Synpr (synaptoporin) - Rat Genome Database

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Gene: Synpr (synaptoporin) Rattus norvegicus
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Symbol: Synpr
Name: synaptoporin
RGD ID: 708366
Description: Involved in modulation of chemical synaptic transmission. Is active in hippocampal mossy fiber to CA3 synapse and synaptic vesicle membrane. Orthologous to human SYNPR (synaptoporin); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC66030; synaptorin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81514,003,861 - 14,330,808 (-)NCBIGRCr8
mRatBN7.21511,573,373 - 11,900,255 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,574,231 - 11,900,243 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,688,000 - 13,865,250 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,646,914 - 14,824,357 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,901,297 - 13,078,555 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01514,558,613 - 14,885,790 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1514,559,471 - 14,737,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01518,562,041 - 18,889,455 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41513,135,331 - 13,314,004 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11513,135,330 - 13,314,004 (-)NCBI
Celera1511,575,871 - 11,752,702 (-)NCBICelera
Cytogenetic Map15p16-p15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Cloning and sequence analysis of the human cDNA encoding the synaptoporin (delta), a highly conservative synaptic vesicle protein. Dai J, etal., Mol Biol Rep 2003 Sep;30(3):185-91.
2. 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.
3. Synaptoporin, a novel putative channel protein of synaptic vesicles. Knaus P, etal., Neuron. 1990 Oct;5(4):453-62.
4. Mossy fiber-CA3 synapses mediate homeostatic plasticity in mature hippocampal neurons. Lee KJ, etal., Neuron. 2013 Jan 9;77(1):99-114. doi: 10.1016/j.neuron.2012.10.033.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Synpr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81514,003,861 - 14,330,808 (-)NCBIGRCr8
mRatBN7.21511,573,373 - 11,900,255 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1511,574,231 - 11,900,243 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1513,688,000 - 13,865,250 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01514,646,914 - 14,824,357 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01512,901,297 - 13,078,555 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01514,558,613 - 14,885,790 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1514,559,471 - 14,737,704 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01518,562,041 - 18,889,455 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41513,135,331 - 13,314,004 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11513,135,330 - 13,314,004 (-)NCBI
Celera1511,575,871 - 11,752,702 (-)NCBICelera
Cytogenetic Map15p16-p15NCBI
SYNPR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38363,200,604 - 63,616,924 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl363,228,315 - 63,616,924 (+)EnsemblGRCh38hg38GRCh38
GRCh37363,263,984 - 63,602,600 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36363,404,064 - 63,577,637 (+)NCBINCBI36Build 36hg18NCBI36
Build 34363,404,063 - 63,577,636NCBI
Celera363,280,648 - 63,619,333 (+)NCBICelera
Cytogenetic Map3p14.2NCBI
HuRef363,360,993 - 63,699,969 (+)NCBIHuRef
CHM1_1363,215,310 - 63,554,108 (+)NCBICHM1_1
T2T-CHM13v2.0363,244,200 - 63,660,530 (+)NCBIT2T-CHM13v2.0
Synpr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39148,854,294 - 9,184,983 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl148,853,423 - 9,184,983 (-)EnsemblGRCm39 Ensembl
GRCm381413,284,780 - 13,615,469 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1413,284,780 - 13,616,340 (+)EnsemblGRCm38mm10GRCm38
MGSCv371414,117,294 - 14,447,983 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361412,078,047 - 12,408,726 (+)NCBIMGSCv36mm8
Celera148,928,251 - 9,266,833 (+)NCBICelera
Cytogenetic Map14A1NCBI
cM Map146.86NCBI
Synpr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555172,261,015 - 2,442,443 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555172,261,080 - 2,442,271 (-)NCBIChiLan1.0ChiLan1.0
SYNPR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2263,205,892 - 63,542,431 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1363,210,686 - 63,547,217 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0363,186,196 - 63,523,267 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1364,569,563 - 64,905,748 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl364,569,397 - 64,908,183 (+)Ensemblpanpan1.1panPan2
SYNPR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12027,572,890 - 27,870,286 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2027,572,873 - 27,870,670 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2027,497,123 - 27,793,776 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02027,809,852 - 28,100,442 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2027,809,849 - 28,101,384 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12027,306,785 - 27,597,138 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02027,656,399 - 27,947,102 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02027,759,805 - 28,049,965 (-)NCBIUU_Cfam_GSD_1.0
Synpr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118164,407,153 - 164,739,359 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366372,796,683 - 3,129,230 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366372,796,707 - 3,128,916 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNPR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1344,841,353 - 45,164,808 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11344,841,224 - 45,164,810 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21349,526,698 - 49,589,538 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYNPR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12224,335,530 - 24,666,503 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2224,496,970 - 24,666,709 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041142,172,137 - 142,509,232 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Synpr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248882,317,425 - 2,608,771 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248882,317,515 - 2,608,719 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Synpr
2569 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:318
Count of miRNA genes:177
Interacting mature miRNAs:206
Transcripts:ENSRNOT00000011307
Prediction methods:Microtar, Miranda
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
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat

Markers in Region
BF415513  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21511,737,666 - 11,737,773 (+)MAPPERmRatBN7.2
Rnor_6.01514,723,493 - 14,723,599NCBIRnor6.0
Rnor_5.01518,727,155 - 18,727,261UniSTSRnor5.0
RGSC_v3.41513,299,790 - 13,299,896UniSTSRGSC3.4
Celera1511,738,477 - 11,738,583UniSTS
RH 3.4 Map1595.8UniSTS
Cytogenetic Map15p16UniSTS


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 9 47 111 55 53 23 25 23 6 176 92 91 44 54 30

Sequence


Ensembl Acc Id: ENSRNOT00000011307   ⟹   ENSRNOP00000011307
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1511,574,231 - 11,751,881 (-)Ensembl
Rnor_6.0 Ensembl1514,559,471 - 14,737,704 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000086502   ⟹   ENSRNOP00000071839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1511,574,231 - 11,712,530 (-)Ensembl
Rnor_6.0 Ensembl1514,559,997 - 14,622,587 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100360   ⟹   ENSRNOP00000076574
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1511,574,231 - 11,900,243 (-)Ensembl
RefSeq Acc Id: NM_023974   ⟹   NP_076464
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81514,004,715 - 14,182,357 (-)NCBI
mRatBN7.21511,574,231 - 11,751,881 (-)NCBI
Rnor_6.01514,559,471 - 14,737,704 (-)NCBI
Rnor_5.01518,562,041 - 18,889,455 (-)NCBI
RGSC_v3.41513,135,331 - 13,314,004 (-)RGD
Celera1511,575,871 - 11,752,702 (-)RGD
Sequence:
RefSeq Acc Id: XM_039093644   ⟹   XP_038949572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81514,003,861 - 14,330,808 (-)NCBI
mRatBN7.21511,573,373 - 11,900,255 (-)NCBI
RefSeq Acc Id: XM_063274618   ⟹   XP_063130688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81514,003,861 - 14,280,170 (-)NCBI
RefSeq Acc Id: NP_076464   ⟸   NM_023974
- Peptide Label: precursor
- UniProtKB: Q9ERH1 (UniProtKB/Swiss-Prot),   P22831 (UniProtKB/Swiss-Prot),   A6K083 (UniProtKB/TrEMBL),   A0A0G2K1H2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071839   ⟸   ENSRNOT00000086502
Ensembl Acc Id: ENSRNOP00000011307   ⟸   ENSRNOT00000011307
RefSeq Acc Id: XP_038949572   ⟸   XM_039093644
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZK40 (UniProtKB/TrEMBL),   A6K082 (UniProtKB/TrEMBL),   A0A0G2K1H2 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000076574   ⟸   ENSRNOT00000100360
RefSeq Acc Id: XP_063130688   ⟸   XM_063274618
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K1H2 (UniProtKB/TrEMBL)
Protein Domains
MARVEL

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P22831-F1-model_v2 AlphaFold P22831 1-265 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:708366 AgrOrtholog
BioCyc Gene G2FUF-14365 BioCyc
Ensembl Genes ENSRNOG00000008203 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011307 ENTREZGENE
  ENSRNOT00000011307.6 UniProtKB/Swiss-Prot
  ENSRNOT00000100360 ENTREZGENE
  ENSRNOT00000127244 ENTREZGENE
InterPro Marvel UniProtKB/Swiss-Prot
  Synaptophysin/porin UniProtKB/Swiss-Prot
KEGG Report rno:66030 UniProtKB/Swiss-Prot
NCBI Gene 66030 ENTREZGENE
PANTHER PTHR10306 UniProtKB/Swiss-Prot
  SYNAPTOPORIN UniProtKB/Swiss-Prot
Pfam MARVEL UniProtKB/Swiss-Prot
PhenoGen Synpr PhenoGen
PRINTS SYNAPTOPHYSN UniProtKB/Swiss-Prot
PROSITE MARVEL UniProtKB/Swiss-Prot
  SYNAPTOP UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000008203 RatGTEx
UniProt A0A0G2K1H2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZK40 ENTREZGENE, UniProtKB/TrEMBL
  A6K082 ENTREZGENE, UniProtKB/TrEMBL
  A6K083 ENTREZGENE, UniProtKB/TrEMBL
  A6K084_RAT UniProtKB/TrEMBL
  P22831 ENTREZGENE
  Q9ERH1 ENTREZGENE
  SYNPR_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q9ERH1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-04-22 Synpr  synaptoporin  LOC66030  synaptorin  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED