Syce3 (synaptonemal complex central element protein 3) - Rat Genome Database

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Gene: Syce3 (synaptonemal complex central element protein 3) Mus musculus
Analyze
Symbol: Syce3
Name: synaptonemal complex central element protein 3
RGD ID: 1623908
MGI Page MGI
Description: Involved in reciprocal meiotic recombination; spermatogenesis; and synaptonemal complex assembly. Acts upstream of or within positive regulation of apoptotic process; positive regulation of developmental process; and positive regulation of reproductive process. Located in central element. Is expressed in embryo; ovary; and testis. Orthologous to human SYCE3 (synaptonemal complex central element protein 3).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700007E06Rik; hypothetical protein LOC75459; testis-specific expressed protein 2; TSEG-2; TSEG2; uncharacterized protein C22orf41 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,274,377 - 89,294,706 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1589,274,377 - 89,294,706 (-)EnsemblGRCm39 Ensembl
GRCm381589,390,174 - 89,410,503 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,390,174 - 89,410,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv371589,220,605 - 89,240,934 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361589,217,932 - 89,238,024 (-)NCBIMGSCv36mm8
Celera1591,519,312 - 91,539,583 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1544.87NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
central element  (IBA,IDA)
chromosome  (IDA)
nucleoplasm  (TAS)
nucleus  (IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. 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:12466851   PMID:12477932   PMID:14610273   PMID:16141072   PMID:16141073   PMID:17660561   PMID:19323366   PMID:20407872  
PMID:21267068   PMID:21637789   PMID:21873635   PMID:22164254   PMID:22826121   PMID:23843628   PMID:24026100   PMID:24413433   PMID:25646409   PMID:27739607   PMID:27796301   PMID:30760716  
PMID:30949703   PMID:34969823   PMID:36635604  


Genomics

Comparative Map Data
Syce3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391589,274,377 - 89,294,706 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1589,274,377 - 89,294,706 (-)EnsemblGRCm39 Ensembl
GRCm381589,390,174 - 89,410,503 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,390,174 - 89,410,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv371589,220,605 - 89,240,934 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361589,217,932 - 89,238,024 (-)NCBIMGSCv36mm8
Celera1591,519,312 - 91,539,583 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1544.87NCBI
SYCE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382250,551,112 - 50,562,919 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2250,551,112 - 50,562,919 (-)EnsemblGRCh38hg38GRCh38
GRCh372250,989,541 - 51,001,348 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362249,336,407 - 49,348,194 (-)NCBINCBI36Build 36hg18NCBI36
Celera2234,865,573 - 34,877,362 (-)NCBICelera
Cytogenetic Map22q13.33NCBI
HuRef2233,880,565 - 33,892,331 (-)NCBIHuRef
CHM1_12250,948,234 - 50,960,066 (-)NCBICHM1_1
T2T-CHM13v2.02251,061,619 - 51,073,448 (-)NCBIT2T-CHM13v2.0
Syce3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87122,336,427 - 122,362,608 (-)NCBIGRCr8
mRatBN7.27120,456,800 - 120,482,882 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7120,456,800 - 120,482,973 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7122,208,296 - 122,216,978 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07124,434,450 - 124,443,132 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07124,397,167 - 124,405,357 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07130,360,511 - 130,386,673 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,360,517 - 130,368,819 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07130,045,693 - 130,071,748 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47127,684,549 - 127,710,970 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7116,929,763 - 116,937,784 (-)NCBICelera
Cytogenetic Map7q34NCBI
Syce3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541333,537,753 - 33,563,373 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541333,537,646 - 33,573,787 (-)NCBIChiLan1.0ChiLan1.0
SYCE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22360,470,925 - 60,483,294 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12263,161,731 - 63,173,877 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02230,797,389 - 30,809,517 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12249,908,095 - 49,920,836 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2249,908,095 - 49,913,903 (-)Ensemblpanpan1.1panPan2
SYCE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11016,748,760 - 16,772,496 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1016,758,528 - 16,772,344 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1016,723,993 - 16,750,303 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01017,472,711 - 17,499,062 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1017,472,395 - 17,499,061 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11017,197,070 - 17,223,364 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01017,520,080 - 17,546,406 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01017,652,265 - 17,678,592 (+)NCBIUU_Cfam_GSD_1.0
Syce3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945261,738 - 281,213 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936629264,077 - 281,119 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936629264,077 - 281,119 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl5181,056 - 200,832 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.15168,908 - 201,037 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25110,579,921 - 110,599,695 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYCE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11933,023,956 - 33,038,641 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1933,023,960 - 33,038,600 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604592,305,570 - 92,318,474 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Syce3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624752218,587 - 234,971 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624752204,242 - 235,081 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Syce3
375 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:305
Count of miRNA genes:153
Interacting mature miRNAs:159
Transcripts:ENSMUST00000109314, ENSMUST00000167959
Prediction methods:Miranda, Rnahybrid
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
26884442Sklq6_mskull length QTL 6, 5 week (mouse)156129481100797881Mouse
1357526Hyplip2_mhyperlipidemia 2 (mouse)Not determined1512402203102896555Mouse
26884425Cvht2_mcranial vault height 2, 5 week (mouse)1528800146102008435Mouse
1558985Eae32_mexperimental allergic encephalomyelitis susceptibility 32 (mouse)Not determined1532578416103425899Mouse
26884402Cvht9_mcranial vault height 9, 16 week (mouse)154216339695497881Mouse
26884397Humsd5_mhumerus midshaft diameter 5, 10 week (mouse)154836339698397881Mouse
26884399Humsd1_mhumerus midshaft diameter 1, 5 week (mouse)1548363396101708435Mouse
38501067Tip3_mtuberculosis immunophenotype 3, IFN-g level (mouse)155356339689584203Mouse
1302074Bmd4_mbone mineral density 4 (mouse)Not determined1556186708103425899Mouse
1300800Ses3_msalmonella enteritidis susceptibility 3 (mouse)Not determined155711700591117153Mouse
1357407Pfat4_mpredicted fat percentage 4 (mouse)8.6Body fat amountpredicted fat percentage155711700591117153Mouse
12880420V25Dq8_mvitamin D inactive form serum level QTL 8 (mouse)156158420095584200Mouse
1301601Faq9_mfluctuating asymmetry QTL 9 (mouse)Not determined156316390397163995Mouse
1302197Bhr2_mbronchial hyperresponsiveness 2 (mouse)Not determined1564306334103425899Mouse
4141135Cia35_mcollagen induced arthritis 35 (mouse)Not determined156481182698811946Mouse
1301119Drb7_mdopamine receptor binding 7 (mouse)Not determined156533657899341028Mouse
1301171Brm2_mbrachyury modifier 2 (mouse)Not determined156552537699525499Mouse
4141921Pstc3_mperiosteal circumference 3 (mouse)Not determined1567270698101270847Mouse
1300627Sluc26_msusceptibility to lung cancer 26 (mouse)Not determined1570345653104073951Mouse
1300648Dbsty4_mdiabesity 4 (mouse)Not determined1570349271104073951Mouse
1300726Pitm4_mprion incubation time 4 (mouse)Not determined1570349271104073951Mouse
14747011Mancz13_mmandible centroid size 13 (mouse)1572382669104073951Mouse
12791003Aath8_maortic arch atherosclerosis 8 (mouse)1573430144104073951Mouse
1301472Pain1_mpain 1 (mouse)Not determined157532084690813185Mouse
1300851Heal4_mwound healing/regeneration 4 (mouse)Not determined1577527592104073951Mouse
4142060W3q6_mweight 3 weeks QTL 6 (mouse)Not determined78601103102901704Mouse
1357894Epfpq3_mepididymal fat percentage QTL 3 (mouse)Not determined1578601103102901704Mouse
14928306Manh79_mmandible shape 79 (mouse)1578847557104073951Mouse
12880411V125Dq11_mvitamin D active form serum level QTL 11 (mouse)1578897881104073951Mouse
10402490Dipa5_mdrug induced psychomotor activation 5 (mouse)Not determined1579163411104073951Mouse
4141897Imrfq2_mimmune response to Factor IX QTL 2 (mouse)Not determined79908940104073951Mouse
1301284Cosz3_mcocaine seizure 3 (mouse)Not determined1580313634104073951Mouse
4141902Cia37_mcollagen induced arthritis 37 (mouse)Not determined1580884933104073951Mouse
1300974Pgia9_mproteoglycan induced arthritis 9 (mouse)Not determined1580884933104073951Mouse
4141511Gdcr1_mglycerolphosphate dehydrogenase regulator 1 (mouse)Not determined82615474104073951Mouse
11530037Sluc34a_msusceptibility to lung cancer 34a (mouse)1585896437104073951Mouse
11530038Sluc34b_msusceptibility to lung cancer 34b (mouse)1585896437104073951Mouse
1357614Bmca_mbile mucin accumulation (mouse)Not determined1585896437104073951Mouse
1301918Skull22_mskull morphology 22 (mouse)Not determined1585901546104073951Mouse
1558845Alprf_malcohol preference (mouse)Not determined158734927190274568Mouse
12738413Lfibq10_mliver fibrosis QTL 10 (mouse)158784208589927286Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000109314   ⟹   ENSMUSP00000104937
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1589,274,377 - 89,294,466 (-)Ensembl
GRCm38.p6 Ensembl1589,390,174 - 89,410,263 (-)Ensembl
RefSeq Acc Id: ENSMUST00000167959   ⟹   ENSMUSP00000131766
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1589,274,377 - 89,294,706 (-)Ensembl
GRCm38.p6 Ensembl1589,390,174 - 89,410,503 (-)Ensembl
RefSeq Acc Id: NM_001162880   ⟹   NP_001156352
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391589,274,377 - 89,294,706 (-)NCBI
GRCm381589,390,174 - 89,410,503 (-)NCBI
MGSCv371589,220,605 - 89,240,934 (-)RGD
Celera1591,519,312 - 91,539,583 (-)RGD
cM Map15 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001162882   ⟹   NP_001156354
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391589,274,377 - 89,294,466 (-)NCBI
GRCm381589,390,174 - 89,410,263 (-)NCBI
MGSCv371589,220,605 - 89,240,934 (-)RGD
Celera1591,519,312 - 91,539,583 (-)RGD
cM Map15 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001156352   ⟸   NM_001162880
- UniProtKB: B5KM66 (UniProtKB/Swiss-Prot),   E7D6R1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001156354   ⟸   NM_001162882
- UniProtKB: B5KM66 (UniProtKB/Swiss-Prot),   E7D6R1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000104937   ⟸   ENSMUST00000109314
RefSeq Acc Id: ENSMUSP00000131766   ⟸   ENSMUST00000167959

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5KM66-F1-model_v2 AlphaFold B5KM66 1-88 view protein structure

Promoters
RGD ID:8684734
Promoter ID:EPDNEW_M20398
Type:multiple initiation site
Name:Syce3_1
Description:Mus musculus synaptonemal complex central element protein 3 ,transcript variant 1, 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
GRCm381589,410,255 - 89,410,315EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1922709 AgrOrtholog
Ensembl Genes ENSMUSG00000078938 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000109314 ENTREZGENE
  ENSMUST00000109314.9 UniProtKB/Swiss-Prot
  ENSMUST00000167959 ENTREZGENE
  ENSMUST00000167959.2 UniProtKB/Swiss-Prot
InterPro Synaptonemal_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:75459 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1922709 ENTREZGENE
NCBI Gene 75459 ENTREZGENE
PANTHER PTHR36686 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Synaptonemal_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Syce3 PhenoGen
UniProt B5KM66 ENTREZGENE
  E7D6R1 ENTREZGENE, UniProtKB/TrEMBL
  SYCE3_MOUSE UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-11 Syce3  synaptonemal complex central element protein 3  1700007E06Rik  RIKEN cDNA 1700007E06 gene  Symbol and/or name change 5135510 APPROVED