Sycn (syncollin) - Rat Genome Database

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Gene: Sycn (syncollin) Mus musculus
Analyze
Symbol: Sycn
Name: syncollin
RGD ID: 733709
MGI Page MGI
Description: Predicted to be involved in exocytosis. Predicted to be located in zymogen granule membrane. Orthologous to human SYCN (syncollin).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 0910001K16Rik; 1810038B08Rik; SYL
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,240,310 - 28,241,635 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl728,240,310 - 28,241,634 (+)EnsemblGRCm39 Ensembl
GRCm38728,540,885 - 28,542,210 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,540,885 - 28,542,209 (+)EnsemblGRCm38mm10GRCm38
MGSCv37729,325,904 - 29,327,229 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36728,249,645 - 28,250,966 (+)NCBIMGSCv36mm8
Celera723,105,986 - 23,107,311 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map716.83NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process
exocytosis  (IEA)

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. MGD IEA MGD IEA
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11839820   PMID:12466851   PMID:12477932   PMID:15462671   PMID:15489334   PMID:16141072   PMID:16141073   PMID:21267068  
PMID:21873635   PMID:25179606   PMID:25186293   PMID:30590051   PMID:37829188  


Genomics

Comparative Map Data
Sycn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39728,240,310 - 28,241,635 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl728,240,310 - 28,241,634 (+)EnsemblGRCm39 Ensembl
GRCm38728,540,885 - 28,542,210 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,540,885 - 28,542,209 (+)EnsemblGRCm38mm10GRCm38
MGSCv37729,325,904 - 29,327,229 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36728,249,645 - 28,250,966 (+)NCBIMGSCv36mm8
Celera723,105,986 - 23,107,311 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map716.83NCBI
SYCN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381939,202,825 - 39,204,263 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1939,202,825 - 39,204,263 (-)EnsemblGRCh38hg38GRCh38
GRCh371939,693,465 - 39,694,903 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361944,385,305 - 44,395,713 (-)NCBINCBI36Build 36hg18NCBI36
Celera1936,497,137 - 36,498,481 (-)NCBICelera
Cytogenetic Map19q13.2NCBI
HuRef1936,140,399 - 36,141,743 (-)NCBIHuRef
CHM1_11939,694,372 - 39,695,716 (-)NCBICHM1_1
T2T-CHM13v2.01942,006,977 - 42,008,415 (-)NCBIT2T-CHM13v2.0
Sycn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8192,950,761 - 92,961,077 (+)NCBIGRCr8
mRatBN7.2183,823,836 - 83,833,542 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl183,832,102 - 83,833,538 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx189,242,458 - 89,243,910 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013,853,314 - 3,854,767 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0190,998,331 - 90,999,783 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0185,219,827 - 85,220,239 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl185,218,803 - 85,220,237 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,434,274 - 86,434,686 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,651,275 - 83,651,687 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1183,729,387 - 83,729,798 (+)NCBI
Celera178,226,789 - 78,227,201 (+)NCBICelera
Cytogenetic Map1q21NCBI
Sycn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955468350,601 - 352,957 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955468350,601 - 352,966 (+)NCBIChiLan1.0ChiLan1.0
SYCN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22045,499,011 - 45,501,279 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11947,369,618 - 47,371,880 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01936,301,867 - 36,303,720 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11944,851,863 - 44,882,227 (-)NCBIpanpan1.1PanPan1.1panPan2
SYCN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11113,987,711 - 113,989,112 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1113,987,739 - 113,989,111 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1113,389,177 - 113,390,562 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01114,587,136 - 114,588,522 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1114,587,148 - 114,588,521 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11114,145,246 - 114,146,628 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01113,778,359 - 113,779,743 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01114,773,516 - 114,774,873 (+)NCBIUU_Cfam_GSD_1.0
Sycn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934913,633,233 - 13,634,382 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366612,061,357 - 2,062,451 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366612,061,281 - 2,062,451 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl647,931,042 - 47,932,708 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1647,931,030 - 47,933,405 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2643,338,879 - 43,340,582 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYCN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1633,792,011 - 33,794,188 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607311,820,477 - 11,822,739 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sycn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479412,517,762 - 12,521,856 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sycn
93 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:190
Count of miRNA genes:180
Interacting mature miRNAs:190
Transcripts:ENSMUST00000119180
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
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7351172887142720Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1303248547032621Mouse
1301041Prnr2_mprion resistance 2 (mouse)Not determined71872879439674033Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72267388756674033Mouse
1301969Lbw5_mlupus NZB x NZW 5 (mouse)Not determined72684761560851775Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71928001553280104Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72306653157066531Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360299972549748Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71333392547349748Mouse
7394747asp3_maudiogenic seizure prone 3 (mouse)Not determined72730579836842367Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71248087746480877Mouse
12790989Tgl6_mtriglyceride 6 (mouse)72754054961540549Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined71984225053842367Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71313520447135204Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
1301572Sluc30_msusceptibility to lung cancer 30 (mouse)Not determined7243169636431844Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined7998886743988984Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71248087746480877Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71030579844305936Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72288857256888716Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71663729349159331Mouse

Markers in Region
PMC134703P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38728,541,271 - 28,541,437UniSTSGRCm38
MGSCv37729,326,290 - 29,326,456UniSTSGRCm37
Celera723,106,372 - 23,106,538UniSTS
Cytogenetic Map7A3UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000119180   ⟹   ENSMUSP00000112770
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl728,240,310 - 28,241,634 (+)Ensembl
GRCm38.p6 Ensembl728,540,885 - 28,542,209 (+)Ensembl
RefSeq Acc Id: NM_026716   ⟹   NP_080992
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39728,240,310 - 28,241,635 (+)NCBI
GRCm38728,540,885 - 28,542,210 (+)ENTREZGENE
MGSCv37729,325,904 - 29,327,229 (+)RGD
Celera723,105,986 - 23,107,311 (+)RGD
cM Map7 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_080992 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH19567 (Get FASTA)   NCBI Sequence Viewer  
  EDL24130 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000112770
  ENSMUSP00000112770.3
GenBank Protein Q8VCK7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_080992   ⟸   NM_026716
- Peptide Label: precursor
- UniProtKB: Q8VCK7 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000112770   ⟸   ENSMUST00000119180

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8VCK7-F1-model_v2 AlphaFold Q8VCK7 1-134 view protein structure

Promoters
RGD ID:6892466
Promoter ID:EPDNEW_M9684
Type:initiation region
Name:Sycn_1
Description:Mus musculus syncollin , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38728,540,878 - 28,540,938EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915666 AgrOrtholog
Ensembl Genes ENSMUSG00000084174 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000119180 ENTREZGENE
  ENSMUST00000119180.4 UniProtKB/Swiss-Prot
Gene3D-CATH Crystallins UniProtKB/Swiss-Prot
InterPro Syncollin UniProtKB/Swiss-Prot
KEGG Report mmu:68416 UniProtKB/Swiss-Prot
MGD MGI:1915666 ENTREZGENE
NCBI Gene 68416 ENTREZGENE
PANTHER PTHR17503 UniProtKB/Swiss-Prot
  SYNCOLLIN UniProtKB/Swiss-Prot
Pfam Syncollin UniProtKB/Swiss-Prot
PhenoGen Sycn PhenoGen
UniProt Q8VCK7 ENTREZGENE, UniProtKB/Swiss-Prot