.48112,935,031 - 112,935,303UniSTSRGSC3.4
Celera8107,666,789 - 107,667,061UniSTS
Cytogenetic Map8q32UniSTS
D3S4519  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,360,799 - 108,361,413 (+)MAPPER
Rnor_6.08116,443,167 - 116,443,780NCBIRnor6.0
Rnor_5.08115,798,277 - 115,798,890UniSTSRnor5.0
RGSC_v3.48112,935,283 - 112,935,896UniSTSRGSC3.4
Celera8107,667,041 - 107,667,654UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8110212979116947981Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:370
Count of miRNA genes:209
Interacting mature miRNAs:243
Transcripts:ENSRNOT00000024193
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 4 4 4 47 20 31 11
Low 3 41 51 35 19 35 8 11 27 15 10 8
Below cutoff 2 2 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000024193   ⟹   ENSRNOP00000024193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8116,439,996 - 116,469,915 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085915   ⟹   ENSRNOP00000071565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8116,437,696 - 116,465,801 (-)Ensembl
RefSeq Acc Id: NM_001108185   ⟹   NP_001101655
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,357,629 - 108,387,083 (-)NCBI
Rnor_6.08116,439,996 - 116,469,915 (-)NCBI
Rnor_5.08115,795,106 - 115,824,684 (-)NCBI
RGSC_v3.48112,932,112 - 112,962,333 (-)RGD
Celera8107,663,870 - 107,693,466 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243778   ⟹   XP_006243840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,468,558 (-)NCBI
Rnor_5.08115,795,106 - 115,824,684 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766532   ⟹   XP_008764754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,469,320 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595691   ⟹   XP_017451180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,468,558 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595692   ⟹   XP_017451181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,469,302 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595693   ⟹   XP_017451182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,468,558 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595694   ⟹   XP_017451183
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,468,557 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595695   ⟹   XP_017451184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08116,439,996 - 116,449,938 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081588   ⟹   XP_038937516
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,357,629 - 108,386,170 (-)NCBI
RefSeq Acc Id: XM_039081589   ⟹   XP_038937517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,358,450 - 108,386,172 (-)NCBI
RefSeq Acc Id: XM_039081590   ⟹   XP_038937518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,358,450 - 108,386,170 (-)NCBI
RefSeq Acc Id: XM_039081591   ⟹   XP_038937519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,358,554 - 108,386,170 (-)NCBI
RefSeq Acc Id: XM_039081592   ⟹   XP_038937520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,357,629 - 108,367,563 (-)NCBI
RefSeq Acc Id: XM_039081593   ⟹   XP_038937521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,361,375 - 108,386,170 (-)NCBI
RefSeq Acc Id: XR_005487846
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,359,924 - 108,386,170 (-)NCBI
RefSeq Acc Id: XR_005487847
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,359,924 - 108,386,170 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101655   ⟸   NM_001108185
- Peptide Label: precursor
- UniProtKB: D3ZGX9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243840   ⟸   XM_006243778
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008764754   ⟸   XM_008766532
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017451181   ⟸   XM_017595692
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451182   ⟸   XM_017595693
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451180   ⟸   XM_017595691
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451183   ⟸   XM_017595694
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017451184   ⟸   XM_017595695
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000024193   ⟸   ENSRNOT00000024193
RefSeq Acc Id: ENSRNOP00000071565   ⟸   ENSRNOT00000085915
RefSeq Acc Id: XP_038937516   ⟸   XM_039081588
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038937520   ⟸   XM_039081592
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038937517   ⟸   XM_039081589
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937518   ⟸   XM_039081590
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937519   ⟸   XM_039081591
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038937521   ⟸   XM_039081593
- Peptide Label: isoform X5
Protein Domains
Ig-like   Sema

Transcriptome

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


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)
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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
Buf/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
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)
F344/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
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
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)
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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
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)
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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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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/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/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/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
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: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 115796197 115796198 G C snv ZF (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308514 AgrOrtholog
Ensembl Genes ENSRNOG00000017704 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024193 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071565 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024193 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085915 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
KEGG Report rno:315996 UniProtKB/TrEMBL
NCBI Gene 315996 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
Pfam Sema UniProtKB/TrEMBL
PhenoGen Sema3f PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  SEMA UniProtKB/TrEMBL
SMART IGc2 UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP Sema UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K0S6_RAT UniProtKB/TrEMBL
  D3ZGX9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema3f  semaphorin 3F  Sema3f  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema3f  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F   Sema3f_predicted  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema3f_predicted  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F (predicted)      Symbol and Name status set to approved 70820 APPROVED