Syce1l (synaptonemal complex central element protein 1-like) - Rat Genome Database

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Gene: Syce1l (synaptonemal complex central element protein 1-like) Rattus norvegicus
Analyze
Symbol: Syce1l
Name: synaptonemal complex central element protein 1-like
RGD ID: 2320134
Description: Predicted to be involved in synaptonemal complex assembly. Predicted to be located in intermediate filament cytoskeleton. Predicted to be active in synaptonemal complex. Orthologous to human SYCE1L (synaptonemal complex central element protein 1 like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; gentamycin; tetrachloromethane.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100361431; synaptonemal complex central element protein 1 like-like
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
GRCr81958,534,205 - 58,544,651 (+)NCBIGRCr8
mRatBN7.21941,625,074 - 41,635,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1941,617,180 - 41,635,526 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01945,946,422 - 45,956,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1945,946,236 - 45,956,844 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01956,771,120 - 56,781,516 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41943,637,872 - 43,648,192 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1940,940,968 - 40,951,368 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Syce1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81958,534,205 - 58,544,651 (+)NCBIGRCr8
mRatBN7.21941,625,074 - 41,635,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1941,617,180 - 41,635,526 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01945,946,422 - 45,956,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1945,946,236 - 45,956,844 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01956,771,120 - 56,781,516 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41943,637,872 - 43,648,192 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1940,940,968 - 40,951,368 (+)NCBICelera
Cytogenetic Map19q12NCBI
SYCE1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381677,199,408 - 77,213,215 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1677,199,408 - 77,213,215 (+)EnsemblGRCh38hg38GRCh38
GRCh371677,233,305 - 77,247,112 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361675,790,850 - 75,804,477 (+)NCBINCBI36Build 36hg18NCBI36
Celera1661,530,886 - 61,544,503 (+)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1662,989,911 - 63,003,598 (+)NCBIHuRef
CHM1_11678,644,846 - 78,658,492 (+)NCBICHM1_1
T2T-CHM13v2.01683,255,583 - 83,269,389 (+)NCBIT2T-CHM13v2.0
Syce1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398114,369,845 - 114,382,165 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8114,369,845 - 114,382,165 (+)EnsemblGRCm39 Ensembl
GRCm388113,643,213 - 113,655,533 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8113,643,213 - 113,655,533 (+)EnsemblGRCm38mm10GRCm38
MGSCv378116,167,113 - 116,179,433 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368116,528,221 - 116,541,510 (+)NCBIMGSCv36mm8
Celera8117,851,913 - 117,864,253 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map859.65NCBI
Syce1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955522469,418 - 480,090 (+)NCBIChiLan1.0ChiLan1.0
SYCE1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21886,917,543 - 86,931,134 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11692,837,079 - 92,850,651 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01657,774,445 - 57,789,221 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11677,120,694 - 77,135,476 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1677,120,694 - 77,135,476 (+)Ensemblpanpan1.1panPan2
SYCE1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1573,963,333 - 73,976,590 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl573,905,115 - 73,976,564 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha573,917,611 - 73,931,109 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0574,270,520 - 74,284,259 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1574,211,239 - 74,224,878 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0574,045,080 - 74,058,597 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0574,535,981 - 74,549,676 (-)NCBIUU_Cfam_GSD_1.0
Syce1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934933,931,715 - 33,952,184 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493647525,636,979 - 25,649,132 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCE1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1610,700,594 - 10,716,772 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2610,731,141 - 10,748,453 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYCE1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1562,681,266 - 62,699,020 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl562,685,006 - 62,698,946 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604713,353,610 - 13,368,814 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syce1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247469,660,721 - 9,730,316 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syce1l
36 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:44
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000044044, ENSRNOT00000045250
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
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat

Markers in Region
RH129790  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21941,625,173 - 41,625,332 (+)MAPPERmRatBN7.2
Rnor_6.01945,946,474 - 45,946,632NCBIRnor6.0
Rnor_5.01956,771,174 - 56,771,332UniSTSRnor5.0
RGSC_v3.41943,637,912 - 43,638,070UniSTSRGSC3.4
Celera1940,941,020 - 40,941,178UniSTS
RH 3.4 Map19545.0UniSTS
Cytogenetic Map19q12UniSTS
RH130613  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21941,625,020 - 41,625,204 (+)MAPPERmRatBN7.2
Rnor_6.01945,946,321 - 45,946,504NCBIRnor6.0
Rnor_5.01956,771,021 - 56,771,204UniSTSRnor5.0
RGSC_v3.41943,637,759 - 43,637,942UniSTSRGSC3.4
Celera1940,940,867 - 40,941,050UniSTS
RH 3.4 Map19544.6UniSTS
Cytogenetic Map19q12UniSTS
RH140107  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21941,626,203 - 41,626,397 (+)MAPPERmRatBN7.2
Rnor_6.01945,947,504 - 45,947,697NCBIRnor6.0
Rnor_5.01956,772,204 - 56,772,397UniSTSRnor5.0
RGSC_v3.41943,638,942 - 43,639,135UniSTSRGSC3.4
Celera1940,942,050 - 40,942,243UniSTS
RH 3.4 Map19535.7UniSTS


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 2 6 3 3 56 1 20 3
Low 1 37 54 41 16 41 8 11 18 34 21 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045250   ⟹   ENSRNOP00000045083
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1941,617,180 - 41,635,526 (+)Ensembl
Rnor_6.0 Ensembl1945,946,236 - 45,956,844 (+)Ensembl
RefSeq Acc Id: XM_006255676   ⟹   XP_006255738
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81958,534,205 - 58,544,651 (+)NCBI
mRatBN7.21941,625,074 - 41,635,541 (+)NCBI
Rnor_6.01945,946,422 - 45,956,822 (+)NCBI
Rnor_5.01956,771,120 - 56,781,516 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006255738 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000045083
  ENSRNOP00000045083.5
Reference Protein Sequences
RefSeq Acc Id: XP_006255738   ⟸   XM_006255676
- UniProtKB: D4AAR3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000045083   ⟸   ENSRNOT00000045250

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAR3-F1-model_v2 AlphaFold D4AAR3 1-245 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:2320134 AgrOrtholog
BioCyc Gene G2FUF-5603 BioCyc
Ensembl Genes ENSRNOG00000031097 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045250.6 UniProtKB/TrEMBL
InterPro SYCE1 UniProtKB/TrEMBL
NCBI Gene 100361431 ENTREZGENE
PANTHER PTHR21731 UniProtKB/TrEMBL
  SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 1-LIKE UniProtKB/TrEMBL
Pfam SYCE1 UniProtKB/TrEMBL
PhenoGen Syce1l PhenoGen
RatGTEx ENSRNOG00000031097 RatGTEx
UniProt D4AAR3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-13 Syce1l  synaptonemal complex central element protein 1-like  LOC100361431  synaptonemal complex central element protein 1 like-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361431  synaptonemal complex central element protein 1 like-like      Symbol and Name status set to provisional 70820 PROVISIONAL