Sema6d (semaphorin 6D) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Sema6d (semaphorin 6D) Rattus norvegicus
Analyze
Symbol: Sema6d
Name: semaphorin 6D
RGD ID: 1310910
Description: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including negative regulation of axon extension involved in axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to act upstream of or within negative regulation of smooth muscle cell migration; positive regulation of smooth muscle cell migration; and ventricular system development. Predicted to be located in Golgi apparatus and cell surface. Predicted to be active in plasma membrane. Orthologous to human SEMA6D (semaphorin 6D); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83131,801,680 - 132,394,578 (+)NCBIGRCr8
mRatBN7.23111,883,415 - 111,941,100 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3115,741,529 - 115,798,821 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03124,337,085 - 124,394,381 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03121,997,462 - 122,054,751 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,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 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
antimycin A  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
azoxystrobin  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
clofibric acid  (EXP)
coumarin  (EXP)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenpyroximate  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
lead(0)  (ISO)
melphalan  (ISO)
methapyrilene  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phenylephrine  (EXP)
picoxystrobin  (ISO)
poly(I:C)  (EXP)
potassium chromate  (ISO)
propiconazole  (EXP)
pyrimidifen  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tebufenpyrad  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell surface  (ISO)
cytoplasm  (ISO)
Golgi apparatus  (IEA,ISO)
plasma membrane  (IBA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12110693   PMID:14977921   PMID:17145500   PMID:22880013   PMID:25931508   PMID:35757507  


Genomics

Comparative Map Data
Sema6d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83131,801,680 - 132,394,578 (+)NCBIGRCr8
mRatBN7.23111,883,415 - 111,941,100 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3115,741,529 - 115,798,821 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03124,337,085 - 124,394,381 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03121,997,462 - 122,054,751 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381547,184,089 - 47,774,228 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1547,184,101 - 47,774,228 (+)EnsemblGRCh38hg38GRCh38
GRCh371547,476,286 - 48,066,425 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361545,797,978 - 45,853,712 (+)NCBINCBI36Build 36hg18NCBI36
Celera1524,903,126 - 24,958,881 (+)NCBICelera
Cytogenetic Map15q21.1NCBI
HuRef1524,302,572 - 24,898,941 (+)NCBIHuRef
CHM1_11547,594,350 - 48,184,622 (+)NCBICHM1_1
T2T-CHM13v2.01544,992,008 - 45,582,270 (+)NCBIT2T-CHM13v2.0
Sema6d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392123,931,089 - 124,509,711 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2123,931,889 - 124,509,690 (+)EnsemblGRCm39 Ensembl
GRCm382124,089,943 - 124,667,789 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2124,089,969 - 124,667,770 (+)EnsemblGRCm38mm10GRCm38
MGSCv372124,436,032 - 124,493,506 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362124,301,737 - 124,359,211 (+)NCBIMGSCv36mm8
Celera2125,867,812 - 125,925,326 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map260.69NCBI
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
NHGRI_mPanPan1-v21636,429,165 - 37,017,139 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11540,606,996 - 41,198,548 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01526,135,344 - 26,725,571 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11544,877,322 - 45,050,169 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1544,994,073 - 45,050,169 (+)Ensemblpanpan1.1panPan2
SEMA6D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13013,489,896 - 14,059,623 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3014,005,124 - 14,057,202 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3013,809,483 - 13,981,345 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03014,020,140 - 14,192,698 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3014,136,625 - 14,192,698 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13014,061,291 - 14,115,720 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03014,060,041 - 14,231,809 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03014,170,816 - 14,342,932 (+)NCBIUU_Cfam_GSD_1.0
Sema6d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864091,663,555 - 92,243,636 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647110,077,222 - 10,089,286 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647110,036,279 - 10,091,699 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA6D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1123,987,528 - 124,043,986 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12635,511,593 - 36,095,816 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2635,511,594 - 35,526,130 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048105,001,970 - 105,583,476 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema6d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473111,914,422 - 11,970,138 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473111,914,530 - 12,269,463 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sema6d
300 total Variants
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.


QTLs in Region (mRatBN7.2)
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)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
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)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)396127817115665732Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3102200529115665732Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat

Markers in Region
D3Rat220  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23111,694,243 - 111,694,464 (+)MAPPERmRatBN7.2
Rnor_6.03116,715,770 - 116,715,990NCBIRnor6.0
Rnor_5.03123,240,660 - 123,240,880UniSTSRnor5.0
RGSC_v3.43111,606,319 - 111,606,540RGDRGSC3.4
RGSC_v3.43111,606,320 - 111,606,540UniSTSRGSC3.4
RGSC_v3.13111,511,893 - 111,512,113RGD
Celera3110,556,435 - 110,556,655UniSTS
RH 3.4 Map3979.3RGD
RH 3.4 Map3979.3UniSTS
RH 2.0 Map3629.6RGD
SHRSP x BN Map354.0398RGD
Cytogenetic Map3q35UniSTS
D15S1223  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23111,940,885 - 111,941,067 (+)MAPPERmRatBN7.2
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
mRatBN7.23111,793,910 - 111,794,095 (+)MAPPERmRatBN7.2
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
RH 3.4 Map3982.7UniSTS
Cytogenetic Map3q35UniSTS


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

Nucleotide Sequences
RefSeq Transcripts NM_001107768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066101   ⟹   ENSRNOP00000062577
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,090 (+)Ensembl
Rnor_6.0 Ensembl3116,899,906 - 116,958,050 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090802   ⟹   ENSRNOP00000070994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)Ensembl
Rnor_6.0 Ensembl3116,899,878 - 116,956,169 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098848   ⟹   ENSRNOP00000082908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,090 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102426   ⟹   ENSRNOP00000094338
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109949   ⟹   ENSRNOP00000093722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113650   ⟹   ENSRNOP00000083343
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3111,883,872 - 111,941,094 (+)Ensembl
RefSeq Acc Id: NM_001107768   ⟹   NP_001101238
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,337,356 - 132,394,571 (+)NCBI
mRatBN7.23111,883,872 - 111,941,090 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762172   ⟹   XP_008760394
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762174   ⟹   XP_008760396
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762175   ⟹   XP_008760397
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,489 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591743   ⟹   XP_017447232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591744   ⟹   XP_017447233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
Rnor_6.03116,939,488 - 116,958,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104982   ⟹   XP_038960910
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,337,262 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
RefSeq Acc Id: XM_039104983   ⟹   XP_038960911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
mRatBN7.23111,926,950 - 111,941,100 (+)NCBI
RefSeq Acc Id: XM_039104984   ⟹   XP_038960912
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,337,261 - 132,394,578 (+)NCBI
mRatBN7.23111,883,890 - 111,941,097 (+)NCBI
RefSeq Acc Id: XM_039104985   ⟹   XP_038960913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,336,893 - 132,394,578 (+)NCBI
mRatBN7.23111,883,415 - 111,941,097 (+)NCBI
RefSeq Acc Id: XM_063283739   ⟹   XP_063139809
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,337,262 - 132,394,578 (+)NCBI
RefSeq Acc Id: XM_063283741   ⟹   XP_063139811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83131,801,680 - 132,394,578 (+)NCBI
RefSeq Acc Id: XM_063283742   ⟹   XP_063139812
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
RefSeq Acc Id: XM_063283743   ⟹   XP_063139813
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,337,262 - 132,394,578 (+)NCBI
RefSeq Acc Id: XM_063283744   ⟹   XP_063139814
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,394,578 (+)NCBI
RefSeq Acc Id: XM_063283745   ⟹   XP_063139815
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83132,380,432 - 132,389,050 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001101238   ⟸   NM_001107768
- Peptide Label: precursor
- UniProtKB: D3ZDA2 (UniProtKB/TrEMBL),   A6HPV2 (UniProtKB/TrEMBL),   A0A8I5ZWU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760393   ⟸   XM_008762171
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JZC4 (UniProtKB/TrEMBL),   A0A8I6GKS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760394   ⟸   XM_008762172
- Peptide Label: isoform X4
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760396   ⟸   XM_008762174
- Peptide Label: isoform X11
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760397   ⟸   XM_008762175
- Peptide Label: isoform X13
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447232   ⟸   XM_017591743
- Peptide Label: isoform X10
- UniProtKB: A0A8I6AKL1 (UniProtKB/TrEMBL),   A0A8I5ZWU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447233   ⟸   XM_017591744
- Peptide Label: isoform X12
- UniProtKB: A0A8I5ZVU9 (UniProtKB/TrEMBL),   A0A8I5ZWU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070994   ⟸   ENSRNOT00000090802
RefSeq Acc Id: ENSRNOP00000062577   ⟸   ENSRNOT00000066101
RefSeq Acc Id: XP_038960913   ⟸   XM_039104985
- Peptide Label: isoform X6
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960912   ⟸   XM_039104984
- Peptide Label: isoform X6
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960910   ⟸   XM_039104982
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038960911   ⟸   XM_039104983
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GKS5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083343   ⟸   ENSRNOT00000113650
RefSeq Acc Id: ENSRNOP00000093722   ⟸   ENSRNOT00000109949
RefSeq Acc Id: ENSRNOP00000082908   ⟸   ENSRNOT00000098848
RefSeq Acc Id: ENSRNOP00000094338   ⟸   ENSRNOT00000102426
RefSeq Acc Id: XP_063139811   ⟸   XM_063283741
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063139809   ⟸   XM_063283739
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063139813   ⟸   XM_063283743
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063139812   ⟸   XM_063283742
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063139814   ⟸   XM_063283744
- Peptide Label: isoform X9
RefSeq Acc Id: XP_063139815   ⟸   XM_063283745
- Peptide Label: isoform X14
Protein Domains
Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZC4-F1-model_v2 AlphaFold A0A0G2JZC4 1-1069 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310910 AgrOrtholog
BioCyc Gene G2FUF-48067 BioCyc
Ensembl Genes ENSRNOG00000004812 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066101 ENTREZGENE
  ENSRNOT00000066101.2 UniProtKB/TrEMBL
  ENSRNOT00000090802.2 UniProtKB/TrEMBL
  ENSRNOT00000098848.1 UniProtKB/TrEMBL
  ENSRNOT00000102426.1 UniProtKB/TrEMBL
  ENSRNOT00000109949.1 UniProtKB/TrEMBL
  ENSRNOT00000113650.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  ligand-binding face of the semaphorins, domain 2 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
  SEMAPHORIN-6D UniProtKB/TrEMBL
Pfam PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PhenoGen Sema6d PhenoGen
PROSITE SEMA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004812 RatGTEx
SMART Sema UniProtKB/TrEMBL
Superfamily-SCOP Plexin repeat UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
UniProt A0A0G2JZC4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZVU9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZWU1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AKL1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GKS5 ENTREZGENE, UniProtKB/TrEMBL
  A6HPV2 ENTREZGENE, 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