Synb (syncytin b) - Rat Genome Database

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Gene: Synb (syncytin b) Rattus norvegicus
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Symbol: Synb
Name: syncytin b
RGD ID: 1566115
Description: Predicted to be involved in syncytium formation by plasma membrane fusion.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: endogenous retrovirus group FRD, member 1; envelope glycoprotein syncytin-B; Ervfrd-1; Herv-frd; HERV-FRD provirus ancestral Env polyprotein; LOC290348; RGD1566115; syncytin 2
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81550,989,313 - 50,996,237 (-)NCBIGRCr8
mRatBN7.21544,580,818 - 44,588,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,583,476 - 44,585,345 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1548,701,396 - 48,703,265 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,812,888 - 49,814,757 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,672,221 - 46,674,090 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,174,986 - 51,222,929 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,174,989 - 51,176,858 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01554,904,788 - 54,952,331 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,853,767 - 49,855,636 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1544,266,431 - 44,268,300 (-)NCBICelera
Cytogenetic Map15p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15644441   PMID:22032925   PMID:27589388   PMID:28604758  


Genomics

Comparative Map Data
Synb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81550,989,313 - 50,996,237 (-)NCBIGRCr8
mRatBN7.21544,580,818 - 44,588,417 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,583,476 - 44,585,345 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1548,701,396 - 48,703,265 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,812,888 - 49,814,757 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,672,221 - 46,674,090 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,174,986 - 51,222,929 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,174,989 - 51,176,858 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01554,904,788 - 54,952,331 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,853,767 - 49,855,636 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1544,266,431 - 44,268,300 (-)NCBICelera
Cytogenetic Map15p11NCBI
Gm27174
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391469,760,100 - 69,792,776 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1469,783,698 - 69,792,812 (-)EnsemblGRCm39 Ensembl
GRCm381469,508,628 - 69,555,417 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,508,632 - 69,512,549 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,546,249 - 69,555,332 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,289,344 - 69,294,299 (-)EnsemblGRCm38mm10GRCm38
MGSCv371469,908,455 - 69,912,356 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361468,243,728 - 68,247,629 (-)NCBIMGSCv36mm8
Celera1467,069,330 - 67,073,231 (-)NCBICelera
Cytogenetic Map14D2NCBI

Variants

.
Variants in Synb
18 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:19
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000038845
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat


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
Low 48 2
Below cutoff 1 22 24 17 10 17 2 2 22 16 32 6 2

Sequence


RefSeq Acc Id: ENSRNOT00000038845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1544,583,476 - 44,585,345 (-)Ensembl
Rnor_6.0 Ensembl1551,174,989 - 51,176,858 (-)Ensembl
RefSeq Acc Id: NM_001024239   ⟹   NP_001019410
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81550,993,279 - 50,995,148 (-)NCBI
mRatBN7.21544,583,476 - 44,585,345 (-)NCBI
Rnor_6.01551,174,989 - 51,176,858 (-)NCBI
Rnor_5.01554,904,788 - 54,952,331 (-)NCBI
RGSC_v3.41549,853,767 - 49,855,636 (-)RGD
Celera1544,266,431 - 44,268,300 (-)RGD
Sequence:
RefSeq Acc Id: XM_039093147   ⟹   XP_038949075
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81550,989,313 - 50,996,237 (-)NCBI
mRatBN7.21544,580,818 - 44,588,417 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001019410 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949075 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAW62451 (Get FASTA)   NCBI Sequence Viewer  
  EDM02185 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000085548
  ENSRNOP00000085548.1
RefSeq Acc Id: NP_001019410   ⟸   NM_001024239
- Peptide Label: precursor
- UniProtKB: A0A8I6A443 (UniProtKB/TrEMBL),   A6HTH2 (UniProtKB/TrEMBL),   Q5G5D0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038949075   ⟸   XM_039093147
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A443 (UniProtKB/TrEMBL),   A6HTH2 (UniProtKB/TrEMBL),   Q5G5D0 (UniProtKB/TrEMBL)

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-13264 BioCyc
Ensembl Genes ENSRNOG00000021823 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038845 ENTREZGENE
  ENSRNOT00000038845.6 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.210 UniProtKB/TrEMBL
InterPro TLV/ENV_coat_polyprotein UniProtKB/TrEMBL
KEGG Report rno:290348 UniProtKB/TrEMBL
NCBI Gene 290348 ENTREZGENE
PANTHER PTHR10424 UniProtKB/TrEMBL
  SYNCYTIN-2 UniProtKB/TrEMBL
Pfam TLV_coat UniProtKB/TrEMBL
PhenoGen Synb PhenoGen
RatGTEx ENSRNOG00000021823 RatGTEx
Superfamily-SCOP Virus ectodomain UniProtKB/TrEMBL
UniProt A0A8I6A443 ENTREZGENE, UniProtKB/TrEMBL
  A6HTH2 ENTREZGENE, UniProtKB/TrEMBL
  Q5G5D0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-02-25 Synb  syncytin b  Ervfrd-1  endogenous retrovirus group FRD, member 1  Name and Symbol changed 629549 APPROVED
2011-08-02 Ervfrd-1  endogenous retrovirus group FRD, member 1  Herv-frd  HERV-FRD provirus ancestral Env polyprotein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Herv-frd  HERV-FRD provirus ancestral Env polyprotein  RGD1566115_predicted  envelope glycoprotein syncytin-B (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566115_predicted  envelope glycoprotein syncytin-B (predicted)  LOC290348  envelope glycoprotein syncytin-B  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC290348  envelope glycoprotein syncytin-B      Symbol and Name status set to provisional 70820 PROVISIONAL