Sema6b (semaphorin 6B) - Rat Genome Database

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Gene: Sema6b (semaphorin 6B) Rattus norvegicus
Analyze
Symbol: Sema6b
Name: semaphorin 6B
RGD ID: 69278
Description: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy. Orthologous to human SEMA6B (semaphorin 6B); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: sema domain transmembrane domain (TM) and cytoplasmic domain (semaphorin) 6B; sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B; sema Z; semaphorin-6B; semaphorin-Z
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,038,103 - 1,055,063 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,038,103 - 1,048,868 (-)EnsemblGRCr8
mRatBN7.29950,939 - 967,905 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9950,939 - 961,521 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,397,335 - 1,406,976 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,744,614 - 6,754,255 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,702,372 - 5,712,013 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,934,273 - 10,951,252 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,941,613 - 10,951,252 (+)Ensemblrn6Rnor6.0
Rnor_5.099,921,231 - 9,938,199 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera97,547,095 - 7,556,706 (+)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
plasma membrane  (IBA,IEA)

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. Molecular cloning of a novel member of semaphorin family genes, semaphorin Z. Kikuchi K, etal., Brain Res Mol Brain Res 1997 Nov;51(1-2):229-37.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:15814794  


Genomics

Comparative Map Data
Sema6b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,038,103 - 1,055,063 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,038,103 - 1,048,868 (-)EnsemblGRCr8
mRatBN7.29950,939 - 967,905 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9950,939 - 961,521 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,397,335 - 1,406,976 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,744,614 - 6,754,255 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,702,372 - 5,712,013 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,934,273 - 10,951,252 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,941,613 - 10,951,252 (+)Ensemblrn6Rnor6.0
Rnor_5.099,921,231 - 9,938,199 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera97,547,095 - 7,556,706 (+)NCBICelera
Cytogenetic Map9q11NCBI
SEMA6B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,542,593 - 4,559,684 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,542,588 - 4,581,784 (-)Ensemblhg38GRCh38
GRCh37194,542,605 - 4,559,696 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,493,600 - 4,509,503 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34194,493,599 - 4,509,503NCBI
Celera194,481,386 - 4,497,296 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,304,316 - 4,321,196 (-)NCBIHuRef
CHM1_1194,542,791 - 4,559,971 (-)NCBICHM1_1
T2T-CHM13v2.0194,526,261 - 4,543,368 (-)NCBIT2T-CHM13v2.0
Sema6b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,430,085 - 56,447,343 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,430,085 - 56,447,343 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381756,123,085 - 56,140,343 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,123,085 - 56,140,343 (-)Ensemblmm10GRCm38
MGSCv371756,262,508 - 56,279,766 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361755,716,378 - 55,726,158 (-)NCBIMGSCv36mm8
Celera1759,541,746 - 59,547,130 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.17NCBI
Sema6b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,388,516 - 4,399,313 (+)Ensembl
ChiLan1.0NW_0049554954,387,147 - 4,399,430 (+)NCBIChiLan1.0ChiLan1.0
SEMA6B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2208,937,116 - 8,975,577 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,166,915 - 8,205,350 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,562,673 - 3,600,981 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,510,286 - 4,528,178 (-)NCBIPanPan1.1PanPan1.1panPan2
SEMA6B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,151,913 - 55,173,434 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,161,818 - 55,173,135 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2054,874,562 - 54,901,970 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02055,803,993 - 55,831,315 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,820,883 - 55,831,921 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,881,306 - 54,893,886 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,346,572 - 55,374,433 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,545,006 - 55,572,679 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sema6b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,172,541 - 215,192,053 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,642,859 - 2,653,742 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,642,730 - 2,654,520 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA6B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,258,439 - 74,296,385 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1274,262,303 - 74,296,386 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SEMA6B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,276,548 - 4,304,738 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660813,880,980 - 3,921,504 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sema6b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,182,812 - 5,192,486 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248285,170,745 - 5,193,568 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sema6b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1487,511,871 - 87,528,714 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sema6b
47 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:128
Interacting mature miRNAs:159
Transcripts:ENSRNOT00000070794
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631533Iresp3Immunoglobin response QTL316.2blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)916094576Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat

Markers in Region
D9Wox41  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29951,427 - 951,555 (-)MAPPERmRatBN7.2
Rnor_6.0910,950,636 - 10,950,763NCBIRnor6.0
Rnor_5.099,937,583 - 9,937,710UniSTSRnor5.0
Celera97,556,090 - 7,556,217UniSTS
Cytogenetic Map9q11UniSTS
RH135075  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29951,032 - 951,223 (-)MAPPERmRatBN7.2
Rnor_6.0910,950,968 - 10,951,158NCBIRnor6.0
Rnor_5.099,937,915 - 9,938,105UniSTSRnor5.0
Celera97,556,422 - 7,556,612UniSTS
Cytogenetic Map9q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 66 163 91 90 59 92 59 6 352 191 11 142 78 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000070794   ⟹   ENSRNOP00000067668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,038,103 - 1,047,742 (-)Ensembl
mRatBN7.2 Ensembl9950,939 - 960,579 (-)Ensembl
Rnor_6.0 Ensembl910,941,613 - 10,951,252 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107355   ⟹   ENSRNOP00000078468
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,038,103 - 1,048,868 (-)Ensembl
mRatBN7.2 Ensembl9950,939 - 961,521 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000144717   ⟹   ENSRNOP00000098799
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,038,103 - 1,048,868 (-)Ensembl
RefSeq Acc Id: NM_053471   ⟹   NP_445923
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,038,103 - 1,047,742 (-)NCBI
mRatBN7.29950,939 - 960,579 (-)NCBI
Rnor_6.0910,941,613 - 10,951,252 (+)NCBI
Rnor_5.099,921,231 - 9,938,199 (+)NCBI
Celera97,547,095 - 7,556,706 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244348   ⟹   XP_006244410
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,038,104 - 1,048,968 (-)NCBI
mRatBN7.29950,940 - 961,655 (-)NCBI
Rnor_6.0910,939,712 - 10,951,251 (+)NCBI
Rnor_5.099,921,231 - 9,938,199 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244349   ⟹   XP_006244411
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,038,104 - 1,055,063 (-)NCBI
mRatBN7.29950,940 - 967,905 (-)NCBI
Rnor_6.0910,934,273 - 10,951,251 (+)NCBI
Rnor_5.099,921,231 - 9,938,199 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_445923 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244410 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244411 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA25687 (Get FASTA)   NCBI Sequence Viewer  
  EDL83655 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067668
  ENSRNOP00000078468
GenBank Protein O70141 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_445923   ⟸   NM_053471
- Peptide Label: precursor
- UniProtKB: O70141 (UniProtKB/Swiss-Prot),   A0A8L2QYG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244411   ⟸   XM_006244349
- Peptide Label: isoform X2
- UniProtKB: O70141 (UniProtKB/Swiss-Prot),   A0A8L2QYG3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244410   ⟸   XM_006244348
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZKZ1 (UniProtKB/TrEMBL),   A6KQZ7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000067668   ⟸   ENSRNOT00000070794
Ensembl Acc Id: ENSRNOP00000078468   ⟸   ENSRNOT00000107355
Ensembl Acc Id: ENSRNOP00000098799   ⟸   ENSRNOT00000144717
Protein Domains
Sema

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O70141-F1-model_v2 AlphaFold O70141 1-887 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:69278 AgrOrtholog
BioCyc Gene G2FUF-28560 BioCyc
Ensembl Genes ENSRNOG00000045998 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000070794 ENTREZGENE
  ENSRNOT00000107355 ENTREZGENE
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
  ligand-binding face of the semaphorins, domain 2 UniProtKB/Swiss-Prot
InterPro Plexin_repeat UniProtKB/Swiss-Prot
  Semap_dom UniProtKB/Swiss-Prot
  Semap_dom_sf UniProtKB/Swiss-Prot
  Semaphorin UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:84609 UniProtKB/Swiss-Prot
NCBI Gene 84609 ENTREZGENE
PANTHER PTHR11036 UniProtKB/Swiss-Prot
  SEMAPHORIN-6B UniProtKB/Swiss-Prot
Pfam PSI UniProtKB/Swiss-Prot
  Sema UniProtKB/Swiss-Prot
PhenoGen Sema6b PhenoGen
PROSITE SEMA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000045998 RatGTEx
SMART Sema UniProtKB/Swiss-Prot
Superfamily-SCOP Plexin repeat UniProtKB/Swiss-Prot
  SSF101912 UniProtKB/Swiss-Prot
TIGR TC227747
UniProt A0A8I5ZKZ1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QYG3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LCQ5_RAT UniProtKB/TrEMBL
  A6KQZ7 ENTREZGENE, UniProtKB/TrEMBL
  O70141 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema6b  semaphorin 6B  Sema6b  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Sema6b  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B  Sema6b  semaphorin 6B  Name updated 1299863 APPROVED
2004-09-10 Sema6b  sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B    semaphorin 6B  Name updated 1299863 APPROVED
2002-06-10 Sema6b  semaphorin 6B      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of the semaphorin/collapsin family of proteins 68847