Sema5a (semaphorin 5A) - Rat Genome Database

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Gene: Sema5a (semaphorin 5A) Rattus norvegicus
Analyze
Symbol: Sema5a
Name: semaphorin 5A
RGD ID: 1308650
Description: Enables chondroitin sulfate proteoglycan binding activity; heparan sulfate proteoglycan binding activity; and syndecan binding activity. Involved in nervous system development; regulation of axon extension involved in axon guidance; and signal clustering. Located in membrane. Orthologous to human SEMA5A (semaphorin 5A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC310207; sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A; sema F; semaphorin-5A; semaphorin-F
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8285,020,724 - 85,451,938 (+)NCBIGRCr8
mRatBN7.2283,309,843 - 83,741,084 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl283,309,843 - 83,741,084 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx290,354,073 - 90,791,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0288,475,679 - 88,913,259 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0283,531,943 - 83,969,519 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0285,377,318 - 85,808,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl285,377,318 - 85,808,970 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02105,049,343 - 105,480,370 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4284,725,092 - 85,158,599 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1284,835,136 - 85,097,066 (+)NCBI
Celera278,800,990 - 79,231,054 (+)NCBICelera
Cytogenetic Map2q23NCBI
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
(R)-lipoic acid  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4-diaminotoluene  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetohydrazide  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
antimycin A  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
cadmium atom  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
choline  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
DDT  (EXP)
dibutyl phthalate  (EXP,ISO)
diethyl malate  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
esketamine  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
glycidol  (EXP)
glyphosate  (ISO)
hypochlorous acid  (ISO)
inulin  (ISO)
isoprenaline  (ISO)
L-methionine  (ISO)
Licochalcone B  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
N,N-diethyl-m-toluamide  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
SB 431542  (ISO)
selenomethionine  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenate  (ISO)
succimer  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
toluene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IDA,IEA,ISO)
plasma membrane  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Semaphorin 5A is a bifunctional axon guidance cue regulated by heparan and chondroitin sulfate proteoglycans. Kantor DB, etal., Neuron. 2004 Dec 16;44(6):961-75.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Molecular cloning and mapping of human semaphorin F from the Cri-du-chat candidate interval. Simmons AD, etal., Biochem Biophys Res Commun. 1998 Jan 26;242(3):685-91.
Additional References at PubMed
PMID:12506007   PMID:15218527   PMID:15743826   PMID:16144627   PMID:19850054   PMID:21835343   PMID:22871113   PMID:23376485   PMID:23533145   PMID:25931508  


Genomics

Comparative Map Data
Sema5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8285,020,724 - 85,451,938 (+)NCBIGRCr8
mRatBN7.2283,309,843 - 83,741,084 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl283,309,843 - 83,741,084 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx290,354,073 - 90,791,652 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0288,475,679 - 88,913,259 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0283,531,943 - 83,969,519 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0285,377,318 - 85,808,970 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl285,377,318 - 85,808,970 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02105,049,343 - 105,480,370 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4284,725,092 - 85,158,599 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1284,835,136 - 85,097,066 (+)NCBI
Celera278,800,990 - 79,231,054 (+)NCBICelera
Cytogenetic Map2q23NCBI
SEMA5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3859,035,033 - 9,546,075 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl59,035,033 - 9,546,075 (-)EnsemblGRCh38hg38GRCh38
GRCh3759,035,145 - 9,546,187 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3659,088,138 - 9,599,233 (-)NCBINCBI36Build 36hg18NCBI36
Build 3459,091,858 - 9,599,158NCBI
Celera59,075,672 - 9,586,506 (-)NCBICelera
Cytogenetic Map5p15.31NCBI
HuRef59,020,618 - 9,529,962 (-)NCBIHuRef
CHM1_159,034,070 - 9,546,215 (-)NCBICHM1_1
T2T-CHM13v2.058,974,898 - 9,485,916 (-)NCBIT2T-CHM13v2.0
Sema5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391532,244,959 - 32,696,487 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1532,244,956 - 32,696,487 (+)EnsemblGRCm39 Ensembl
GRCm381532,244,813 - 32,696,341 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1532,244,810 - 32,696,341 (+)EnsemblGRCm38mm10GRCm38
MGSCv371532,174,568 - 32,626,096 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361532,361,948 - 32,640,922 (+)NCBIMGSCv36mm8
Celera1532,949,262 - 33,396,657 (+)NCBICelera
Cytogenetic Map15B3.1NCBI
cM Map1513.02NCBI
Sema5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555046,350,866 - 6,762,104 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555046,343,747 - 6,691,945 (-)NCBIChiLan1.0ChiLan1.0
SEMA5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v249,272,092 - 9,780,658 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan157,425,701 - 7,935,102 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v059,349,473 - 9,852,183 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.159,168,549 - 9,672,779 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl59,168,549 - 9,564,356 (-)Ensemblpanpan1.1panPan2
SEMA5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1344,612,202 - 5,089,071 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl344,612,142 - 5,082,280 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha349,122,860 - 9,593,613 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0344,522,038 - 4,992,481 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl344,521,503 - 4,998,657 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1344,573,215 - 5,048,444 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0344,553,933 - 5,029,831 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0344,776,835 - 5,250,400 (+)NCBIUU_Cfam_GSD_1.0
Sema5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213237,599,219 - 238,050,371 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366431,355,070 - 1,637,151 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366431,352,401 - 1,803,553 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1672,756,383 - 73,328,981 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11672,796,453 - 73,335,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21678,742,131 - 79,220,468 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.148,598,680 - 9,095,346 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl48,600,959 - 9,095,423 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606419,470,071 - 19,975,962 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247516,436,854 - 6,738,216 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247516,429,814 - 6,913,673 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sema5a
3171 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:828
Count of miRNA genes:313
Interacting mature miRNAs:402
Transcripts:ENSRNOT00000016506
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
5684990Bmd82Bone mineral density QTL 822.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)259324377103795077Rat
5684996Bmd85Bone mineral density QTL 854.70.024tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)259324377103795077Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
631500Bp99Blood pressure QTL 992.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)259324719102755241Rat
1578777Stresp15Stress response QTL 1520.05blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)259846005104846005Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)264366971109366971Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)267942638112942638Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)27478666494359546Rat
1359034Bp274Blood pressure QTL 274arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)27478666494359546Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)276539322102785628Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)276539322102785628Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat

Markers in Region
D2Mgh19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2283,575,072 - 83,575,226 (+)MAPPERmRatBN7.2
Rnor_6.0285,642,517 - 85,642,672NCBIRnor6.0
Rnor_5.02105,313,917 - 105,314,072UniSTSRnor5.0
RGSC_v3.4284,991,829 - 84,991,982RGDRGSC3.4
RGSC_v3.4284,991,830 - 84,991,985UniSTSRGSC3.4
RGSC_v3.1284,936,791 - 84,936,944RGD
Celera279,065,698 - 79,065,847UniSTS
RH 3.4 Map2526.5UniSTS
RH 3.4 Map2526.5RGD
RH 2.0 Map2427.8RGD
SHRSP x BN Map235.4298RGD
Cytogenetic Map2q23UniSTS
D2Rat328  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2283,468,750 - 83,468,912 (+)MAPPERmRatBN7.2
Rnor_6.0285,536,218 - 85,536,379NCBIRnor6.0
Rnor_5.02105,208,031 - 105,208,192UniSTSRnor5.0
RGSC_v3.4284,885,630 - 84,885,792RGDRGSC3.4
RGSC_v3.4284,885,631 - 84,885,792UniSTSRGSC3.4
RGSC_v3.1284,830,592 - 84,830,754RGD
Celera278,959,432 - 78,959,593UniSTS
SHRSP x BN Map235.4298RGD
SHRSP x BN Map235.4298UniSTS
Cytogenetic Map2q23UniSTS
RH141406  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2283,735,110 - 83,735,317 (+)MAPPERmRatBN7.2
Rnor_6.0285,802,997 - 85,803,203NCBIRnor6.0
Rnor_5.02105,474,397 - 105,474,603UniSTSRnor5.0
RGSC_v3.4285,152,626 - 85,152,832UniSTSRGSC3.4
Celera279,225,073 - 79,225,279UniSTS
RH 3.4 Map2523.7UniSTS
Cytogenetic Map2q23UniSTS
UniSTS:496014  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2283,596,708 - 83,596,799 (+)MAPPERmRatBN7.2
Rnor_6.0285,664,155 - 85,664,245NCBIRnor6.0
Rnor_5.02105,335,555 - 105,335,645UniSTSRnor5.0
RGSC_v3.4285,013,469 - 85,013,559UniSTSRGSC3.4
Celera279,087,335 - 79,087,425UniSTS
Cytogenetic Map2q23UniSTS


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 14 12 4 5 4 1 1 72 35 34 8 1
Low 3 29 40 32 14 32 7 9 2 7 3 7
Below cutoff 5 5 5 1

Sequence


RefSeq Acc Id: ENSRNOT00000016506   ⟹   ENSRNOP00000016506
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl283,309,843 - 83,741,084 (+)Ensembl
Rnor_6.0 Ensembl285,377,318 - 85,808,970 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085094   ⟹   ENSRNOP00000074231
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl283,309,843 - 83,736,489 (+)Ensembl
Rnor_6.0 Ensembl285,377,341 - 85,802,558 (+)Ensembl
RefSeq Acc Id: NM_001107659   ⟹   NP_001101129
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8285,020,724 - 85,451,938 (+)NCBI
mRatBN7.2283,309,843 - 83,741,084 (+)NCBI
Rnor_6.0285,377,318 - 85,808,970 (+)NCBI
Rnor_5.02105,049,343 - 105,480,370 (+)NCBI
RGSC_v3.4284,725,092 - 85,158,599 (+)RGD
Celera278,800,990 - 79,231,054 (+)RGD
Sequence:
RefSeq Acc Id: XM_063281754   ⟹   XP_063137824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8285,021,080 - 85,451,935 (+)NCBI
RefSeq Acc Id: XM_063281755   ⟹   XP_063137825
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8285,021,390 - 85,451,935 (+)NCBI
RefSeq Acc Id: NP_001101129   ⟸   NM_001107659
- Peptide Label: precursor
- UniProtKB: D3ZTD8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074231   ⟸   ENSRNOT00000085094
RefSeq Acc Id: ENSRNOP00000016506   ⟸   ENSRNOT00000016506
RefSeq Acc Id: XP_063137824   ⟸   XM_063281754
- Peptide Label: isoform X1
- UniProtKB: D3ZTD8 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063137825   ⟸   XM_063281755
- Peptide Label: isoform X1
- UniProtKB: D3ZTD8 (UniProtKB/Swiss-Prot)
Protein Domains
PSI   Sema   TSP type-1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTD8-F1-model_v2 AlphaFold D3ZTD8 1-1074 view protein structure

Transcriptome

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

Promoters
RGD ID:13691214
Promoter ID:EPDNEW_R1739
Type:multiple initiation site
Name:Sema5a_1
Description:semaphorin 5A
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_6.0285,377,333 - 85,377,393EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308650 AgrOrtholog
BioCyc Gene G2FUF-53846 BioCyc
Ensembl Genes ENSRNOG00000011977 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055025467 UniProtKB/Swiss-Prot
  ENSRNOG00060020174 UniProtKB/Swiss-Prot
  ENSRNOG00065013025 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000016506 ENTREZGENE
  ENSRNOT00000016506.6 UniProtKB/Swiss-Prot
  ENSRNOT00000085094.2 UniProtKB/TrEMBL
  ENSRNOT00055043984 UniProtKB/Swiss-Prot
  ENSRNOT00060034937 UniProtKB/Swiss-Prot
  ENSRNOT00065021346 UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.20.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ligand-binding face of the semaphorins, domain 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Plexin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema5A_sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semaphorin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:310207 UniProtKB/Swiss-Prot
NCBI Gene 310207 ENTREZGENE
PANTHER PTHR11036 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEMAPHORIN-5A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sema5a PhenoGen
PRINTS TSP1REPEAT UniProtKB/Swiss-Prot
PROSITE SEMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011977 RatGTEx
  ENSRNOG00055025467 RatGTEx
  ENSRNOG00060020174 RatGTEx
  ENSRNOG00065013025 RatGTEx
SMART PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Plexin repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF101912 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82895 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K7J5_RAT UniProtKB/TrEMBL
  D3ZTD8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema5a  semaphorin 5A  Sema5a  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema5a  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A   Sema5a_predicted  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema5a_predicted  sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A (predicted)      Symbol and Name status set to approved 70820 APPROVED