Sema3c (semaphorin 3C) - Rat Genome Database

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Gene: Sema3c (semaphorin 3C) Rattus norvegicus
Analyze
Symbol: Sema3c
Name: semaphorin 3C
RGD ID: 1309343
Description: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including mesenchymal cell differentiation; negative regulation of axon extension involved in axon guidance; and outflow tract septum morphogenesis. Predicted to act upstream of or within several processes, including chordate embryonic development; circulatory system development; and dichotomous subdivision of terminal units involved in salivary gland branching. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA3C (semaphorin 3C); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC296787; MGC189535; sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C; semaphorin-3C
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
mRatBN7.2417,583,212 - 17,747,234 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl417,583,212 - 17,746,534 (-)Ensembl
Rnor_6.0414,318,276 - 14,490,438 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl414,318,274 - 14,490,446 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0414,315,785 - 14,464,552 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0414,293,370 - 14,301,988 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4413,739,659 - 13,914,636 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1413,742,156 - 13,940,776 (-)NCBI
Celera413,120,876 - 13,281,356 (-)NCBICelera
Cytogenetic Map4q11NCBI
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
(+)-schisandrin B  (EXP)
(-)-alpha-phellandrene  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-diaminotoluene  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
aconitine  (EXP)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-phellandrene  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arotinoid acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
CHIR 99021  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clorgyline  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
cortisol  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
dibenz[a,h]anthracene  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gentamycin  (EXP)
GW 4064  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
mercury dibromide  (ISO)
methapyrilene  (EXP)
microcystin-LR  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (EXP)
sirolimus  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
titanium dioxide  (ISO)
toxaphene  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
XAV939  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Identification of human semaphorin E gene expression in rheumatoid synovial cells by mRNA differential display. Mangasser-Stephan K, etal., Biochem Biophys Res Commun. 1997 May 8;234(1):153-6.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Increased prevalence of semaphorin 3C, a repellent of sympathetic nerve fibers, in the synovial tissue of patients with rheumatoid arthritis. Miller LE, etal., Arthritis Rheum. 2004 Apr;50(4):1156-63.
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11688556   PMID:12477932   PMID:15239958   PMID:17021275   PMID:17626059   PMID:18041777   PMID:18308469   PMID:19666519   PMID:23533145   PMID:23840631   PMID:24006456   PMID:26053665  


Genomics

Comparative Map Data
Sema3c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2417,583,212 - 17,747,234 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl417,583,212 - 17,746,534 (-)Ensembl
Rnor_6.0414,318,276 - 14,490,438 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl414,318,274 - 14,490,446 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0414,315,785 - 14,464,552 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0414,293,370 - 14,301,988 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4413,739,659 - 13,914,636 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1413,742,156 - 13,940,776 (-)NCBI
Celera413,120,876 - 13,281,356 (-)NCBICelera
Cytogenetic Map4q11NCBI
SEMA3C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38780,742,538 - 80,922,389 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl780,742,538 - 80,922,359 (-)EnsemblGRCh38hg38GRCh38
GRCh37780,371,854 - 80,551,705 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36780,209,790 - 80,386,603 (-)NCBINCBI36hg18NCBI36
Build 34780,016,505 - 80,193,318NCBI
Celera775,072,464 - 75,249,324 (-)NCBI
Cytogenetic Map7q21.11NCBI
HuRef774,974,724 - 75,151,804 (-)NCBIHuRef
CHM1_1780,302,304 - 80,479,089 (-)NCBICHM1_1
T2T-CHM13v2.0781,993,843 - 82,173,749 (-)NCBI
CRA_TCAGchr7v2779,703,271 - 79,880,104 (-)NCBI
Sema3c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39517,779,814 - 17,935,266 (+)NCBIGRCm39mm39
GRCm39 Ensembl517,779,279 - 17,935,266 (+)Ensembl
GRCm38517,574,816 - 17,730,268 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl517,574,281 - 17,730,268 (+)EnsemblGRCm38mm10GRCm38
MGSCv37517,080,634 - 17,236,086 (+)NCBIGRCm37mm9NCBIm37
MGSCv36517,086,640 - 17,242,092 (+)NCBImm8
Celera514,560,250 - 14,706,435 (+)NCBICelera
Cytogenetic Map5A3NCBI
Sema3c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554104,794,477 - 4,954,906 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554104,795,658 - 4,953,460 (+)NCBIChiLan1.0ChiLan1.0
SEMA3C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1786,369,036 - 86,545,580 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl786,368,753 - 86,545,580 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0772,706,615 - 72,884,163 (-)NCBIMhudiblu_PPA_v0panPan3
SEMA3C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11820,457,683 - 20,748,008 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1820,459,925 - 20,635,276 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1820,127,137 - 20,308,722 (-)NCBI
ROS_Cfam_1.01820,902,897 - 21,081,564 (-)NCBI
ROS_Cfam_1.0 Ensembl1820,902,900 - 21,079,854 (-)Ensembl
UMICH_Zoey_3.11820,529,290 - 20,710,735 (-)NCBI
UNSW_CanFamBas_1.01820,081,763 - 20,263,578 (-)NCBI
UU_Cfam_GSD_1.01820,737,406 - 20,919,731 (-)NCBI
Sema3c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511862,334,007 - 62,493,720 (-)NCBI
SpeTri2.0NW_004936810903,306 - 1,063,024 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA3C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl999,251,714 - 99,433,230 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1999,114,649 - 99,432,683 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29109,599,201 - 109,733,310 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA3C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12167,974,074 - 68,154,383 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2167,974,317 - 68,154,439 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604235,792,898 - 35,971,861 (-)NCBIVero_WHO_p1.0
Sema3c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473929,484,461 - 29,626,619 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473929,484,557 - 29,642,981 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134319  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2417,583,460 - 17,583,677 (+)MAPPERmRatBN7.2
Rnor_6.0414,318,525 - 14,318,741NCBIRnor6.0
Rnor_5.0414,293,619 - 14,293,835UniSTSRnor5.0
RGSC_v3.4413,739,908 - 13,740,124UniSTSRGSC3.4
Celera413,121,126 - 13,121,342UniSTS
Cytogenetic Map4q11UniSTS
RH138101  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2417,584,079 - 17,584,204 (+)MAPPERmRatBN7.2
Rnor_6.0414,319,144 - 14,319,268NCBIRnor6.0
Rnor_5.0414,438,283 - 14,438,407UniSTSRnor5.0
Rnor_5.0414,294,238 - 14,294,362UniSTSRnor5.0
RGSC_v3.4413,740,527 - 13,740,651UniSTSRGSC3.4
RGSC_v3.4413,887,628 - 13,887,752UniSTSRGSC3.4
Celera413,121,745 - 13,121,869UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:775
Count of miRNA genes:312
Interacting mature miRNAs:402
Transcripts:ENSRNOT00000009132
Prediction methods:Microtar, Miranda
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 37 7 2 2 2 8 10 60 34 38 11 8
Low 1 6 38 27 17 27 1 14 1 3
Below cutoff 12 12 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009132   ⟹   ENSRNOP00000009132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl417,583,212 - 17,746,521 (-)Ensembl
Rnor_6.0 Ensembl414,318,274 - 14,490,446 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102073   ⟹   ENSRNOP00000086874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl417,584,168 - 17,746,534 (-)Ensembl
RefSeq Acc Id: NM_001106578   ⟹   NP_001100048
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,583,212 - 17,744,401 (-)NCBI
Rnor_6.0414,318,276 - 14,488,225 (-)NCBI
Rnor_5.0414,293,370 - 14,301,988 (-)NCBI
Rnor_5.0414,315,785 - 14,464,552 (-)NCBI
RGSC_v3.4413,739,659 - 13,914,636 (-)RGD
Celera413,120,876 - 13,281,356 (-)RGD
Sequence:
RefSeq Acc Id: XM_008762645   ⟹   XP_008760867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,583,212 - 17,747,230 (-)NCBI
Rnor_6.0414,318,276 - 14,490,438 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762646   ⟹   XP_008760868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,583,212 - 17,747,234 (-)NCBI
Rnor_6.0414,318,276 - 14,490,436 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100048 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760867 (Get FASTA)   NCBI Sequence Viewer  
  XP_008760868 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI69108 (Get FASTA)   NCBI Sequence Viewer  
  EDL99454 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100048   ⟸   NM_001106578
- Peptide Label: precursor
- UniProtKB: B5DFL7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760867   ⟸   XM_008762645
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008760868   ⟸   XM_008762646
- Peptide Label: isoform X2
- UniProtKB: F7FHT4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009132   ⟸   ENSRNOT00000009132
RefSeq Acc Id: ENSRNOP00000086874   ⟸   ENSRNOT00000102073
Protein Domains
Ig-like   Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F7FHT4-F1-model_v2 AlphaFold F7FHT4 1-757 view protein structure

Transcriptome

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

Promoters
RGD ID:13692821
Promoter ID:EPDNEW_R3345
Type:initiation region
Name:Sema3c_1
Description:semaphorin 3C
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_6.0414,490,375 - 14,490,435EPDNEW

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)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 13808019 13808020 T C snv FHL/EurMcwi (MCW)
4 13808023 13808024 C A snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309343 AgrOrtholog
BioCyc Gene G2FUF-45912 BioCyc
Ensembl Genes ENSRNOG00000006526 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009132 ENTREZGENE
  ENSRNOP00000009132.6 UniProtKB/TrEMBL
  ENSRNOP00000086874 ENTREZGENE
  ENSRNOP00000086874.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009132 ENTREZGENE
  ENSRNOT00000009132.7 UniProtKB/TrEMBL
  ENSRNOT00000102073 ENTREZGENE
  ENSRNOT00000102073.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
KEGG Report rno:296787 UniProtKB/TrEMBL
NCBI Gene 296787 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
Pfam I-set UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PhenoGen Sema3c PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  SEMA UniProtKB/TrEMBL
SMART IGc2 UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP Sema UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6A4P5_RAT UniProtKB/TrEMBL
  B5DFL7 ENTREZGENE, UniProtKB/TrEMBL
  F7FHT4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema3c  semaphorin 3C  Sema3c  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema3c  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C   Sema3c_predicted  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema3c_predicted  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C (predicted)      Symbol and Name status set to approved 70820 APPROVED