Sema6d (semaphorin 6D) - Rat Genome Database
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Gene: Sema6d (semaphorin 6D) Rattus norvegicus
Analyze
Symbol: Sema6d
Name: semaphorin 6D
RGD ID: 1310910
Description: Predicted to have chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; neural crest cell migration; and regulation of smooth muscle cell migration. Predicted to localize to several cellular components, including Golgi apparatus; cell surface; and extracellular space. Orthologous to human SEMA6D (semaphorin 6D); INTERACTS WITH 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC311384; sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D; semaphorin-6D
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_6.03116,899,906 - 116,958,059 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3116,899,878 - 116,958,050 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03123,424,951 - 123,482,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43111,890,235 - 111,948,388 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13111,742,306 - 111,851,550 (+)NCBI
Celera3110,744,441 - 110,801,657 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
clofibric acid  (EXP)
coumarin  (EXP)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
melphalan  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
phenylephrine  (EXP)
poly(I:C)  (EXP)
potassium chromate  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

References

Additional References at PubMed
PMID:12110693   PMID:14977921   PMID:17145500   PMID:22880013   PMID:25931508  


Genomics

Comparative Map Data
Sema6d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03116,899,906 - 116,958,059 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3116,899,878 - 116,958,050 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03123,424,951 - 123,482,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43111,890,235 - 111,948,388 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13111,742,306 - 111,851,550 (+)NCBI
Celera3110,744,441 - 110,801,657 (+)NCBICelera
Cytogenetic Map3q36NCBI
SEMA6D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1547,184,101 - 47,774,223 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1547,184,101 - 47,774,228 (+)EnsemblGRCh38hg38GRCh38
GRCh381547,184,089 - 47,774,228 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371547,476,403 - 48,066,420 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361545,797,978 - 45,853,712 (+)NCBINCBI36hg18NCBI36
Celera1524,903,126 - 24,958,881 (+)NCBI
Cytogenetic Map15q21.1NCBI
HuRef1524,302,572 - 24,898,941 (+)NCBIHuRef
CHM1_11547,594,350 - 48,184,622 (+)NCBICHM1_1
Sema6d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392123,931,089 - 124,509,709 (+)NCBIGRCm39mm39
GRCm382124,089,943 - 124,667,789 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2124,089,969 - 124,667,770 (+)EnsemblGRCm38mm10GRCm38
MGSCv372124,436,032 - 124,493,506 (+)NCBIGRCm37mm9NCBIm37
MGSCv362124,301,737 - 124,359,211 (+)NCBImm8
Celera2125,867,812 - 125,925,326 (+)NCBICelera
Cytogenetic Map2F1NCBI
Sema6d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554096,086,113 - 6,143,713 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554096,086,178 - 6,143,702 (-)NCBIChiLan1.0ChiLan1.0
SEMA6D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11544,877,322 - 45,050,169 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1544,994,073 - 45,050,169 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01526,135,344 - 26,725,571 (+)NCBIMhudiblu_PPA_v0panPan3
SEMA6D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3014,005,124 - 14,057,202 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13013,489,896 - 14,059,623 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sema6d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647110,036,279 - 10,091,699 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA6D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1123,987,530 - 124,307,241 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11123,987,528 - 124,586,062 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21138,042,345 - 138,421,863 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA6D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12635,511,593 - 36,095,816 (-)NCBI
ChlSab1.1 Ensembl2635,511,594 - 35,526,130 (-)Ensembl
Sema6d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473111,914,530 - 12,269,463 (-)NCBI

Position Markers
D3Rat220  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03116,715,770 - 116,715,990NCBIRnor6.0
Rnor_5.03123,240,660 - 123,240,880UniSTSRnor5.0
RGSC_v3.43111,606,320 - 111,606,540UniSTSRGSC3.4
RGSC_v3.43111,606,319 - 111,606,540RGDRGSC3.4
RGSC_v3.13111,511,893 - 111,512,113RGD
Celera3110,556,435 - 110,556,655UniSTS
Cytogenetic Map3q35UniSTS
RH 3.4 Map3979.3RGD
RH 3.4 Map3979.3UniSTS
RH 2.0 Map3629.6RGD
SHRSP x BN Map354.0398RGD
D15S1223  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03116,957,846 - 116,958,027NCBIRnor6.0
Rnor_5.03123,482,578 - 123,482,759UniSTSRnor5.0
RGSC_v3.43111,948,184 - 111,948,365UniSTSRGSC3.4
Celera3110,801,453 - 110,801,634UniSTS
Cytogenetic Map3q35UniSTS
BF393068  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03116,815,525 - 116,815,709NCBIRnor6.0
Rnor_5.03123,340,691 - 123,340,875UniSTSRnor5.0
RGSC_v3.43111,796,901 - 111,797,085UniSTSRGSC3.4
Celera3110,656,172 - 110,656,356UniSTS
Cytogenetic Map3q35UniSTS
RH 3.4 Map3982.7UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)354630948119830094Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)366711607119830094Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)366711607119830094Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)383817637119509260Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3100730984119830094Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3106900427119830094Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:346
Count of miRNA genes:189
Interacting mature miRNAs:255
Transcripts:ENSRNOT00000066101
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 31 9 6 11 6 1 1 74 26 34 11 1
Low 2 12 48 35 8 35 7 10 9 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066101   ⟹   ENSRNOP00000062577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3116,899,906 - 116,958,050 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090802   ⟹   ENSRNOP00000070994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3116,899,878 - 116,956,169 (+)Ensembl
RefSeq Acc Id: NM_001107768   ⟹   NP_001101238
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,899,906 - 116,958,050 (+)NCBI
Rnor_5.03123,424,951 - 123,482,791 (+)NCBI
RGSC_v3.43111,890,235 - 111,948,388 (+)RGD
Celera3110,744,441 - 110,801,657 (+)RGD
Sequence:
RefSeq Acc Id: XM_008762171   ⟹   XP_008760393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762172   ⟹   XP_008760394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762173   ⟹   XP_008760395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762174   ⟹   XP_008760396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762175   ⟹   XP_008760397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,489 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591743   ⟹   XP_017447232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591744   ⟹   XP_017447233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001101238   ⟸   NM_001107768
- Peptide Label: precursor
- UniProtKB: D3ZDA2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760393   ⟸   XM_008762171
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008760394   ⟸   XM_008762172
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008760396   ⟸   XM_008762174
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008760395   ⟸   XM_008762173
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008760397   ⟸   XM_008762175
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017447232   ⟸   XM_017591743
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017447233   ⟸   XM_017591744
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000070994   ⟸   ENSRNOT00000090802
RefSeq Acc Id: ENSRNOP00000062577   ⟸   ENSRNOT00000066101
Protein Domains
Sema

Transcriptome

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

Promoters
RGD ID:13692376
Promoter ID:EPDNEW_R2900
Type:initiation region
Name:Sema6d_1
Description:semaphorin 6D
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_6.03116,899,908 - 116,899,968EPDNEW

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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 116955407 116955408 G A snv GH/OmrMcwi (MCW), WAG/Rij (RGD), BBDP/Wor (RGD), WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310910 AgrOrtholog
Ensembl Genes ENSRNOG00000004812 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062577 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070994 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066101 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090802 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro Plexin_repeat UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
KEGG Report rno:311384 UniProtKB/TrEMBL
NCBI Gene 311384 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
Pfam PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PhenoGen Sema6d PhenoGen
PROSITE SEMA UniProtKB/TrEMBL
SMART Sema UniProtKB/TrEMBL
Superfamily-SCOP Sema UniProtKB/TrEMBL
UniGene Rn.8257 ENTREZGENE
UniProt A0A0G2JZC4_RAT UniProtKB/TrEMBL
  D3ZDA2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema6d  semaphorin 6D  Sema6d  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema6d  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D   Sema6d_predicted  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema6d_predicted  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D (predicted)      Symbol and Name status set to approved 70820 APPROVED