Sema4d (semaphorin 4D) - Rat Genome Database

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Gene: Sema4d (semaphorin 4D) Rattus norvegicus
Analyze
Symbol: Sema4d
Name: semaphorin 4D
RGD ID: 1310554
Description: Predicted to enable identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Predicted to be involved in several processes, including positive regulation of intracellular signal transduction; positive regulation of nervous system development; and regulation of peptidyl-tyrosine phosphorylation. Predicted to act upstream of or within positive regulation of axonogenesis. Is active in postsynaptic membrane. Orthologous to human SEMA4D (semaphorin 4D); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC103694042; LOC306790; sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D; semaphorin-4D; uncharacterized LOC103694042
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
GRCr81713,582,085 - 13,688,889 (+)NCBIGRCr8
mRatBN7.21713,430,324 - 13,537,146 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1713,430,379 - 13,537,138 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1713,427,656 - 13,450,343 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01715,038,325 - 15,061,123 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01713,354,447 - 13,377,136 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01713,516,276 - 13,538,513 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1713,488,376 - 13,553,974 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01715,590,977 - 15,613,214 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41719,352,632 - 19,373,179 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11719,332,919 - 19,373,283 (+)NCBI
Celera1713,255,006 - 13,277,562 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
amitrole  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
folic acid  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
kainic acid  (EXP)
lipopolysaccharide  (ISO)
lycorine  (ISO)
maneb  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
Monobutylphthalate  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Semaphorin 4D/plexin-B1 induces endothelial cell migration through the activation of PYK2, Src, and the phosphatidylinositol 3-kinase-Akt pathway. Basile JR, etal., Mol Cell Biol. 2005 Aug;25(16):6889-98.
2. Sema4D induces angiogenesis through Met recruitment by Plexin B1. Conrotto P, etal., Blood. 2005 Jun 1;105(11):4321-9. Epub 2005 Jan 4.
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. The transmembrane semaphorin Sema4D/CD100, an inhibitor of axonal growth, is expressed on oligodendrocytes and upregulated after CNS lesion. Moreau-Fauvarque C, etal., J Neurosci. 2003 Oct 8;23(27):9229-39.
7. Sema4D localizes to synapses and regulates GABAergic synapse development as a membrane-bound molecule in the mammalian hippocampus. Raissi AJ, etal., Mol Cell Neurosci. 2013 Nov;57:23-32. doi: 10.1016/j.mcn.2013.08.004. Epub 2013 Sep 10.
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8876214   PMID:8889548   PMID:11254688   PMID:15218527   PMID:15330859   PMID:15613544   PMID:19788569   PMID:20610402   PMID:20877282   PMID:22019888   PMID:23699507   PMID:23949850  
PMID:24549858   PMID:26489627   PMID:28624895   PMID:29981480   PMID:36970799  


Genomics

Comparative Map Data
Sema4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81713,582,085 - 13,688,889 (+)NCBIGRCr8
mRatBN7.21713,430,324 - 13,537,146 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1713,430,379 - 13,537,138 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1713,427,656 - 13,450,343 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01715,038,325 - 15,061,123 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01713,354,447 - 13,377,136 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01713,516,276 - 13,538,513 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1713,488,376 - 13,553,974 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01715,590,977 - 15,613,214 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41719,352,632 - 19,373,179 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11719,332,919 - 19,373,283 (+)NCBI
Celera1713,255,006 - 13,277,562 (+)NCBICelera
Cytogenetic Map17p14NCBI
SEMA4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38989,360,787 - 89,498,113 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl989,360,787 - 89,498,130 (-)EnsemblGRCh38hg38GRCh38
GRCh37991,975,702 - 92,113,028 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36991,181,972 - 91,284,431 (-)NCBINCBI36Build 36hg18NCBI36
Build 34989,221,705 - 89,324,165NCBI
Celera962,560,599 - 62,677,697 (-)NCBICelera
Cytogenetic Map9q22.2NCBI
HuRef961,809,649 - 61,812,817 (-)NCBIHuRef
HuRef961,823,373 - 61,926,322 (-)NCBIHuRef
CHM1_1992,124,533 - 92,243,431 (-)NCBICHM1_1
T2T-CHM13v2.09101,524,564 - 101,662,071 (-)NCBIT2T-CHM13v2.0
Sema4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391351,839,565 - 51,947,823 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1351,839,565 - 51,947,783 (-)EnsemblGRCm39 Ensembl
GRCm381351,685,529 - 51,793,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1351,685,529 - 51,793,747 (-)EnsemblGRCm38mm10GRCm38
MGSCv371351,796,617 - 51,889,013 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361351,713,744 - 51,806,140 (-)NCBIMGSCv36mm8
Celera1352,773,981 - 52,868,989 (-)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1326.16NCBI
Sema4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555152,608,331 - 2,689,326 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555152,573,816 - 2,676,387 (+)NCBIChiLan1.0ChiLan1.0
SEMA4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21149,962,438 - 50,099,628 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1949,964,928 - 50,102,016 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0960,451,420 - 60,588,519 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1988,497,528 - 88,611,374 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl988,497,528 - 88,560,811 (-)Ensemblpanpan1.1panPan2
SEMA4D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1196,825,963 - 96,878,956 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl196,814,674 - 96,878,968 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha197,278,644 - 97,342,104 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0197,427,590 - 97,490,619 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl197,432,133 - 97,490,753 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1197,055,805 - 97,118,887 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0196,774,870 - 96,838,078 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0197,533,063 - 97,596,441 (+)NCBIUU_Cfam_GSD_1.0
Sema4d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494411,158,121 - 11,231,467 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936780317,948 - 350,113 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936780317,926 - 350,113 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA4D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14957,081 - 1,078,508 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114957,074 - 1,078,522 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2141,174,861 - 1,259,699 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA4D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11299,872,725 - 99,951,441 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1299,874,189 - 99,900,982 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603888,195,884 - 88,316,203 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema4d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476523,197,462 - 23,229,922 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476523,097,771 - 23,244,778 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sema4d
678 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:629
Count of miRNA genes:276
Interacting mature miRNAs:344
Transcripts:ENSRNOT00000018378
Prediction methods:Microtar, Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001170563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063276348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063276349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063276350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063276351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063276352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BQ780932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO395136 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO404183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DN935876 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000018378   ⟹   ENSRNOP00000018378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1713,499,205 - 13,521,684 (+)Ensembl
Rnor_6.0 Ensembl1713,516,456 - 13,537,114 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1713,488,376 - 13,516,561 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076794   ⟹   ENSRNOP00000068126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1713,430,379 - 13,537,138 (+)Ensembl
Rnor_6.0 Ensembl1713,519,130 - 13,553,974 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101493   ⟹   ENSRNOP00000079766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1713,499,025 - 13,521,684 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000106280   ⟹   ENSRNOP00000091940
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1713,430,379 - 13,537,138 (+)Ensembl
RefSeq Acc Id: NM_001170563   ⟹   NP_001164034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,650,781 - 13,673,435 (+)NCBI
mRatBN7.21713,499,025 - 13,521,684 (+)NCBI
Rnor_6.01713,516,276 - 13,538,513 (+)NCBI
Rnor_5.01715,590,977 - 15,613,214 (+)NCBI
Celera1713,255,006 - 13,277,562 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095639   ⟹   XP_038951567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,673,437 (+)NCBI
mRatBN7.21713,430,325 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095640   ⟹   XP_038951568
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,641,591 - 13,673,437 (+)NCBI
mRatBN7.21713,490,376 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095641   ⟹   XP_038951569
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,626,657 - 13,673,437 (+)NCBI
mRatBN7.21713,474,851 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095642   ⟹   XP_038951570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,618,871 - 13,673,437 (+)NCBI
mRatBN7.21713,467,108 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095643   ⟹   XP_038951571
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,615,022 - 13,673,437 (+)NCBI
mRatBN7.21713,464,554 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095644   ⟹   XP_038951572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,621,064 - 13,673,437 (+)NCBI
mRatBN7.21713,469,425 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095645   ⟹   XP_038951573
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,642,487 - 13,673,437 (+)NCBI
mRatBN7.21713,490,735 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_039095647   ⟹   XP_038951575
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,688,889 (+)NCBI
mRatBN7.21713,430,325 - 13,537,146 (+)NCBI
RefSeq Acc Id: XM_039095648   ⟹   XP_038951576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,688,889 (+)NCBI
mRatBN7.21713,430,324 - 13,537,146 (+)NCBI
RefSeq Acc Id: XM_039095649   ⟹   XP_038951577
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,683,819 (+)NCBI
mRatBN7.21713,430,325 - 13,532,072 (+)NCBI
RefSeq Acc Id: XM_039095650   ⟹   XP_038951578
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,085 - 13,688,889 (+)NCBI
mRatBN7.21713,430,325 - 13,537,146 (+)NCBI
RefSeq Acc Id: XM_039095651   ⟹   XP_038951579
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,626,661 - 13,688,889 (+)NCBI
mRatBN7.21713,474,857 - 13,537,146 (+)NCBI
RefSeq Acc Id: XM_039095652   ⟹   XP_038951580
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,091 - 13,673,437 (+)NCBI
mRatBN7.21713,430,326 - 13,521,686 (+)NCBI
RefSeq Acc Id: XM_063276348   ⟹   XP_063132418
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,639,955 - 13,673,437 (+)NCBI
RefSeq Acc Id: XM_063276349   ⟹   XP_063132419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,679,635 (+)NCBI
RefSeq Acc Id: XM_063276350   ⟹   XP_063132420
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,618,877 - 13,688,889 (+)NCBI
RefSeq Acc Id: XM_063276351   ⟹   XP_063132421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,616,375 - 13,688,889 (+)NCBI
RefSeq Acc Id: XM_063276352   ⟹   XP_063132422
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81713,582,090 - 13,688,889 (+)NCBI
RefSeq Acc Id: NP_001164034   ⟸   NM_001170563
- Peptide Label: precursor
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018378   ⟸   ENSRNOT00000018378
Ensembl Acc Id: ENSRNOP00000068126   ⟸   ENSRNOT00000076794
RefSeq Acc Id: XP_038951576   ⟸   XM_039095648
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951575   ⟸   XM_039095647
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GJZ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951578   ⟸   XM_039095650
- Peptide Label: isoform X5
- UniProtKB: A0A096MJH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951577   ⟸   XM_039095649
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038951567   ⟸   XM_039095639
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951580   ⟸   XM_039095652
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038951571   ⟸   XM_039095643
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951570   ⟸   XM_039095642
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951572   ⟸   XM_039095644
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951569   ⟸   XM_039095641
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951579   ⟸   XM_039095651
- Peptide Label: isoform X5
- UniProtKB: A0A096MJH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951568   ⟸   XM_039095640
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038951573   ⟸   XM_039095645
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL),   D3ZYR4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091940   ⟸   ENSRNOT00000106280
Ensembl Acc Id: ENSRNOP00000079766   ⟸   ENSRNOT00000101493
RefSeq Acc Id: XP_063132422   ⟸   XM_063276352
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063132419   ⟸   XM_063276349
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063132421   ⟸   XM_063276351
- Peptide Label: isoform X5
- UniProtKB: A0A096MJH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063132420   ⟸   XM_063276350
- Peptide Label: isoform X5
- UniProtKB: A0A096MJH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063132418   ⟸   XM_063276348
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G5Q1 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYR4-F1-model_v2 AlphaFold D3ZYR4 1-862 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:1310554 AgrOrtholog
BioCyc Gene G2FUF-10075 BioCyc
Ensembl Genes ENSRNOG00000013679 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018378.9 UniProtKB/TrEMBL
  ENSRNOT00000076794.2 UniProtKB/TrEMBL
  ENSRNOT00000101493.1 UniProtKB/TrEMBL
  ENSRNOT00000106280.1 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
  ligand-binding face of the semaphorins, domain 2 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Immunoglobulin UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  Plexin_repeat 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:306790 UniProtKB/TrEMBL
NCBI Gene 306790 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
  SEMAPHORIN-4D UniProtKB/TrEMBL
Pfam PF00047 UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PhenoGen Sema4d PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  SEMA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013679 RatGTEx
SMART IGc2 UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
Superfamily-SCOP Plexin repeat UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A096MJH1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G5Q1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GJZ1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYR4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Sema4d  semaphorin 4D  LOC103694042  uncharacterized LOC103694042  Data merged from RGD:9120378 737654 PROVISIONAL
2016-01-21 Sema4d  semaphorin 4D  Sema4d  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694042  uncharacterized LOC103694042      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Sema4d  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D   Sema4d_predicted  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sema4d_predicted  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (predicted)      Symbol and Name status set to approved 70820 APPROVED