Sema5b (semaphorin 5B) - Rat Genome Database

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Gene: Sema5b (semaphorin 5B) Rattus norvegicus
Analyze
Symbol: Sema5b
Name: semaphorin 5B
RGD ID: 1308914
Description: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including axonogenesis; negative regulation of axon extension involved in axon guidance; and neural crest cell migration. Predicted to act upstream of or within detection of light stimulus involved in visual perception; neuron projection extension; and neuron projection guidance. Predicted to be integral component of membrane. Orthologous to human SEMA5B (semaphorin 5B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC303901; sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B; semaphorin-5B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21165,102,031 - 65,225,456 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1165,102,031 - 65,225,311 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1173,924,601 - 74,048,131 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01166,586,861 - 66,710,396 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01165,618,128 - 65,741,669 (-)NCBIRnor_WKY
Rnor_6.01168,304,844 - 68,435,109 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1168,306,659 - 68,349,238 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01171,394,318 - 71,522,385 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41166,944,881 - 67,070,820 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11167,003,918 - 67,047,091 (-)NCBI
Celera1164,564,164 - 64,686,394 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21835343  


Genomics

Comparative Map Data
Sema5b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21165,102,031 - 65,225,456 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1165,102,031 - 65,225,311 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1173,924,601 - 74,048,131 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01166,586,861 - 66,710,396 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01165,618,128 - 65,741,669 (-)NCBIRnor_WKY
Rnor_6.01168,304,844 - 68,435,109 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1168,306,659 - 68,349,238 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01171,394,318 - 71,522,385 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41166,944,881 - 67,070,820 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11167,003,918 - 67,047,091 (-)NCBI
Celera1164,564,164 - 64,686,394 (-)NCBICelera
Cytogenetic Map11q22NCBI
SEMA5B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383122,909,082 - 123,028,605 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3122,909,082 - 123,028,605 (-)EnsemblGRCh38hg38GRCh38
GRCh373122,627,929 - 122,747,452 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363124,110,733 - 124,229,266 (-)NCBINCBI36Build 36hg18NCBI36
Build 343124,110,732 - 124,230,142NCBI
Celera3121,038,150 - 121,153,367 (-)NCBICelera
Cytogenetic Map3q21.1NCBI
HuRef3120,001,447 - 120,120,673 (-)NCBIHuRef
CHM1_13122,591,693 - 122,711,128 (-)NCBICHM1_1
T2T-CHM13v2.03125,628,273 - 125,748,681 (-)NCBIT2T-CHM13v2.0
Sema5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391635,361,517 - 35,484,631 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1635,361,515 - 35,485,102 (+)EnsemblGRCm39 Ensembl
GRCm381635,541,154 - 35,664,261 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1635,541,145 - 35,664,732 (+)EnsemblGRCm38mm10GRCm38
MGSCv371635,541,448 - 35,664,344 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361635,461,318 - 35,583,448 (+)NCBIMGSCv36mm8
Celera1636,009,886 - 36,133,535 (+)NCBICelera
Cytogenetic Map16B3NCBI
Sema5b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542722,109,607 - 22,180,602 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542722,109,946 - 22,219,497 (-)NCBIChiLan1.0ChiLan1.0
SEMA5B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13126,900,966 - 127,020,453 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3126,900,966 - 126,986,186 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03119,996,933 - 120,116,899 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SEMA5B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13325,971,178 - 26,041,842 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3325,970,764 - 26,091,087 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3325,994,711 - 26,113,704 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03326,204,184 - 26,323,925 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3326,204,204 - 26,288,684 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13326,001,281 - 26,042,529 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03326,044,260 - 26,163,787 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03326,603,554 - 26,722,607 (-)NCBIUU_Cfam_GSD_1.0
Sema5b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602128,244,898 - 128,362,085 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367252,229,772 - 2,270,458 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA5B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13137,455,346 - 137,590,831 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113137,443,982 - 137,586,962 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213147,290,589 - 147,312,252 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA5B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12257,915,118 - 57,968,900 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2257,915,344 - 57,967,793 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041108,381,214 - 108,501,229 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema5b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249121,244,801 - 1,280,609 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249121,244,801 - 1,370,253 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
D11Rat95  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,223,112 - 65,223,335 (+)MAPPERmRatBN7.2
Rnor_6.01168,432,909 - 68,433,133NCBIRnor6.0
Rnor_5.01171,520,185 - 71,520,409UniSTSRnor5.0
RGSC_v3.41167,068,619 - 67,068,844RGDRGSC3.4
RGSC_v3.41167,068,620 - 67,068,844UniSTSRGSC3.4
RGSC_v3.11167,126,208 - 67,126,433RGD
Celera1164,684,197 - 64,684,422UniSTS
SHRSP x BN Map1129.8399RGD
SHRSP x BN Map1129.8399UniSTS
Cytogenetic Map11q22UniSTS
D11Got55  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,123,953 - 65,124,130 (+)MAPPERmRatBN7.2
Rnor_6.01168,328,812 - 68,328,988NCBIRnor6.0
Rnor_5.01171,416,429 - 71,416,605UniSTSRnor5.0
RGSC_v3.41166,969,009 - 66,969,186RGDRGSC3.4
RGSC_v3.41166,969,010 - 66,969,186UniSTSRGSC3.4
RGSC_v3.11167,026,599 - 67,026,775RGD
Celera1164,585,529 - 64,585,705UniSTS
RH 3.4 Map11452.5UniSTS
RH 3.4 Map11452.5RGD
RH 2.0 Map11172.5RGD
Cytogenetic Map11q22UniSTS
D11Got57  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,163,249 - 65,163,545 (+)MAPPERmRatBN7.2
Rnor_6.01168,368,056 - 68,368,351NCBIRnor6.0
Rnor_5.01171,455,565 - 71,455,860UniSTSRnor5.0
RGSC_v3.41167,008,299 - 67,008,595RGDRGSC3.4
RGSC_v3.41167,008,300 - 67,008,595UniSTSRGSC3.4
RGSC_v3.11167,065,889 - 67,066,184RGD
Celera1164,624,873 - 64,625,168UniSTS
RH 3.4 Map11458.3UniSTS
RH 3.4 Map11458.3RGD
RH 2.0 Map11181.3RGD
Cytogenetic Map11q22UniSTS
D16Mit211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,140,643 - 65,140,753 (+)MAPPERmRatBN7.2
Rnor_6.01168,345,460 - 68,345,571NCBIRnor6.0
Rnor_5.01171,433,077 - 71,433,188UniSTSRnor5.0
RGSC_v3.41166,985,721 - 66,985,832UniSTSRGSC3.4
Celera1164,602,257 - 64,602,368UniSTS
Cytogenetic Map11q22UniSTS
AI893641  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.41166,945,659 - 66,945,743UniSTSRGSC3.4
Celera1164,564,948 - 64,565,032UniSTS
Cytogenetic Map11q22UniSTS
BI290062  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,220,663 - 65,220,812 (+)MAPPERmRatBN7.2
Rnor_6.01168,430,460 - 68,430,608NCBIRnor6.0
Rnor_5.01171,517,736 - 71,517,884UniSTSRnor5.0
RGSC_v3.41167,066,171 - 67,066,319UniSTSRGSC3.4
Celera1164,681,748 - 64,681,896UniSTS
RH 3.4 Map11442.9UniSTS
Cytogenetic Map11q22UniSTS
AU048424  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21165,149,978 - 65,150,169 (+)MAPPERmRatBN7.2
Rnor_6.01168,354,798 - 68,354,988NCBIRnor6.0
Rnor_5.01171,442,415 - 71,442,605UniSTSRnor5.0
RGSC_v3.41166,995,062 - 66,995,252UniSTSRGSC3.4
Celera1164,611,597 - 64,611,787UniSTS
Cytogenetic Map11q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:110
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000030074
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 56 27
Low 40 11 2 3 2 2 5 18 34 14 10 2
Below cutoff 3 3 41 34 15 34 6 6 1 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030074   ⟹   ENSRNOP00000033170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1165,102,031 - 65,225,311 (-)Ensembl
Rnor_6.0 Ensembl1168,306,659 - 68,349,238 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095740   ⟹   ENSRNOP00000091837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1165,102,480 - 65,225,311 (-)Ensembl
RefSeq Acc Id: NM_001107091   ⟹   NP_001100561
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21165,102,031 - 65,225,311 (-)NCBI
Rnor_6.01168,304,844 - 68,435,109 (-)NCBI
Rnor_5.01171,394,318 - 71,522,385 (-)NCBI
RGSC_v3.41166,944,881 - 67,070,820 (-)RGD
Celera1164,564,164 - 64,686,394 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088339   ⟹   XP_038944267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21165,102,532 - 65,225,454 (-)NCBI
RefSeq Acc Id: XM_039088340   ⟹   XP_038944268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21165,102,532 - 65,225,455 (-)NCBI
RefSeq Acc Id: XM_039088341   ⟹   XP_038944269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21165,106,749 - 65,225,456 (-)NCBI
RefSeq Acc Id: XR_005491027
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21165,106,592 - 65,225,456 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100561   ⟸   NM_001107091
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000033170   ⟸   ENSRNOT00000030074
RefSeq Acc Id: XP_038944268   ⟸   XM_039088340
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944267   ⟸   XM_039088339
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944269   ⟸   XM_039088341
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000091837   ⟸   ENSRNOT00000095740
Protein Domains
Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEM7-F1-model_v2 AlphaFold D4AEM7 1-1092 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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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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
DA/OlaHsd (2019)
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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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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)
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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)
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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/Stm (2019)
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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)
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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
FXLE16/Stm (2020)
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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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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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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)
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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)
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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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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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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)
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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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)
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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)
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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)
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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)
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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 65115591 65115592 C T snv WKY/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308914 AgrOrtholog
BioCyc Gene G2FUF-21194 BioCyc
Ensembl Genes ENSRNOG00000002238 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000033170 ENTREZGENE
  ENSRNOP00000033170.7 UniProtKB/TrEMBL
  ENSRNOP00000091837 ENTREZGENE
  ENSRNOP00000091837.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030074 ENTREZGENE
  ENSRNOT00000030074.7 UniProtKB/TrEMBL
  ENSRNOT00000095740 ENTREZGENE
  ENSRNOT00000095740.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.20.100.10 UniProtKB/TrEMBL
InterPro Plexin-like_fold UniProtKB/TrEMBL
  Plexin_repeat UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
  Thrombospondin_1_rpt UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
NCBI Gene 303901 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
Pfam PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  TSP_1 UniProtKB/TrEMBL
PhenoGen Sema5b PhenoGen
PROSITE SEMA UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
SMART PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
Superfamily-SCOP Sema UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
UniProt A0A8I6AGW5_RAT UniProtKB/TrEMBL
  D4AEM7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema5b  semaphorin 5B  Sema5b  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema5b  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B   Sema5b_predicted  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema5b_predicted  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B (predicted)      Symbol and Name status set to approved 70820 APPROVED