Syna (syncytin a) - Rat Genome Database

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Gene: Syna (syncytin a) Mus musculus
Analyze
Symbol: Syna
Name: syncytin a
RGD ID: 1615713
MGI Page MGI
Description: Acts upstream of or within labyrinthine layer development and myoblast fusion. Predicted to be located in plasma membrane. Is expressed in several structures, including extraembryonic component; ganglia; heart ventricle; musculoskeletal system; and placenta. Orthologous to human ERVFRD-1 (endogenous retrovirus group FRD member 1, envelope).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: envelope glycoprotein syncytin-A; Gm453; Gm52; syncy; syncytin-A
RGD Orthologs
Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,586,108 - 134,605,891 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5134,587,000 - 134,589,025 (-)EnsemblGRCm39 Ensembl
GRCm385134,557,254 - 134,577,038 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,558,146 - 134,560,171 (-)EnsemblGRCm38mm10GRCm38
MGSCv375135,034,110 - 135,035,963 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365134,842,867 - 134,844,720 (-)NCBIMGSCv36mm8
Celera5131,565,945 - 131,567,798 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.67NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15644441   PMID:17105734   PMID:17762178   PMID:18077339   PMID:18167345   PMID:18448564   PMID:19564597   PMID:20652949   PMID:20685850   PMID:21238448   PMID:21267068  
PMID:21435445   PMID:21558372   PMID:21606200   PMID:21729874   PMID:21873635   PMID:21972064   PMID:22032925   PMID:22109522   PMID:22684254   PMID:23364048   PMID:23610556   PMID:23807393  
PMID:23830620   PMID:25078604   PMID:26292834   PMID:26476147   PMID:26812015   PMID:26907377   PMID:27542691   PMID:27589388   PMID:27930960   PMID:27991852   PMID:28526753   PMID:28679758  
PMID:28935154   PMID:29500366   PMID:30158284   PMID:30718289   PMID:31338035   PMID:31360740   PMID:31675530   PMID:32513715   PMID:32798765   PMID:32959379   PMID:33842485   PMID:34767447  
PMID:34850819   PMID:34957089   PMID:34963058   PMID:35493107   PMID:37019373   PMID:37060937   PMID:38374152  


Genomics

Comparative Map Data
Syna
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,586,108 - 134,605,891 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5134,587,000 - 134,589,025 (-)EnsemblGRCm39 Ensembl
GRCm385134,557,254 - 134,577,038 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,558,146 - 134,560,171 (-)EnsemblGRCm38mm10GRCm38
MGSCv375135,034,110 - 135,035,963 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365134,842,867 - 134,844,720 (-)NCBIMGSCv36mm8
Celera5131,565,945 - 131,567,798 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.67NCBI
Ervfrd-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81227,787,680 - 27,794,732 (+)NCBIGRCr8
mRatBN7.21222,151,211 - 22,158,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1222,151,211 - 22,158,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1223,294,443 - 23,301,347 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01223,905,524 - 23,912,428 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01222,972,115 - 22,979,027 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,161,130 - 25,168,182 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,161,130 - 25,168,182 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,161,524 - 27,168,576 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,220,471 - 23,222,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1223,915,041 - 23,922,023 (+)NCBICelera
Cytogenetic Map12q12NCBI

Variants

.
Variants in Syna
793 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:423
Count of miRNA genes:295
Interacting mature miRNAs:336
Transcripts:ENSMUST00000149604
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301715Elmaz2_melevated maze behavior 2 (mouse)Not determined5125178229141700466Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572857343139985755Mouse
10412191Bbaa24_mB.burgdorferi-associated arthritis 24 (mouse)Not determined5119945037141700466Mouse
13464143Bbaa2b_mB.burgdorferi-associated arthritis 2b (mouse)5133052969140709801Mouse
11528552Scram1_mspinal cord resistance to astrocytoma modifier 1 (mouse)5121455402151758149Mouse
1300827Cora1_mcorrelation in cytokine production 1 (mouse)Not determined5115156883149157015Mouse
14746986Manh58_mmandible shape 58 (mouse)5102446283136446283Mouse
10412239Alpq7_malcohol preference QTL 7 (mouse)Not determined5104705939138705939Mouse
12880406Jcdq2_mjoint cartilage degeneration QTL 2 (mouse)5129787831151758149Mouse
4141218Ath24_matherosclerosis 24 (mouse)Not determined129520084151758149Mouse
12859290Criq2_mCitrobacter rodentium infection QTL 2 (mouse)5101332579135332579Mouse
1301363Pbwg13_mpostnatal body weight growth 13 (mouse)Not determined5125133457151758149Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589418876146787935Mouse
1300913Bwefm_mbody weight females and males day 10 (mouse)Not determined5109439348143439459Mouse
4141081Nidd7k_mNidd7 on KK-A (mouse)Not determined119945037149347326Mouse
1301624Aevm2_mautoimmune extremity vasculitis in MRL mice 2 (mouse)Not determined5101863832135864028Mouse
10043890Trigq4_mtriglyceride QTL 4 (mouse)Not determined5107906299141906412Mouse
1302079Lbw3_mlupus NZB x NZW 3 (mouse)Not determined5124700335151758149Mouse
11532736Sluc33b_msusceptibility to lung cancer 33b (mouse)5102945037136945196Mouse
1301986Bpq4_mblood pressure QTL 4 (mouse)Not determined5121555236151758149Mouse
1301857Bglq14_mbody growth late QTL 14 (mouse)Not determined5118948964151758149Mouse
1301543Hypch_mhypercholesterolemia (mouse)Not determined5109238624139118905Mouse
10412202Bbaa26_mB.burgdorferi-associated arthritis 26 (mouse)Not determined5104583688138555455Mouse
12904945Tammq2_mtibialis anterior muscle mass QTL 2 (mouse)5100665965134665965Mouse
4142473Chlq11_mcirculating hormone level QTL 11 (mouse)Not determined5107906299141906412Mouse
13464251Ahl21_mage related hearing loss, early onset 21 (mouse)5109167240143167381Mouse
1301226Bbaa2_mB.burgdorferi-associated arthritis 2 (mouse)Not determined5115156883149157015Mouse
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526441234138455402Mouse
10412197Bbaa25_mB.burgdorferi-associated arthritis 25 (mouse)Not determined5109167240143167381Mouse
12904959Smmq1_msoleus muscle mass QTL 1 (mouse)5100665965134665965Mouse
1301102Cia14_mcollagen induced arthritis 14 (mouse)Not determined5113320385138555455Mouse
11049557Lmr26_mleishmaniasis resistance 26 (mouse)5133925558151758149Mouse
13464243Ahl20_mage related hearing loss, early onset 20 (mouse)5107906299141906412Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000149604   ⟹   ENSMUSP00000116437
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5134,587,000 - 134,589,025 (-)Ensembl
GRCm38.p6 Ensembl5134,558,146 - 134,560,171 (-)Ensembl
RefSeq Acc Id: NM_001013751   ⟹   NP_001013773
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,589,025 (-)NCBI
GRCm385134,557,254 - 134,560,171 (-)NCBI
MGSCv375135,034,110 - 135,035,963 (-)RGD
Celera5131,564,959 - 131,567,876 (-)ENTREZGENE
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006504404   ⟹   XP_006504467
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006504406   ⟹   XP_006504469
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011240874   ⟹   XP_011239176
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011240875   ⟹   XP_011239177
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011240877   ⟹   XP_011239179
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030254356   ⟹   XP_030110216
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,592,955 (-)NCBI
GRCm385134,557,254 - 134,564,102 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030254357   ⟹   XP_030110217
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395134,586,108 - 134,605,891 (-)NCBI
GRCm385134,557,254 - 134,577,037 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001013773   ⟸   NM_001013751
- Peptide Label: precursor
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006504467   ⟸   XM_006504404
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006504469   ⟸   XM_006504406
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011239177   ⟸   XM_011240875
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011239176   ⟸   XM_011240874
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011239179   ⟸   XM_011240877
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030110217   ⟸   XM_030254357
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_030110216   ⟸   XM_030254356
- Peptide Label: isoform X1
- UniProtKB: Q5G5D5 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSMUSP00000116437   ⟸   ENSMUST00000149604

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5G5D5-F1-model_v2 AlphaFold Q5G5D5 1-617 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2684898 AgrOrtholog
Ensembl Genes ENSMUSG00000085957 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000149604 ENTREZGENE
  ENSMUST00000149604.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.287.210 UniProtKB/Swiss-Prot
InterPro TLV/ENV_coat_polyprotein UniProtKB/Swiss-Prot
KEGG Report mmu:214292 UniProtKB/Swiss-Prot
MGD MGI:2684898 ENTREZGENE
NCBI Gene 214292 ENTREZGENE
PANTHER ENDOGENOUS RETROVIRUS GROUP S71 MEMBER 1 ENV POLYPROTEIN-RELATED UniProtKB/Swiss-Prot
  PTHR10424 UniProtKB/Swiss-Prot
Pfam TLV_coat UniProtKB/Swiss-Prot
PhenoGen Syna PhenoGen
Superfamily-SCOP Virus ectodomain UniProtKB/Swiss-Prot
UniProt Q5G5D5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-18 Syna  syncytin a  Gm52  predicted gene 52  Symbol and/or name change 5135510 APPROVED