Syce2 (synaptonemal complex central element protein 2) - Rat Genome Database
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Gene: Syce2 (synaptonemal complex central element protein 2) Mus musculus
Analyze
Symbol: Syce2
Name: synaptonemal complex central element protein 2
RGD ID: 1323548
MGI Page MGI
Description: Predicted to be involved in synaptonemal complex assembly. Localizes to central element. Is expressed in primary spermatocyte and spermatocyte. Orthologous to human SYCE2 (synaptonemal complex central element protein 2); INTERACTS WITH 1,1-dichloroethene; 4-hydroxyphenyl retinamide; carbon nanotube.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 1700013H19Rik; AA407907; central element synaptonemal complex 1; Cesc1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,598,740 - 85,614,075 (+)NCBIGRCm39mm39
GRCm38884,872,111 - 84,887,446 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,872,111 - 84,888,221 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,396,010 - 87,411,345 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,762,216 - 87,777,500 (+)NCBImm8
Celera889,171,634 - 89,187,006 (+)NCBICelera
Cytogenetic Map8C3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15489334   PMID:15944401   PMID:16141072  
PMID:16141073   PMID:16968740   PMID:17339376   PMID:18799693   PMID:19851446   PMID:21478856   PMID:21637789   PMID:21677750   PMID:21873635   PMID:22164254   PMID:22854038   PMID:22863743  
PMID:23810942   PMID:24026100   PMID:24797475   PMID:25646409   PMID:25795304   PMID:26496610   PMID:30949703  


Genomics

Comparative Map Data
Syce2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,598,740 - 85,614,075 (+)NCBIGRCm39mm39
GRCm38884,872,111 - 84,887,446 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,872,111 - 84,888,221 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,396,010 - 87,411,345 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,762,216 - 87,777,500 (+)NCBImm8
Celera889,171,634 - 89,187,006 (+)NCBICelera
Cytogenetic Map8C3NCBI
SYCE2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1912,898,786 - 12,919,293 (-)EnsemblGRCh38hg38GRCh38
GRCh381912,898,229 - 12,919,674 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,009,894 - 13,030,116 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361912,870,894 - 12,891,086 (-)NCBINCBI36hg18NCBI36
Celera1912,899,602 - 12,919,804 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,581,761 - 12,601,966 (-)NCBIHuRef
CHM1_11913,010,391 - 13,030,583 (-)NCBICHM1_1
Syce2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01925,982,003 - 26,002,399 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,983,169 - 26,001,317 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,956,382 - 36,976,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41924,925,123 - 24,943,271 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11924,930,880 - 24,948,097 (-)NCBI
Celera1922,825,765 - 22,843,913 (-)NCBICelera
Cytogenetic Map19q11NCBI
Syce2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541531,957,489 - 31,969,859 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541531,957,244 - 31,969,922 (-)NCBIChiLan1.0ChiLan1.0
SYCE2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,203,069 - 13,224,138 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,203,595 - 13,224,052 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,459,646 - 12,481,833 (-)NCBIMhudiblu_PPA_v0panPan3
SYCE2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2049,281,773 - 49,283,880 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12049,267,985 - 49,285,986 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Syce2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366591,962,055 - 1,978,743 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCE2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl266,128,492 - 66,131,447 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1266,118,439 - 66,133,454 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,467,419 - 66,470,050 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYCE2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,581,915 - 11,599,770 (-)NCBI
Syce2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901478,860 - 491,577 (-)NCBI

Position Markers
AI266902  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,886,647 - 84,886,745UniSTSGRCm38
MGSCv37887,410,546 - 87,410,644UniSTSGRCm37
Cytogenetic Map8C3UniSTS
cM Map838.6UniSTS
Whitehead/MRC_RH81013.31UniSTS
D17825  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,886,761 - 84,886,911UniSTSGRCm38
MGSCv37887,410,660 - 87,410,810UniSTSGRCm37
Celera889,186,321 - 89,186,471UniSTS
Cytogenetic Map8C3UniSTS
cM Map838.6UniSTS
Whitehead/MRC_RH81007.26UniSTS
RH124647  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,886,073 - 84,887,204UniSTSGRCm38
MGSCv37887,409,972 - 87,411,103UniSTSGRCm37
Celera889,185,630 - 89,186,764UniSTS
Cytogenetic Map8C3UniSTS
cM Map838.6UniSTS
UniSTS:235945  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,887,581 - 84,887,787UniSTSGRCm38
MGSCv37887,411,480 - 87,411,686UniSTSGRCm37
Celera889,187,132 - 89,187,338UniSTS
Cytogenetic Map8C3UniSTS
cM Map838.6UniSTS
Gcdh  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,886,619 - 84,886,781UniSTSGRCm38
MGSCv37887,410,518 - 87,410,680UniSTSGRCm37
Celera889,186,176 - 89,186,341UniSTS
Cytogenetic Map8C3UniSTS
cM Map838.6UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse
1558780Idd22_minsulin dependent diabetes susceptibility 22 (mouse)Not determined871102903105103009Mouse
4141395Char2a_mP. chabaudi malaria resistance QTL 2a (mouse)Not determined7113678390202598Mouse
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
1301872Cd4ts3_mCD4 T cell subset 3 (mouse)Not determined871396181105396393Mouse
1300920Pitm3_mprion incubation time 3 (mouse)Not determined873202495107202598Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse
1558890Lith18_mlithogenic gene 18 (mouse)Not determined875675517109675623Mouse
1357470Obq16_mobesity QTL 16 (mouse)Not determined875685348109685497Mouse
1301808Nhdlq1_mnon-HDL QTL 1 (mouse)Not determined875685348109685497Mouse
1301874Hdlq16_mHDL QTL 16 (mouse)Not determined875685348109685497Mouse
10412234Nhdlq14_mnon-HDL QTL 14 (mouse)Not determined875685348109685497Mouse
1301099Cbm2_mcerebellum weight 2 (mouse)Not determined878518613112518703Mouse
1301581Char2_mP. chabaudi malaria resistance QTL 2 (mouse)Not determined879082178113082403Mouse
12904012Cfq10_mconditioned fear QTL 10 (mouse)88006677589014359Mouse
10755530Wbc2_mwhite blood cell count 2 (mouse)881092664115092664Mouse
10755519Wbc1_mwhite blood cell count 1 (mouse)881619151115619151Mouse
1301766Desp1_mdespair 1 (mouse)Not determined884759576118759741Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1260
Count of miRNA genes:515
Interacting mature miRNAs:626
Transcripts:ENSMUST00000003922, ENSMUST00000136026, ENSMUST00000144466, ENSMUST00000170296
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000003922   ⟹   ENSMUSP00000003922
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,872,193 - 84,887,456 (+)Ensembl
RefSeq Acc Id: ENSMUST00000136026   ⟹   ENSMUSP00000122159
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,872,111 - 84,888,221 (+)Ensembl
RefSeq Acc Id: ENSMUST00000144466
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,872,438 - 84,886,002 (+)Ensembl
RefSeq Acc Id: ENSMUST00000170296   ⟹   ENSMUSP00000131438
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,872,111 - 84,887,446 (+)Ensembl
RefSeq Acc Id: NM_001168244   ⟹   NP_001161716
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,598,887 - 85,614,075 (+)NCBI
GRCm38884,872,258 - 84,887,446 (+)NCBI
MGSCv37887,396,010 - 87,411,345 (+)RGD
Celera889,171,634 - 89,187,006 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001168246   ⟹   NP_001161718
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,598,740 - 85,614,075 (+)NCBI
GRCm38884,872,111 - 84,887,446 (+)ENTREZGENE
MGSCv37887,396,010 - 87,411,345 (+)RGD
Celera889,171,634 - 89,187,006 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_027954   ⟹   NP_082230
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,598,740 - 85,614,075 (+)NCBI
GRCm38884,872,111 - 84,887,446 (+)ENTREZGENE
MGSCv37887,396,010 - 87,411,345 (+)RGD
Celera889,171,634 - 89,187,006 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_031759
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,598,740 - 85,614,075 (+)NCBI
GRCm38884,872,111 - 84,887,446 (+)ENTREZGENE
MGSCv37887,396,010 - 87,411,345 (+)RGD
Celera889,171,634 - 89,187,006 (+)RGD
cM Map8 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_082230   ⟸   NM_027954
- Peptide Label: isoform 2
- UniProtKB: Q505B8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001161718   ⟸   NM_001168246
- Peptide Label: isoform 1
- UniProtKB: E9PYH4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001161716   ⟸   NM_001168244
- Peptide Label: isoform 3
- UniProtKB: Q505B8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000131438   ⟸   ENSMUST00000170296
RefSeq Acc Id: ENSMUSP00000003922   ⟸   ENSMUST00000003922
RefSeq Acc Id: ENSMUSP00000122159   ⟸   ENSMUST00000136026

Promoters
RGD ID:8667701
Promoter ID:EPDNEW_M11882
Type:initiation region
Name:Syce2_1
Description:Mus musculus synaptonemal complex central element protein 2 ,transcript variant 3, 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
GRCm38884,872,229 - 84,872,289EPDNEW
RGD ID:6843784
Promoter ID:MM_KWN:55103
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   MEF_B6
Transcripts:NM_001168244,   NM_001168246,   OTTMUST00000053070,   OTTMUST00000053071,   OTTMUST00000053072
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36887,395,116 - 87,396,442 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1919096 AgrOrtholog
Ensembl Genes ENSMUSG00000003824 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000003922 UniProtKB/TrEMBL
  ENSMUSP00000122159 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000131438 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000003922 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000136026 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000170296 ENTREZGENE, UniProtKB/TrEMBL
InterPro Syce2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:71846 UniProtKB/Swiss-Prot
MGD MGI:1919096 ENTREZGENE
NCBI Gene 71846 ENTREZGENE
PANTHER PTHR28398 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syce2 PhenoGen
UniGene Mm.229128 ENTREZGENE
UniProt A2RTK0_MOUSE UniProtKB/TrEMBL
  E9PYH4 ENTREZGENE, UniProtKB/TrEMBL
  F8WHI9_MOUSE UniProtKB/TrEMBL
  Q505B8 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3TJR1 UniProtKB/Swiss-Prot
  Q9DAC4 UniProtKB/Swiss-Prot