Cplx1 (complexin 1) - Rat Genome Database

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Gene: Cplx1 (complexin 1) Rattus norvegicus
Analyze
Symbol: Cplx1
Name: complexin 1
RGD ID: 70944
Description: Enables syntaxin-1 binding activity. Involved in synaptic vesicle exocytosis. Located in dendrite; neuronal cell body; and synapse. Part of synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex. Is active in postsynapse and presynapse. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 63. Orthologous to human CPLX1 (complexin 1); INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: complexin I; complexin-1; CPX I; synaphin-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,184,638 - 1,216,392 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx141,083,688 - 1,115,359 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0142,385,452 - 2,417,121 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0141,082,163 - 1,113,835 (+)NCBIRnor_WKY
Rnor_6.0142,194,895 - 2,226,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,194,933 - 2,226,598 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0142,189,521 - 2,220,992 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4141,732,344 - 1,763,172 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1141,732,343 - 1,763,172 (+)NCBI
Celera141,225,465 - 1,255,747 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Munc18-1 binding to the neuronal SNARE complex controls synaptic vesicle priming. Deak F, etal., J Cell Biol. 2009 Mar 9;184(5):751-64. Epub 2009 Mar 2.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Binding of the Munc13-1 MUN domain to membrane-anchored SNARE complexes. Guan R, etal., Biochemistry. 2008 Feb 12;47(6):1474-81. Epub 2008 Jan 18.
5. Distinct regional distribution in the brain of messenger RNAs for the two isoforms of synaphin associated with the docking/fusion complex. Ishizuka T, etal., Neuroscience 1999 Jan;88(1):295-306.
6. Complexins: cytosolic proteins that regulate SNAP receptor function. McMahon HT, etal., Cell 1995 Oct 6;83(1):111-9.
7. Gene Data Set MGD Curation, June 12, 2002
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. Rapid and selective binding to the synaptic SNARE complex suggests a modulatory role of complexins in neuroexocytosis. Pabst S, etal., J Biol Chem 2002 Mar 8;277(10):7838-48.
11. Complexins regulate a late step in Ca2+-dependent neurotransmitter release. Reim K, etal., Cell 2001 Jan 12;104(1):71-81.
12. GOA pipeline RGD automated data pipeline
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
15. Complexin I knockout rats exhibit a complex neurobehavioral phenotype including profound ataxia and marked deficits in lifespan. Xu Y, etal., Pflugers Arch. 2020 Jan;472(1):117-133. doi: 10.1007/s00424-019-02337-5. Epub 2019 Dec 24.
16. Immunohistochemical distribution of the two isoforms of synaphin/complexin involved in neurotransmitter release: localization at the distinct central nervous system regions and synaptic types. Yamada M, etal., Neuroscience. 1999;93(1):7-18.
Additional References at PubMed
PMID:9753100   PMID:10777504   PMID:11832227   PMID:12477932   PMID:15126625   PMID:15489334   PMID:15911881   PMID:16430375   PMID:17828276   PMID:19132534   PMID:22284181   PMID:25122624  
PMID:25716318   PMID:26019341   PMID:27821736   PMID:29476059   PMID:29985126   PMID:30194295   PMID:36675068  


Genomics

Comparative Map Data
Cplx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,184,638 - 1,216,392 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx141,083,688 - 1,115,359 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0142,385,452 - 2,417,121 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0141,082,163 - 1,113,835 (+)NCBIRnor_WKY
Rnor_6.0142,194,895 - 2,226,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,194,933 - 2,226,598 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0142,189,521 - 2,220,992 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4141,732,344 - 1,763,172 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1141,732,343 - 1,763,172 (+)NCBI
Celera141,225,465 - 1,255,747 (+)NCBICelera
Cytogenetic Map14p22NCBI
CPLX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384784,957 - 826,129 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl4784,957 - 826,129 (-)EnsemblGRCh38hg38GRCh38
GRCh374778,745 - 819,917 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364768,745 - 809,945 (-)NCBINCBI36Build 36hg18NCBI36
Build 344768,575 - 809,775NCBI
Celera4715,373 - 756,500 (-)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef4749,326 - 788,854 (-)NCBIHuRef
CHM1_14775,692 - 816,930 (-)NCBICHM1_1
T2T-CHM13v2.04782,738 - 823,932 (-)NCBIT2T-CHM13v2.0
Cplx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395108,666,420 - 108,697,893 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5108,666,420 - 108,697,890 (-)EnsemblGRCm39 Ensembl
GRCm385108,518,554 - 108,550,027 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5108,518,554 - 108,550,024 (-)EnsemblGRCm38mm10GRCm38
MGSCv375108,947,573 - 108,979,046 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365108,758,861 - 108,790,234 (-)NCBIMGSCv36mm8
Celera5105,640,079 - 105,671,475 (-)NCBICelera
Cytogenetic Map5FNCBI
Cplx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955514359,174 - 376,916 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955514359,174 - 376,916 (-)NCBIChiLan1.0ChiLan1.0
CPLX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan141,057,716 - 1,098,985 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04889,037 - 930,046 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14819,833 - 858,953 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4819,833 - 858,953 (-)Ensemblpanpan1.1panPan2
CPLX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1391,635,953 - 91,658,084 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl391,638,515 - 91,656,737 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha394,100,889 - 94,123,599 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0392,634,899 - 92,657,654 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl392,636,465 - 92,657,651 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1391,806,223 - 91,828,878 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0391,859,863 - 91,882,527 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0392,243,776 - 92,266,460 (+)NCBIUU_Cfam_GSD_1.0
Cplx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528568,613,608 - 68,636,796 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647722,316,018 - 22,338,475 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647722,315,827 - 22,338,488 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPLX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8197,882 - 205,371 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18197,876 - 231,721 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2831,143 - 64,220 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CPLX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12747,959,109 - 48,002,338 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2747,959,091 - 48,002,527 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660514,341,575 - 4,386,462 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cplx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475526,266,614 - 26,288,079 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475526,265,590 - 26,286,203 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cplx1
100 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:448
Count of miRNA genes:211
Interacting mature miRNAs:274
Transcripts:ENSRNOT00000061720
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat

Markers in Region
AI454690  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2141,216,075 - 1,216,280 (+)MAPPERmRatBN7.2
Rnor_6.0142,226,294 - 2,226,498NCBIRnor6.0
Rnor_5.0142,220,676 - 2,220,880UniSTSRnor5.0
RGSC_v3.4141,762,856 - 1,763,060UniSTSRGSC3.4
Celera141,255,431 - 1,255,635UniSTS
Cytogenetic Map14p22UniSTS


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 64
Low 3 29 14 5 6 5 5 5 10 15 35 10 5
Below cutoff 14 36 29 13 29 3 6 20 6 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061720   ⟹   ENSRNOP00000058432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl142,194,933 - 2,226,598 (+)Ensembl
RefSeq Acc Id: NM_022864   ⟹   NP_074055
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,186,065 - 1,216,392 (+)NCBI
Rnor_6.0142,196,289 - 2,226,610 (+)NCBI
Rnor_5.0142,189,521 - 2,220,992 (+)NCBI
RGSC_v3.4141,732,344 - 1,763,172 (+)RGD
Celera141,225,465 - 1,255,747 (+)RGD
Sequence:
RefSeq Acc Id: XM_006250571   ⟹   XP_006250633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,184,638 - 1,216,382 (+)NCBI
Rnor_6.0142,194,895 - 2,226,600 (+)NCBI
Rnor_5.0142,189,521 - 2,220,992 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_074055   ⟸   NM_022864
- UniProtKB: Q64276 (UniProtKB/Swiss-Prot),   P63041 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250633   ⟸   XM_006250571
- Peptide Label: isoform X1
- UniProtKB: P63041 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058432   ⟸   ENSRNOT00000061720

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P63041-F1-model_v2 AlphaFold P63041 1-134 view protein structure

Transcriptome

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

Promoters
RGD ID:13699149
Promoter ID:EPDNEW_R9673
Type:initiation region
Name:Cplx1_1
Description:complexin 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0142,194,933 - 2,194,993EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70944 AgrOrtholog
BioCyc Gene G2FUF-16678 BioCyc
Ensembl Genes ENSRNOG00000000060 Ensembl
Gene3D-CATH Single Helix bin UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7317504 IMAGE-MGC_LOAD
InterPro Synaphin UniProtKB/Swiss-Prot
KEGG Report rno:64832 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105424 IMAGE-MGC_LOAD
NCBI Gene 64832 ENTREZGENE
PANTHER COMPLEXIN-1 UniProtKB/Swiss-Prot
  PTHR16705 UniProtKB/Swiss-Prot
Pfam Synaphin UniProtKB/Swiss-Prot
PhenoGen Cplx1 PhenoGen
Superfamily-SCOP SNARE fusion complex UniProtKB/Swiss-Prot
UniProt CPLX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q64276 ENTREZGENE
UniProt Secondary O09057 UniProtKB/Swiss-Prot
  O09142 UniProtKB/Swiss-Prot
  Q566D7 UniProtKB/Swiss-Prot
  Q64276 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-07-09 Cplx1  complexin 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference