Sema3a (semaphorin 3A) - Rat Genome Database

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Gene: Sema3a (semaphorin 3A) Rattus norvegicus
Analyze
Symbol: Sema3a
Name: semaphorin 3A
RGD ID: 3657
Description: Predicted to enable chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in negative regulation of axon extension. Acts upstream of or within axon guidance. Located in axon and dendrite. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: sema domain immunoglobulin domain (Ig) short basic domain secreted (semaphorin) 3A; sema domain, immunoglobulin domain (Ig), short basic domain, sec; sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A; sema III; semaphorin III; semaphorin-3A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8422,239,418 - 22,709,907 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl422,245,322 - 22,535,774 (-)EnsemblGRCr8
mRatBN7.2421,282,398 - 21,754,834 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl421,287,982 - 21,494,432 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx426,307,920 - 26,512,008 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0422,234,070 - 22,438,148 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0420,607,687 - 20,811,763 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0418,170,375 - 18,545,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl418,178,656 - 18,396,035 (-)Ensemblrn6Rnor6.0
Rnor_5.0418,133,300 - 18,444,520 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4417,575,112 - 17,790,100 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera416,810,716 - 17,013,648 (-)NCBICelera
RGSC_v3.1417,575,111 - 17,790,100 (-)NCBI
Cytogenetic Map4q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,4'-trichlorobiphenyl  (ISO)
2-hydroxypropanoic acid  (ISO)
2-palmitoylglycerol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acetic acid  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
alpha-amanitin  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (EXP,ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (EXP)
diquat  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
Evodiamine  (ISO)
fentanyl  (EXP)
ferric oxide  (EXP)
ferrostatin-1  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
glucose  (ISO)
hexaconazole  (ISO)
ketoconazole  (EXP)
lipopolysaccharide  (ISO)
medroxyprogesterone acetate  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (EXP)
okadaic acid  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
PCB138  (ISO)
PD 0325901  (ISO)
potassium chromate  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
sirolimus  (EXP,ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon extension involved in axon guidance  (ISO)
axon guidance  (IEA,IGI,ISO)
axonal fasciculation  (ISO)
axonogenesis involved in innervation  (ISO)
basal dendrite arborization  (ISO)
branchiomotor neuron axon guidance  (ISO)
cell differentiation  (IEA)
dendrite morphogenesis  (ISO)
dichotomous subdivision of terminal units involved in salivary gland branching  (ISO)
facial nerve structural organization  (ISO)
facioacoustic ganglion development  (ISO)
gonadotrophin-releasing hormone neuronal migration to the hypothalamus  (ISO)
maintenance of synapse structure  (ISO)
motor neuron axon guidance  (IBA,ISO)
negative chemotaxis  (IBA,ISO)
negative regulation of axon extension  (IDA,ISO)
negative regulation of axon extension involved in axon guidance  (ISO)
negative regulation of developmental process  (IEA)
negative regulation of epithelial cell migration  (ISO)
negative regulation of multicellular organismal process  (IEA)
negative regulation of neuron projection development  (IEA,ISO)
nerve development  (ISO)
nervous system development  (IEA,ISO)
neural crest cell migration  (IBA)
neural crest cell migration involved in autonomic nervous system development  (ISO)
neural crest cell migration involved in sympathetic nervous system development  (ISO)
neuron migration  (ISO)
olfactory bulb development  (IEA,ISO,ISS)
positive regulation of cell migration  (IBA)
positive regulation of male gonad development  (ISO)
positive regulation of neuron migration  (ISO)
regulation of anatomical structure morphogenesis  (IEA)
regulation of axon extension involved in axon guidance  (IEA,ISO)
regulation of heart rate  (ISO)
regulation of multicellular organismal development  (IEA)
regulation of plasma membrane bounded cell projection organization  (IEA)
semaphorin-plexin signaling pathway  (IBA,ISO)
sympathetic ganglion development  (ISO)
sympathetic neuron projection extension  (ISO)
sympathetic neuron projection guidance  (ISO)
synaptic target recognition  (ISO)
trigeminal ganglion development  (ISO)
trigeminal nerve structural organization  (ISO)
ventral trunk neural crest cell migration  (ISO)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Flotillin-mediated endocytic events dictate cell type-specific responses to semaphorin 3A. Carcea I, etal., J Neurosci. 2010 Nov 10;30(45):15317-29. doi: 10.1523/JNEUROSCI.1821-10.2010.
2. Semaphorin 3A displays a punctate distribution on the surface of neuronal cells and interacts with proteoglycans in the extracellular matrix. De Wit J, etal., Mol Cell Neurosci. 2005 May;29(1):40-55.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Growth cone collapse induced by semaphorin 3A requires 12/15-lipoxygenase. Mikule K, etal., J Neurosci 2002 Jun 15;22(12):4932-41.
7. Involvement of Fes/Fps tyrosine kinase in semaphorin3A signaling. Mitsui N, etal., EMBO J 2002 Jul 1;21(13):3274-85.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Class 3 semaphorins control vascular morphogenesis by inhibiting integrin function. Serini G, etal., Nature. 2003 Jul 24;424(6947):391-7.
14. Anti-semaphorin 3A antibodies rescue retinal ganglion cells from cell death following optic nerve axotomy. Shirvan A, etal., J Biol Chem 2002 Dec 20;277(51):49799-807.
15. Evidence that Sema3A and Sema3F regulate the migration of GABAergic neurons in the developing neocortex. Tamamaki N, etal., J Comp Neurol 2003 Jan 6;455(2):238-48.
Additional References at PubMed
PMID:7748561   PMID:8915837   PMID:9753685   PMID:11683995   PMID:12372285   PMID:12435358   PMID:12591607   PMID:12821384   PMID:12852851   PMID:14727128   PMID:14749426   PMID:14755522  
PMID:15094469   PMID:15155748   PMID:15239958   PMID:15604101   PMID:15814794   PMID:15869472   PMID:16217616   PMID:16467521   PMID:16677822   PMID:16906543   PMID:17417650   PMID:17428830  
PMID:17626059   PMID:18041777   PMID:18053124   PMID:18059265   PMID:18356247   PMID:18550718   PMID:18804103   PMID:18815803   PMID:19325129   PMID:19386662   PMID:19515904   PMID:19652227  
PMID:19855168   PMID:20298787   PMID:20331965   PMID:21059704   PMID:21593320   PMID:21828096   PMID:21835341   PMID:21865583   PMID:21933622   PMID:22416012   PMID:22683681   PMID:22790009  
PMID:22997549   PMID:23049211   PMID:23085379   PMID:23139269   PMID:23711091   PMID:23766263   PMID:23940048   PMID:24006456   PMID:24599038   PMID:24899721   PMID:25161316   PMID:25843720  
PMID:26638837   PMID:26787044   PMID:26950444   PMID:27143756   PMID:27787858   PMID:27787862   PMID:29203371   PMID:29457037   PMID:29774455   PMID:29940213   PMID:30747413   PMID:30816586  
PMID:31078154   PMID:31251980   PMID:31814697   PMID:32242249   PMID:33566267   PMID:37128697   PMID:37864189   PMID:38430015  


Genomics

Comparative Map Data
Sema3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8422,239,418 - 22,709,907 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl422,245,322 - 22,535,774 (-)EnsemblGRCr8
mRatBN7.2421,282,398 - 21,754,834 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl421,287,982 - 21,494,432 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx426,307,920 - 26,512,008 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0422,234,070 - 22,438,148 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0420,607,687 - 20,811,763 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0418,170,375 - 18,545,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl418,178,656 - 18,396,035 (-)Ensemblrn6Rnor6.0
Rnor_5.0418,133,300 - 18,444,520 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4417,575,112 - 17,790,100 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera416,810,716 - 17,013,648 (-)NCBICelera
RGSC_v3.1417,575,111 - 17,790,100 (-)NCBI
Cytogenetic Map4q12NCBI
SEMA3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38783,955,777 - 84,492,725 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl783,955,777 - 84,492,939 (-)Ensemblhg38GRCh38
GRCh37783,585,093 - 83,824,105 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36783,425,595 - 83,662,153 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34783,235,140 - 83,468,560NCBI
Celera778,289,042 - 78,525,324 (-)NCBICelera
Cytogenetic Map7q21.11NCBI
HuRef778,196,709 - 78,433,239 (-)NCBIHuRef
CHM1_1783,517,590 - 83,754,442 (-)NCBICHM1_1
T2T-CHM13v2.0785,206,156 - 85,764,887 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2782,919,781 - 83,156,009 (-)NCBI
Sema3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39513,174,789 - 13,653,453 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl513,175,381 - 13,652,533 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38513,124,822 - 13,603,485 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl513,125,414 - 13,602,565 (+)Ensemblmm10GRCm38
MGSCv37513,399,309 - 13,602,571 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36513,405,315 - 13,608,571 (+)NCBIMGSCv36mm8
Celera1223,770,632 - 23,979,473 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map54.31NCBI
Sema3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554102,144,388 - 2,338,973 (+)Ensembl
ChiLan1.0NW_0049554102,146,088 - 2,344,342 (+)NCBIChiLan1.0ChiLan1.0
SEMA3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26101,817,901 - 102,371,663 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17150,082,605 - 150,636,262 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0775,929,699 - 76,484,246 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1789,590,353 - 89,827,253 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl789,590,359 - 90,004,122 (-)EnsemblpanPan2panpan1.1
SEMA3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11823,411,607 - 23,866,631 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1823,414,576 - 23,867,098 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1823,096,760 - 23,551,325 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01823,872,684 - 24,326,815 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1823,872,709 - 24,071,806 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11823,522,022 - 23,975,809 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01823,035,644 - 23,490,231 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01823,702,159 - 24,157,050 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
SEMA3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl996,181,770 - 96,387,950 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1995,934,937 - 96,387,950 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SEMA3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12164,723,860 - 64,942,705 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2164,784,039 - 64,939,682 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604239,053,607 - 39,576,492 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473932,105,824 - 32,309,271 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473932,104,014 - 32,426,980 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Sema3a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v16144,021,609 - 144,219,712 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sema3a
3191 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:34
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000034692
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)41308014658080146Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41564430960644309Rat
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)4132668025Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4128392287Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4132668025Rat
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)41103870656038706Rat
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)4134142783Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4134142783Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41103870656038706Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42228845340471598Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4589457557613242Rat
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)41103870656038706Rat
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)41170660492690519Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4131106810Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41890069763900697Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4128392287Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4145429897Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41103870656038706Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4132668025Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42228845363245191Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)41890069763900697Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41103870656038706Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4128392287Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4140471598Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4842855130449094Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4588999950889999Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41891315163913151Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4133538816Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42192515166925151Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)4163900697Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41103870656038706Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4132668025Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42228845345429897Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41075870140490708Rat

Markers in Region
D4Mgh1  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8422,288,453 - 22,288,599 (+)Marker Load Pipeline
mRatBN7.2421,333,343 - 21,333,491 (+)MAPPERmRatBN7.2
Rnor_6.0418,222,187 - 18,222,332NCBIRnor6.0
Rnor_5.0418,184,531 - 18,184,676UniSTSRnor5.0
RGSC_v3.4417,617,956 - 17,618,102RGDRGSC3.4
RGSC_v3.4417,617,957 - 17,618,102UniSTSRGSC3.4
Celera416,853,169 - 16,853,313UniSTS
RGSC_v3.1417,617,956 - 17,618,102RGD
RH 3.4 Map4588.2RGD
RH 3.4 Map4588.2UniSTS
Cytogenetic Map4q12UniSTS
RH69031  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2421,290,898 - 21,291,112 (+)MAPPERmRatBN7.2
Rnor_6.0418,178,878 - 18,179,091NCBIRnor6.0
Rnor_5.0418,141,803 - 18,142,016UniSTSRnor5.0
RGSC_v3.4417,575,136 - 17,575,349UniSTSRGSC3.4
Celera416,810,740 - 16,810,953UniSTS
Cytogenetic Map4q12UniSTS
UniSTS:224589  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2421,493,449 - 21,493,575 (+)MAPPERmRatBN7.2
Rnor_6.0418,395,341 - 18,395,466NCBIRnor6.0
Rnor_5.0418,354,718 - 18,354,843UniSTSRnor5.0
RGSC_v3.4417,790,276 - 17,790,401UniSTSRGSC3.4
Celera417,013,824 - 17,013,949UniSTS
Cytogenetic Map4q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 149 91 90 59 26 59 6 278 126 11 128 69 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000034692   ⟹   ENSRNOP00000036472
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl422,245,322 - 22,448,643 (-)Ensembl
mRatBN7.2 Ensembl421,289,798 - 21,494,432 (-)Ensembl
Rnor_6.0 Ensembl418,178,656 - 18,396,035 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096965   ⟹   ENSRNOP00000085581
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl422,245,322 - 22,448,643 (-)Ensembl
mRatBN7.2 Ensembl421,287,982 - 21,493,560 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115447   ⟹   ENSRNOP00000090740
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl422,245,322 - 22,448,643 (-)Ensembl
mRatBN7.2 Ensembl421,287,982 - 21,493,560 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000152075   ⟹   ENSRNOP00000107058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl422,245,322 - 22,535,774 (-)Ensembl
RefSeq Acc Id: NM_017310   ⟹   NP_059006
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8422,245,322 - 22,448,657 (-)NCBI
mRatBN7.2421,290,212 - 21,493,560 (-)NCBI
Rnor_6.0418,178,854 - 18,395,165 (-)NCBI
Rnor_5.0418,133,300 - 18,444,520 (-)NCBI
RGSC_v3.4417,575,112 - 17,790,100 (-)RGD
Celera416,810,716 - 17,013,648 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235990   ⟹   XP_006236052
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8422,239,418 - 22,449,297 (-)NCBI
mRatBN7.2421,282,398 - 21,494,200 (-)NCBI
Rnor_6.0418,170,375 - 18,396,018 (-)NCBI
Rnor_5.0418,133,300 - 18,444,520 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762702   ⟹   XP_008760924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8422,239,418 - 22,709,907 (-)NCBI
mRatBN7.2421,282,398 - 21,754,834 (-)NCBI
Rnor_6.0418,170,375 - 18,545,190 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063285863   ⟹   XP_063141933
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8422,239,418 - 22,548,568 (-)NCBI
RefSeq Acc Id: NP_059006   ⟸   NM_017310
- Peptide Label: precursor
- UniProtKB: Q63548 (UniProtKB/Swiss-Prot),   A6K213 (UniProtKB/TrEMBL),   A0A8L2QL58 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236052   ⟸   XM_006235990
- Peptide Label: isoform X1
- UniProtKB: Q63548 (UniProtKB/Swiss-Prot),   A6K213 (UniProtKB/TrEMBL),   A0A8L2QL58 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760924   ⟸   XM_008762702
- Peptide Label: isoform X1
- UniProtKB: Q63548 (UniProtKB/Swiss-Prot),   A6K213 (UniProtKB/TrEMBL),   A0A8L2QL58 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000036472   ⟸   ENSRNOT00000034692
Ensembl Acc Id: ENSRNOP00000085581   ⟸   ENSRNOT00000096965
Ensembl Acc Id: ENSRNOP00000090740   ⟸   ENSRNOT00000115447
RefSeq Acc Id: XP_063141933   ⟸   XM_063285863
- Peptide Label: isoform X1
- UniProtKB: Q63548 (UniProtKB/Swiss-Prot),   A6K213 (UniProtKB/TrEMBL),   A0A8L2QL58 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107058   ⟸   ENSRNOT00000152075
Protein Domains
Ig-like   Ig-like C2-type   Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63548-F1-model_v2 AlphaFold Q63548 1-772 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3657 AgrOrtholog
BioCyc Gene G2FUF-45867 BioCyc
Ensembl Genes ENSRNOG00000023337 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000034692 ENTREZGENE
  ENSRNOT00000096965.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
  2.60.40.10 UniProtKB/Swiss-Prot
  ligand-binding face of the semaphorins, domain 2 UniProtKB/Swiss-Prot
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  IL-1RAcP-like_ig UniProtKB/Swiss-Prot
  PSI UniProtKB/Swiss-Prot
  Sema3A_sema UniProtKB/Swiss-Prot
  Semap_dom UniProtKB/Swiss-Prot
  Semap_dom_sf UniProtKB/Swiss-Prot
  Semaphorin UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:29751 UniProtKB/Swiss-Prot
NCBI Gene 29751 ENTREZGENE
PANTHER PTHR11036 UniProtKB/Swiss-Prot
  SEMAPHORIN-3A UniProtKB/Swiss-Prot
Pfam Ig_6 UniProtKB/Swiss-Prot
  Sema UniProtKB/Swiss-Prot
PhenoGen Sema3a PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
  SEMA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000023337 RatGTEx
SMART PSI UniProtKB/Swiss-Prot
  Sema UniProtKB/Swiss-Prot
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP Plexin repeat UniProtKB/Swiss-Prot
  SSF101912 UniProtKB/Swiss-Prot
  SSF48726 UniProtKB/Swiss-Prot
UniProt A0A8I6AE44_RAT UniProtKB/TrEMBL
  A0A8L2QL58 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L9H4_RAT UniProtKB/TrEMBL
  A6K213 ENTREZGENE, UniProtKB/TrEMBL
  Q63548 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema3a  semaphorin 3A  Sema3a  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Sema3a  sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A    Semaphorin 3a  Name updated 1299863 APPROVED
2002-06-10 Sema3a  Semaphorin 3a      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function binds and activates a receptor complex consisting of neuropilin-1 (NP-1) and plexin A and serves as a neurite repellent factor 628318
gene_process Sema3A treatment increases the synthesis of the eicosanoid, 12(S)-hydroxyeicosatetraenoic acid (HETE) 628318
gene_process involved in mediating axonal guidance, cell migration, and neoplastic transformation 628318
gene_process causes localized collapse of growth cone to direct neurites away from a repellent 628318
gene_product class III secreted polypeptide 628318