Sema6c (semaphorin 6C) - Rat Genome Database

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Gene: Sema6c (semaphorin 6C) Rattus norvegicus
Analyze
Symbol: Sema6c
Name: semaphorin 6C
RGD ID: 3659
Description: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in axon guidance. Predicted to be located in cell surface and cytoplasm. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6C (semaphorin 6C); INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: sema domain transmembrane domain (TM) and cytoplasmic domain (semaphorin) 6C; sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C; Sema Y; semaphorin-6C; semaphorin-Y
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
mRatBN7.22182,733,635 - 182,750,066 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2182,737,474 - 182,746,856 (+)Ensembl
Rnor_6.02196,330,777 - 196,347,218 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2196,334,626 - 196,344,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02215,827,260 - 215,843,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42190,069,489 - 190,078,845 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12190,032,242 - 190,041,599 (+)NCBI
Celera2175,271,228 - 175,280,584 (+)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:17145500  


Genomics

Comparative Map Data
Sema6c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22182,733,635 - 182,750,066 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2182,737,474 - 182,746,856 (+)Ensembl
Rnor_6.02196,330,777 - 196,347,218 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2196,334,626 - 196,344,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02215,827,260 - 215,843,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42190,069,489 - 190,078,845 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12190,032,242 - 190,041,599 (+)NCBI
Celera2175,271,228 - 175,280,584 (+)NCBICelera
Cytogenetic Map2q34NCBI
SEMA6C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381151,131,685 - 151,146,631 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1151,131,685 - 151,146,631 (-)EnsemblGRCh38hg38GRCh38
GRCh371151,104,183 - 151,119,107 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361149,370,785 - 149,385,728 (-)NCBINCBI36hg18NCBI36
Build 341147,917,234 - 147,932,177NCBI
Celera1124,219,448 - 124,234,432 (-)NCBI
Cytogenetic Map1q21.3NCBI
HuRef1122,481,473 - 122,496,449 (-)NCBIHuRef
CHM1_11152,499,488 - 152,514,467 (-)NCBICHM1_1
T2T-CHM13v2.01150,255,406 - 150,270,332 (-)NCBI
Sema6c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39395,067,731 - 95,081,361 (+)NCBIGRCm39mm39
GRCm39 Ensembl395,067,768 - 95,081,335 (+)Ensembl
GRCm38395,160,420 - 95,174,050 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl395,160,457 - 95,174,024 (+)EnsemblGRCm38mm10GRCm38
MGSCv37394,968,296 - 94,977,238 (+)NCBIGRCm37mm9NCBIm37
MGSCv36395,249,778 - 95,258,720 (+)NCBImm8
Celera396,595,452 - 96,604,393 (+)NCBICelera
Cytogenetic Map3F2.1NCBI
Sema6c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955588490,615 - 500,189 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955588490,581 - 504,436 (-)NCBIChiLan1.0ChiLan1.0
SEMA6C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11130,127,696 - 130,142,611 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1130,128,185 - 130,138,458 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01126,480,899 - 126,496,032 (-)NCBIMhudiblu_PPA_v0panPan3
SEMA6C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11760,195,798 - 60,208,630 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1760,195,785 - 60,208,630 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1759,638,597 - 59,652,183 (-)NCBI
ROS_Cfam_1.01761,211,121 - 61,224,719 (-)NCBI
ROS_Cfam_1.0 Ensembl1761,212,560 - 61,224,719 (-)Ensembl
UMICH_Zoey_3.11760,039,846 - 60,053,446 (-)NCBI
UNSW_CanFamBas_1.01760,125,203 - 60,138,789 (-)NCBI
UU_Cfam_GSD_1.01760,853,137 - 60,866,736 (-)NCBI
Sema6c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505822,303,469 - 22,316,961 (-)NCBI
SpeTri2.0NW_0049365801,331,950 - 1,347,327 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA6C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl498,107,391 - 98,122,348 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1498,107,316 - 98,121,464 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24107,360,109 - 107,374,242 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA6C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12012,542,234 - 12,557,041 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2012,546,281 - 12,560,674 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603812,122,909 - 12,137,660 (+)NCBIVero_WHO_p1.0
Sema6c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477218,707,744 - 18,720,731 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462477218,707,723 - 18,720,661 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2143657569184114274Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072185122374Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072185122374Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072185122374Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072185122374Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2152413072185122374Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168354880185122374Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2172710921184114403Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:46
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000028645, ENSRNOT00000050914
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 2 8 11 58 10 34 8
Low 3 43 55 39 19 39 16 24 7 11
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590806 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590807 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB000817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB014074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC117098 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF363971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000028645   ⟹   ENSRNOP00000028645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,737,474 - 182,746,835 (+)Ensembl
Rnor_6.0 Ensembl2196,334,626 - 196,343,987 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000050914   ⟹   ENSRNOP00000050221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,737,474 - 182,746,835 (+)Ensembl
Rnor_6.0 Ensembl2196,334,626 - 196,343,987 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090729   ⟹   ENSRNOP00000071511
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,737,479 - 182,746,856 (+)Ensembl
Rnor_6.0 Ensembl2196,334,631 - 196,344,008 (+)Ensembl
RefSeq Acc Id: NM_017308   ⟹   NP_059004
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,737,479 - 182,746,835 (+)NCBI
Rnor_6.02196,334,631 - 196,343,987 (+)NCBI
Rnor_5.02215,827,260 - 215,843,686 (+)NCBI
RGSC_v3.42190,069,489 - 190,078,845 (+)RGD
Celera2175,271,228 - 175,280,584 (+)RGD
Sequence:
RefSeq Acc Id: XM_006232858   ⟹   XP_006232920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Rnor_5.02215,827,260 - 215,843,686 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232861   ⟹   XP_006232923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Rnor_5.02215,827,260 - 215,843,686 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232869   ⟹   XP_006232931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,740,312 - 182,750,066 (+)NCBI
Rnor_6.02196,337,106 - 196,347,218 (+)NCBI
Rnor_5.02215,827,260 - 215,843,686 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761293   ⟹   XP_008759515
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590800   ⟹   XP_017446289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590802   ⟹   XP_017446291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590804   ⟹   XP_017446293
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590806   ⟹   XP_017446295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590807   ⟹   XP_017446296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590808   ⟹   XP_017446297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590809   ⟹   XP_017446298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Rnor_6.02196,330,777 - 196,347,218 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102126   ⟹   XP_038958054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
RefSeq Acc Id: XM_039102128   ⟹   XP_038958056
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
RefSeq Acc Id: XM_039102129   ⟹   XP_038958057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22182,733,635 - 182,750,066 (+)NCBI
Protein Sequences
Protein RefSeqs NP_059004 (Get FASTA)   NCBI Sequence Viewer  
  XP_006232920 (Get FASTA)   NCBI Sequence Viewer  
  XP_006232923 (Get FASTA)   NCBI Sequence Viewer  
  XP_006232931 (Get FASTA)   NCBI Sequence Viewer  
  XP_008759515 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446289 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446291 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446293 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446295 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446296 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446297 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446298 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958054 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958056 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958057 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL99669 (Get FASTA)   NCBI Sequence Viewer  
  BAA76293 (Get FASTA)   NCBI Sequence Viewer  
  BAA76295 (Get FASTA)   NCBI Sequence Viewer  
  EDL85733 (Get FASTA)   NCBI Sequence Viewer  
  EDL85734 (Get FASTA)   NCBI Sequence Viewer  
  EDL85735 (Get FASTA)   NCBI Sequence Viewer  
  EDL85736 (Get FASTA)   NCBI Sequence Viewer  
  EDL85737 (Get FASTA)   NCBI Sequence Viewer  
  EDL85738 (Get FASTA)   NCBI Sequence Viewer  
  EDL85739 (Get FASTA)   NCBI Sequence Viewer  
  EDL85740 (Get FASTA)   NCBI Sequence Viewer  
  EDL85741 (Get FASTA)   NCBI Sequence Viewer  
  EDL85742 (Get FASTA)   NCBI Sequence Viewer  
  EDL85743 (Get FASTA)   NCBI Sequence Viewer  
  EDL85744 (Get FASTA)   NCBI Sequence Viewer  
  EDL85745 (Get FASTA)   NCBI Sequence Viewer  
  EDL85746 (Get FASTA)   NCBI Sequence Viewer  
  EDL85747 (Get FASTA)   NCBI Sequence Viewer  
  Q9WTL3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_059004   ⟸   NM_017308
- Peptide Label: precursor
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006232920   ⟸   XM_006232858
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006232923   ⟸   XM_006232861
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006232931   ⟸   XM_006232869
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008759515   ⟸   XM_008761293
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446289   ⟸   XM_017590800
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446293   ⟸   XM_017590804
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446291   ⟸   XM_017590802
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446295   ⟸   XM_017590806
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446296   ⟸   XM_017590807
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446298   ⟸   XM_017590809
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017446297   ⟸   XM_017590808
- Peptide Label: isoform X1
- UniProtKB: Q9WTL3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028645   ⟸   ENSRNOT00000028645
RefSeq Acc Id: ENSRNOP00000071511   ⟸   ENSRNOT00000090729
RefSeq Acc Id: ENSRNOP00000050221   ⟸   ENSRNOT00000050914
RefSeq Acc Id: XP_038958057   ⟸   XM_039102129
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958054   ⟸   XM_039102126
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958056   ⟸   XM_039102128
- Peptide Label: isoform X1
Protein Domains
Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9WTL3-F1-model_v2 AlphaFold Q9WTL3 1-960 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)
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/NCrl (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
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)
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
LEXF11/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
M520/NRrrcMcwi (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
MR/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
MWF/Hsd (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
PVG/Seac (2019)
Visual CSV TAB Printer
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)
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
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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)
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
WKY/NCrl (2019)
Visual CSV TAB Printer
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3659 AgrOrtholog
BioCyc Gene G2FUF-52110 BioCyc
Ensembl Genes ENSRNOG00000021101 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028645 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000050221 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071511 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028645 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000050914 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000090729 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Semap_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semaphorin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semaphorin_6C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29744 UniProtKB/Swiss-Prot
NCBI Gene 29744 ENTREZGENE
PANTHER PTHR11036 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11036:SF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sema6c PhenoGen
PROSITE SEMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF101912 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC230022
UniProt Q8R4U4_RAT UniProtKB/TrEMBL
  Q9WTL3 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9WTM6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema6c  semaphorin 6C  Sema6c  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Sema6c  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C    semaphorin 6c  Name updated 1299863 APPROVED
2002-06-10 Sema6c  semaphorin 6c      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a class VI sema domain 69992
gene_transcript two alternative splicing forms exist that are regulated in a tissue- and age-dependent manner 69992