Sema3d (semaphorin 3D) - Rat Genome Database

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Gene: Sema3d (semaphorin 3D) Ictidomys tridecemlineatus
Analyze
Symbol: Sema3d
Name: semaphorin 3D
RGD ID: 12620398
Description: ENCODES a protein that exhibits chemorepellent activity (inferred); semaphorin receptor binding (inferred); INVOLVED IN axon guidance (inferred); negative regulation of axon extension involved in axon guidance (inferred); neural crest cell migration (inferred); ASSOCIATED WITH CHARGE syndrome (ortholog); epilepsy (ortholog); genetic disease (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred); membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: semaphorin-3D
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511865,778,860 - 65,961,152 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936789933,877 - 1,053,566 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936789872,760 - 1,053,606 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
Sema3d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511865,778,860 - 65,961,152 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936789933,877 - 1,053,566 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936789872,760 - 1,053,606 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA3D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38784,995,553 - 85,250,243 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl784,995,553 - 85,187,056 (-)EnsemblGRCh38hg38GRCh38
GRCh37784,624,869 - 84,879,559 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36784,462,805 - 84,589,183 (-)NCBINCBI36Build 36hg18NCBI36
Build 34784,269,521 - 84,395,898NCBI
Celera779,328,907 - 79,455,300 (-)NCBICelera
Cytogenetic Map7q21.11NCBI
HuRef779,234,320 - 79,360,917 (-)NCBIHuRef
CHM1_1784,555,054 - 84,681,432 (-)NCBICHM1_1
T2T-CHM13v2.0786,245,383 - 86,500,064 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2783,956,759 - 84,083,147 (-)NCBI
Sema3d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39512,433,133 - 12,638,920 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl512,433,352 - 12,638,915 (+)EnsemblGRCm39 Ensembl
GRCm38512,383,161 - 12,588,953 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl512,383,385 - 12,588,948 (+)EnsemblGRCm38mm10GRCm38
MGSCv37512,383,166 - 12,588,943 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36512,389,562 - 12,593,064 (+)NCBIMGSCv36mm8
Celera1222,750,770 - 22,952,639 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map53.97NCBI
Sema3d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8423,271,815 - 23,460,971 (-)NCBIGRCr8
mRatBN7.2422,316,769 - 22,505,930 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl422,316,779 - 22,505,930 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx427,324,703 - 27,511,651 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0423,250,906 - 23,437,865 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0421,624,497 - 21,811,446 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0419,224,378 - 19,413,519 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl419,224,310 - 19,413,484 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0419,169,059 - 19,359,164 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4418,641,725 - 18,832,339 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1418,657,541 - 18,695,693 (-)NCBI
Celera417,832,750 - 18,021,791 (-)NCBICelera
Cytogenetic Map4q12NCBI
Sema3d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554101,400,839 - 1,498,172 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554101,356,787 - 1,510,394 (+)NCBIChiLan1.0ChiLan1.0
SEMA3D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26102,851,559 - 103,042,950 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17151,115,741 - 151,307,498 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0776,964,151 - 77,155,472 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1790,624,393 - 90,750,389 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl790,624,398 - 90,750,389 (-)Ensemblpanpan1.1panPan2
SEMA3D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11824,254,113 - 24,429,767 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1824,262,125 - 24,394,155 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1823,932,740 - 24,149,080 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01824,708,889 - 24,925,861 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1824,719,837 - 24,925,292 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11824,357,283 - 24,573,713 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01823,871,664 - 24,088,431 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01824,538,712 - 24,755,683 (-)NCBIUU_Cfam_GSD_1.0
SEMA3D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl995,280,593 - 95,486,090 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1995,280,637 - 95,486,109 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29105,461,182 - 105,525,530 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA3D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12163,794,289 - 63,923,280 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2163,794,281 - 63,919,352 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604240,083,998 - 40,246,334 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema3d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473932,981,101 - 33,086,376 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473932,981,158 - 33,143,250 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005340343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSSTOT00000006169   ⟹   ENSSTOP00000005518
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_004936789933,877 - 1,053,566 (+)Ensembl
RefSeq Acc Id: XM_005340343   ⟹   XP_005340400
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440511865,778,860 - 65,961,152 (-)NCBI
SpeTri2.0NW_004936789872,760 - 1,053,606 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005340400 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000005518.3
GenBank Protein KAG3277878 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005340400   ⟸   XM_005340343
- UniProtKB: I3M7D6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000005518   ⟸   ENSSTOT00000006169
Protein Domains
Ig-like   Sema


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000006144 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000006169.3 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_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  IL-1RAcP-like_ig UniProtKB/TrEMBL
  PSI UniProtKB/TrEMBL
  Semap_dom UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/TrEMBL
NCBI Gene Sema3d ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
  SEMAPHORIN-3D UniProtKB/TrEMBL
Pfam Ig_6 UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  SEMA UniProtKB/TrEMBL
SMART PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP Plexin repeat UniProtKB/TrEMBL
  SSF101912 UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt I3M7D6 ENTREZGENE, UniProtKB/TrEMBL