Sema3a (sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Sema3a (sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A) Mus musculus
Analyze
Symbol: Sema3a
Name: sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
RGD ID: 730922
MGI Page MGI
Description: Enables chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in several processes, including nervous system development; positive regulation of male gonad development; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including dichotomous subdivision of terminal units involved in salivary gland branching; negative regulation of axon extension involved in axon guidance; and neuron projection development. Located in extracellular space. Is active in cerebellar climbing fiber to Purkinje cell synapse. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; metanephros; and sensory organ. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: col; coll-1; collapsin-1; Hsema-I; Sem; sema D; sema III; SEMA1; Semad; semaphorin III; semaphorin-3A; semaphorin-D; SemD
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39513,174,789 - 13,653,453 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl513,175,381 - 13,652,533 (+)EnsemblGRCm39 Ensembl
GRCm38513,124,822 - 13,603,485 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl513,125,414 - 13,602,565 (+)EnsemblGRCm38mm10GRCm38
MGSCv37513,399,309 - 13,602,571 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36513,405,315 - 13,608,571 (+)NCBIMGSCv36mm8
Celera1223,770,632 - 23,979,473 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map54.31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal atrial thrombosis  (IAGP)
abnormal axon fasciculation  (IAGP)
abnormal branching involved in ureteric bud morphogenesis  (IAGP)
abnormal cerebral cortex morphology  (IAGP)
abnormal cerebral cortex pyramidal cell morphology  (IAGP)
abnormal dendritic cell physiology  (IAGP)
abnormal dorsal root ganglion morphology  (IAGP)
abnormal enteric nervous system morphology  (IAGP)
abnormal neuron differentiation  (IAGP)
abnormal neuronal migration  (IAGP)
abnormal olfactory bulb morphology  (IAGP)
abnormal ophthalmic nerve morphology  (IAGP)
abnormal paravertebral ganglion morphology  (IAGP)
abnormal posture  (IAGP)
abnormal rib morphology  (IAGP)
abnormal sensory neuron innervation pattern  (IAGP)
abnormal spinal nerve morphology  (IAGP)
abnormal sternum morphology  (IAGP)
abnormal T cell physiology  (IAGP)
abnormal trigeminal nerve morphology  (IAGP)
abnormal vagus nerve morphology  (IAGP)
asymmetric sternocostal joints  (IAGP)
cervical vertebral fusion  (IAGP)
decreased body size  (IAGP)
decreased body weight  (IAGP)
decreased brain size  (IAGP)
decreased food intake  (IAGP)
decreased gonadotropin-releasing hormone neuron number  (IAGP)
decreased survivor rate  (IAGP)
dilated heart right atrium  (IAGP)
heart right ventricle hypertrophy  (IAGP)
lethality at weaning, incomplete penetrance  (IAGP)
neonatal lethality, incomplete penetrance  (IAGP)
postnatal lethality, complete penetrance  (IAGP)
postnatal lethality, incomplete penetrance  (IAGP)
premature death  (IAGP)
prenatal lethality, incomplete penetrance  (IAGP)
rib fusion  (IAGP)
small olfactory bulb  (IAGP)
split xiphoid process  (IAGP)
thin cerebral cortex  (IAGP)
weakness  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Neuropilin-2 mediates axonal fasciculation, zonal segregation, but not axonal convergence, of primary accessory olfactory neurons. Cloutier JF, etal., Neuron 2002 Mar 14;33(6):877-92.
2. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. MGD IEA MGD IEA
5. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. Mouse MP Annotation Import Pipeline RGD automated import pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7656991   PMID:7748561   PMID:7748562   PMID:8812066   PMID:8817451   PMID:8849723   PMID:8889548   PMID:9204478   PMID:9331345   PMID:9331348   PMID:9390514   PMID:9675049  
PMID:9753685   PMID:9811588   PMID:10349636   PMID:10495275   PMID:10520994   PMID:10557350   PMID:10804168   PMID:10843805   PMID:10964465   PMID:10985345   PMID:11025205   PMID:11027230  
PMID:11042159   PMID:11076861   PMID:11108845   PMID:11217851   PMID:11231073   PMID:11442635   PMID:11461151   PMID:11486090   PMID:11683995   PMID:11830568   PMID:12023301   PMID:12372285  
PMID:12401447   PMID:12435358   PMID:12477932   PMID:12506007   PMID:12591607   PMID:12598627   PMID:12821380   PMID:12852851   PMID:12879061   PMID:12925274   PMID:14516677   PMID:14659802  
PMID:14681479   PMID:14697657   PMID:14750152   PMID:14755522   PMID:15051154   PMID:15078553   PMID:15080899   PMID:15121176   PMID:15155748   PMID:15229182   PMID:15239958   PMID:15240808  
PMID:15386596   PMID:15473965   PMID:15489334   PMID:15545629   PMID:15545635   PMID:15604101   PMID:15632069   PMID:15788454   PMID:15814794   PMID:15869472   PMID:16141072   PMID:16141073  
PMID:16284245   PMID:16286926   PMID:16360650   PMID:16364899   PMID:16540575   PMID:16541019   PMID:16602821   PMID:16706833   PMID:16774995   PMID:17099709   PMID:17145500   PMID:17182786  
PMID:17362911   PMID:17417650   PMID:17428830   PMID:17582329   PMID:17626059   PMID:17728139   PMID:17921861   PMID:17951031   PMID:17989695   PMID:17997325   PMID:18003833   PMID:18022325  
PMID:18032673   PMID:18053124   PMID:18077678   PMID:18096366   PMID:18180379   PMID:18199763   PMID:18209113   PMID:18249526   PMID:18262512   PMID:18300426   PMID:18356247   PMID:18464795  
PMID:18489001   PMID:18550718   PMID:18574596   PMID:18615113   PMID:18617019   PMID:18662545   PMID:18727829   PMID:18804103   PMID:19020035   PMID:19030180   PMID:19325129   PMID:19332558  
PMID:19386638   PMID:19386662   PMID:19403658   PMID:19454481   PMID:19463158   PMID:19515904   PMID:19538749   PMID:19589963   PMID:19655386   PMID:19809158   PMID:19812329   PMID:19906865  
PMID:20010807   PMID:20071458   PMID:20133938   PMID:20159040   PMID:20345923   PMID:20410128   PMID:20512151   PMID:20643936   PMID:20713502   PMID:20826310   PMID:21059704   PMID:21075075  
PMID:21098092   PMID:21125652   PMID:21205984   PMID:21521879   PMID:21525298   PMID:21658587   PMID:21677750   PMID:21765815   PMID:21793640   PMID:21828096   PMID:21862448   PMID:21873635  
PMID:22000108   PMID:22028026   PMID:22076636   PMID:22082309   PMID:22096573   PMID:22179111   PMID:22234963   PMID:22279234   PMID:22368082   PMID:22492355   PMID:22505034   PMID:22516460  
PMID:22522930   PMID:22547824   PMID:22615927   PMID:22627288   PMID:22632726   PMID:22683681   PMID:22685328   PMID:22723296   PMID:22723300   PMID:22790009   PMID:22955271   PMID:23063659  
PMID:23070608   PMID:23104057   PMID:23142733   PMID:23317887   PMID:23395391   PMID:23430612   PMID:23595275   PMID:23602477   PMID:23644455   PMID:23709645   PMID:23812756   PMID:23922915  
PMID:23954273   PMID:23991118   PMID:23998265   PMID:24006456   PMID:24093675   PMID:24276892   PMID:24332039   PMID:24550112   PMID:24591256   PMID:24618750   PMID:24631295   PMID:24728844  
PMID:24752460   PMID:24776795   PMID:24809797   PMID:24829504   PMID:24831527   PMID:24918638   PMID:24952961   PMID:24998526   PMID:25088775   PMID:25249008   PMID:25475434   PMID:25478809  
PMID:25512301   PMID:25601765   PMID:25839327   PMID:25843547   PMID:25975775   PMID:26102480   PMID:26620267   PMID:26633812   PMID:26686462   PMID:26830346   PMID:26884395   PMID:26945060  
PMID:27143756   PMID:27155222   PMID:27198082   PMID:27246732   PMID:27466379   PMID:27480924   PMID:27578798   PMID:27618676   PMID:27693255   PMID:27772760   PMID:27787851   PMID:27858201  
PMID:28013333   PMID:28103314   PMID:28254884   PMID:28480592   PMID:28540528   PMID:28555754   PMID:28637841   PMID:28683823   PMID:28729362   PMID:28729659   PMID:28731788   PMID:28792937  
PMID:28893946   PMID:28970231   PMID:29016743   PMID:29031500   PMID:29059194   PMID:29111592   PMID:29138447   PMID:29224790   PMID:29358640   PMID:29403069   PMID:29540665   PMID:29774231  
PMID:29898965   PMID:30099044   PMID:30237243   PMID:30353093   PMID:30550785   PMID:30579864   PMID:30627913   PMID:30628891   PMID:30661929   PMID:30735130   PMID:30796970   PMID:30819894  
PMID:30862786   PMID:30862799   PMID:30902550   PMID:30967873   PMID:31025335   PMID:31270650   PMID:31430342   PMID:31474563   PMID:31537704   PMID:31733191   PMID:31929360   PMID:32012286  
PMID:32184710   PMID:32541009   PMID:32561725   PMID:33070651   PMID:33127760   PMID:33143303   PMID:33302058   PMID:33503438   PMID:33649856   PMID:34039996   PMID:34060391   PMID:34321999  
PMID:34338972   PMID:34812142   PMID:34821196   PMID:35294878   PMID:35347234   PMID:35462405   PMID:35654941   PMID:35798870   PMID:35899793   PMID:35927240   PMID:35933488   PMID:36240771  
PMID:36284453   PMID:36598593   PMID:36877136   PMID:36880403   PMID:37052590   PMID:37221130   PMID:37310417   PMID:37421591   PMID:37846569   PMID:38163665   PMID:38165021   PMID:38584583  
PMID:38670629   PMID:38727898   PMID:38910430   PMID:39152112   PMID:39746903  


Genomics

Comparative Map Data
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 Ensembl
GRCm38513,124,822 - 13,603,485 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl513,125,414 - 13,602,565 (+)EnsemblGRCm38mm10GRCm38
MGSCv37513,399,309 - 13,602,571 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36513,405,315 - 13,608,571 (+)NCBIMGSCv36mm8
Celera1223,770,632 - 23,979,473 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map54.31NCBI
SEMA3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38783,955,777 - 84,492,725 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl783,955,777 - 84,492,724 (-)EnsemblGRCh38hg38GRCh38
GRCh37783,585,093 - 83,824,105 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36783,425,595 - 83,662,153 (-)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8422,239,418 - 22,709,907 (-)NCBIGRCr8
mRatBN7.2421,282,398 - 21,754,834 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl421,287,982 - 21,494,432 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx426,307,920 - 26,512,008 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0422,234,070 - 22,438,148 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0420,607,687 - 20,811,763 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0418,170,375 - 18,545,190 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl418,178,656 - 18,396,035 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0418,133,300 - 18,444,520 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4417,575,112 - 17,790,100 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1417,575,111 - 17,790,100 (-)NCBI
Celera416,810,716 - 17,013,648 (-)NCBICelera
Cytogenetic Map4q12NCBI
Sema3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554102,144,388 - 2,338,973 (+)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1823,096,760 - 23,551,325 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01823,872,684 - 24,326,815 (-)NCBIROS_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_1.0
SEMA3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl996,181,770 - 96,387,950 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473932,104,014 - 32,426,980 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sema3a
27877 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1591
Count of miRNA genes:552
Interacting mature miRNAs:728
Transcripts:ENSMUST00000030714, ENSMUST00000095012, ENSMUST00000125629, ENSMUST00000137798, ENSMUST00000141968
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4141207Imrfq1_mimmune response to Factor IX QTL 1 (mouse)Not determined5812411742124239Mouse
7394748Mom5_mmodifier of Min 5 (mouse)Not determined5884767233475637Mouse
4141234Pbwg14_mpostnatal body weight growth 14 (mouse)Not determined5121273552Mouse
12738412Lfibq4_mliver fibrosis QTL 4 (mouse)5315000020799180Mouse
15039371Nmrs21_mNAFLD-associated magnetic resonance shift 21 (mouse)5350482337504823Mouse
1301693Sle6_msystemic lupus erythematosus susceptibility 6 (mouse)Not determined5889069387841837Mouse
1301468Eye1_meye weight 1 (mouse)Not determined5121929650Mouse
10412081Bwq13_mbody weight QTL 13 (mouse)Not determined5123606323Mouse
1357478Kdnw1_mkidney weight 1 (mouse)Not determined5891594940529869Mouse
13442491Mecth1_mmechanosensation threshold 1 (mouse)5451800019834998Mouse
12904958Gmmq8_mgastrocnemius muscle mass QTL 8 (mouse)5129421124Mouse
14696730Kidlq1_mkidney weight, left QTL 1 (mouse)51356315247563152Mouse
10401122Pgia41_mproteoglycan induced arthritis 41 (mouse)Not determined582314434823280Mouse
1301806Actd2_mactivity-distance traveled 2 (mouse)Not determined5538452039384652Mouse

Markers in Region
Sema3a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5A1UniSTS
cM Map5 UniSTS
UniSTS:224589  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38513,399,614 - 13,399,785UniSTSGRCm38
MGSCv37513,399,614 - 13,399,785UniSTSGRCm37
Celera1223,770,937 - 23,771,110UniSTS
Cytogenetic Map5A1UniSTS
UniSTS:224729  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38513,599,749 - 13,599,913UniSTSGRCm38
MGSCv37513,599,749 - 13,599,913UniSTSGRCm37
Celera1223,976,651 - 23,976,815UniSTS
Cytogenetic Map5A1UniSTS
Sema3a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5A1UniSTS
Sema3a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5A1UniSTS
cM Map5 UniSTS
Sema3a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5A1UniSTS


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001243072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001243073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_009152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006503557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006503558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006503559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011240665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036164935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036164936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036164937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC022368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC109165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC121125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC121841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC159971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF164782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK052051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK053115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK137040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK140817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK164242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK166127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK166206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC057588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC090844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY674854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CN460380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D85028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L40484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L41541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X85993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000030714   ⟹   ENSMUSP00000030714
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,449,276 - 13,652,533 (+)Ensembl
GRCm38.p6 Ensembl513,399,309 - 13,602,565 (+)Ensembl
Ensembl Acc Id: ENSMUST00000095012   ⟹   ENSMUSP00000092621
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,446,751 - 13,650,956 (+)Ensembl
GRCm38.p6 Ensembl513,396,784 - 13,600,988 (+)Ensembl
Ensembl Acc Id: ENSMUST00000125629   ⟹   ENSMUSP00000121710
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,448,655 - 13,501,174 (+)Ensembl
GRCm38.p6 Ensembl513,398,688 - 13,451,207 (+)Ensembl
Ensembl Acc Id: ENSMUST00000137798   ⟹   ENSMUSP00000128153
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,448,964 - 13,652,533 (+)Ensembl
GRCm38.p6 Ensembl513,398,997 - 13,599,348 (+)Ensembl
Ensembl Acc Id: ENSMUST00000141968   ⟹   ENSMUSP00000122621
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,449,291 - 13,501,144 (+)Ensembl
GRCm38.p6 Ensembl513,399,324 - 13,451,177 (+)Ensembl
Ensembl Acc Id: ENSMUST00000195907
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,175,560 - 13,574,674 (+)Ensembl
GRCm38.p6 Ensembl513,125,593 - 13,524,707 (+)Ensembl
Ensembl Acc Id: ENSMUST00000196514
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,175,381 - 13,360,721 (+)Ensembl
GRCm38.p6 Ensembl513,125,414 - 13,310,754 (+)Ensembl
Ensembl Acc Id: ENSMUST00000197582
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,175,459 - 13,343,695 (+)Ensembl
GRCm38.p6 Ensembl513,125,492 - 13,293,728 (+)Ensembl
Ensembl Acc Id: ENSMUST00000200073
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl513,449,544 - 13,546,368 (+)Ensembl
GRCm38.p6 Ensembl513,399,577 - 13,496,401 (+)Ensembl
RefSeq Acc Id: NM_001243072   ⟹   NP_001230001
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,446,751 - 13,653,453 (+)NCBI
GRCm38513,396,784 - 13,603,485 (+)NCBI
Celera1223,767,947 - 23,980,387 (+)NCBI
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001243073   ⟹   NP_001230002
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,448,964 - 13,653,453 (+)NCBI
GRCm38513,398,997 - 13,603,485 (+)NCBI
Celera1223,767,947 - 23,980,387 (+)NCBI
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_009152   ⟹   NP_033178
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,449,276 - 13,653,453 (+)NCBI
GRCm38513,399,309 - 13,603,485 (+)NCBI
MGSCv37513,399,309 - 13,602,571 (+)RGD
Celera1223,767,947 - 23,980,387 (+)NCBI
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006503557   ⟹   XP_006503620
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,174,789 - 13,652,535 (+)NCBI
GRCm38513,124,822 - 13,602,567 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006503558   ⟹   XP_006503621
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,449,194 - 13,652,535 (+)NCBI
GRCm38513,399,186 - 13,602,567 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006503559   ⟹   XP_006503622
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,448,655 - 13,652,535 (+)NCBI
GRCm38513,398,688 - 13,602,567 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011240665   ⟹   XP_011238967
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,326,316 - 13,652,535 (+)NCBI
GRCm38513,280,166 - 13,602,567 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036164935   ⟹   XP_036020828
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,448,962 - 13,652,535 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036164936   ⟹   XP_036020829
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,448,273 - 13,652,535 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036164937   ⟹   XP_036020830
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39513,448,396 - 13,652,535 (+)NCBI
Sequence:
RefSeq Acc Id: NP_033178   ⟸   NM_009152
- Peptide Label: precursor
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001230001   ⟸   NM_001243072
- Peptide Label: precursor
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001230002   ⟸   NM_001243073
- Peptide Label: precursor
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006503620   ⟸   XM_006503557
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006503622   ⟸   XM_006503559
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006503621   ⟸   XM_006503558
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011238967   ⟸   XM_011240665
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000121710   ⟸   ENSMUST00000125629
Ensembl Acc Id: ENSMUSP00000092621   ⟸   ENSMUST00000095012
Ensembl Acc Id: ENSMUSP00000128153   ⟸   ENSMUST00000137798
Ensembl Acc Id: ENSMUSP00000030714   ⟸   ENSMUST00000030714
Ensembl Acc Id: ENSMUSP00000122621   ⟸   ENSMUST00000141968
RefSeq Acc Id: XP_036020829   ⟸   XM_036164936
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_036020830   ⟸   XM_036164937
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_036020828   ⟸   XM_036164935
- Peptide Label: isoform X1
- UniProtKB: Q62215 (UniProtKB/Swiss-Prot),   Q62180 (UniProtKB/Swiss-Prot),   Q5BL08 (UniProtKB/Swiss-Prot),   O08665 (UniProtKB/Swiss-Prot),   E9QK85 (UniProtKB/Swiss-Prot),   A0A803Z7F8 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   Ig-like C2-type   Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08665-F1-model_v2 AlphaFold O08665 1-772 view protein structure

Promoters
RGD ID:6886000
Promoter ID:EPDNEW_M6451
Type:initiation region
Name:Sema3a_3
Description:Mus musculus sema domain, immunoglobulin domain , short basicdomain, secreted, 3A , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M6452  EPDNEW_M6453  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38513,125,484 - 13,125,544EPDNEW
RGD ID:6886002
Promoter ID:EPDNEW_M6452
Type:single initiation site
Name:Sema3a_2
Description:Mus musculus sema domain, immunoglobulin domain , short basicdomain, secreted, 3A , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M6451  EPDNEW_M6453  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38513,163,765 - 13,163,825EPDNEW
RGD ID:6838306
Promoter ID:MM_KWN:41405
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:MEF_B4,   MEF_B6
Transcripts:NM_009152,   OTTMUST00000050497,   OTTMUST00000050498,   UC008WMB.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36513,398,526 - 13,399,497 (+)MPROMDB
RGD ID:6886004
Promoter ID:EPDNEW_M6453
Type:initiation region
Name:Sema3a_1
Description:Mus musculus sema domain, immunoglobulin domain , short basicdomain, secreted, 3A , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M6451  EPDNEW_M6452  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38513,399,406 - 13,399,466EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:107558 AgrOrtholog
Ensembl Genes ENSMUSG00000028883 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000030714 ENTREZGENE
  ENSMUST00000095012 ENTREZGENE
  ENSMUST00000137798 ENTREZGENE
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 mmu:20346 UniProtKB/Swiss-Prot
MGD MGI:107558 ENTREZGENE
NCBI Gene 20346 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
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 A0A803Z7F8 ENTREZGENE, UniProtKB/TrEMBL
  D3Z2A7_MOUSE UniProtKB/TrEMBL
  D3Z4Q3_MOUSE UniProtKB/TrEMBL
  E9Q668_MOUSE UniProtKB/TrEMBL
  E9QK85 ENTREZGENE
  O08665 ENTREZGENE
  Q5BL08 ENTREZGENE
  Q62180 ENTREZGENE
  Q62215 ENTREZGENE
  SEM3A_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary E9QK85 UniProtKB/Swiss-Prot
  Q5BL08 UniProtKB/Swiss-Prot
  Q62180 UniProtKB/Swiss-Prot
  Q62215 UniProtKB/Swiss-Prot