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

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Gene: Syce3 (synaptonemal complex central element protein 3) Rattus norvegicus
Analyze
Symbol: Syce3
Name: synaptonemal complex central element protein 3
RGD ID: 1586367
Description: Predicted to be involved in reciprocal meiotic recombination; spermatogenesis; and synaptonemal complex assembly. Predicted to act upstream of or within positive regulation of apoptotic process; positive regulation of developmental process; and positive regulation of reproductive process. Predicted to be located in chromosome and nucleus. Predicted to be active in central element. Orthologous to human SYCE3 (synaptonemal complex central element protein 3); INTERACTS WITH bisphenol A; fenvalerate; furan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC689933; LOC689933; uncharacterized protein LOC689933
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87122,336,427 - 122,362,608 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7122,336,427 - 122,344,820 (-)EnsemblGRCr8
mRatBN7.27120,456,800 - 120,482,882 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7120,456,800 - 120,482,973 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7122,208,296 - 122,216,978 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07124,434,450 - 124,443,132 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07124,397,167 - 124,405,357 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07130,360,511 - 130,386,673 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,360,517 - 130,368,819 (-)Ensemblrn6Rnor6.0
Rnor_5.07130,045,693 - 130,071,748 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47127,684,549 - 127,710,970 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7116,929,763 - 116,937,784 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse:




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

Biological Process

Cellular Component
central element  (IBA,IEA,ISO)
chromosome  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Function

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. 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:20407872   PMID:21637789   PMID:22164254  


Genomics

Comparative Map Data
Syce3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87122,336,427 - 122,362,608 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7122,336,427 - 122,344,820 (-)EnsemblGRCr8
mRatBN7.27120,456,800 - 120,482,882 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7120,456,800 - 120,482,973 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7122,208,296 - 122,216,978 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07124,434,450 - 124,443,132 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07124,397,167 - 124,405,357 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07130,360,511 - 130,386,673 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7130,360,517 - 130,368,819 (-)Ensemblrn6Rnor6.0
Rnor_5.07130,045,693 - 130,071,748 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47127,684,549 - 127,710,970 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7116,929,763 - 116,937,784 (-)NCBICelera
Cytogenetic Map7q34NCBI
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 (-)Ensemblhg38GRCh38
GRCh372250,989,541 - 51,001,348 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362249,336,407 - 49,348,194 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm381589,390,174 - 89,410,503 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1589,390,174 - 89,410,503 (-)Ensemblmm10GRCm38
MGSCv371589,220,605 - 89,240,934 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361589,217,932 - 89,238,024 (-)NCBIMGSCv36mm8
Celera1591,519,312 - 91,539,583 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1544.87NCBI
Syce3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541333,537,753 - 33,563,373 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1016,723,993 - 16,750,303 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01017,472,711 - 17,499,062 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624752204,242 - 235,081 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Syce3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11258,689,465 - 258,714,802 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Syce3
158 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:147
Interacting mature miRNAs:158
Transcripts:ENSRNOT00000064328
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7121393075137014596Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7119280025135560836Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7118556868125929417Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
11 5 28 71 73 83 56 62 56 4 196 98 1 69 27 60 27 5 5

Sequence


Ensembl Acc Id: ENSRNOT00000064328   ⟹   ENSRNOP00000062544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7122,336,427 - 122,344,820 (-)Ensembl
mRatBN7.2 Ensembl7120,456,800 - 120,482,973 (-)Ensembl
Rnor_6.0 Ensembl7130,360,517 - 130,368,819 (-)Ensembl
RefSeq Acc Id: NM_001135253   ⟹   NP_001128725
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87122,336,427 - 122,344,734 (-)NCBI
mRatBN7.27120,456,800 - 120,465,107 (-)NCBI
Rnor_6.07130,360,511 - 130,368,819 (-)NCBI
Rnor_5.07130,045,693 - 130,071,748 (-)NCBI
RGSC_v3.47127,684,549 - 127,710,970 (-)RGD
Celera7116,929,763 - 116,937,784 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242244   ⟹   XP_006242306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87122,336,758 - 122,362,608 (-)NCBI
mRatBN7.27120,456,800 - 120,482,860 (-)NCBI
Rnor_6.07130,360,511 - 130,386,669 (-)NCBI
Rnor_5.07130,045,693 - 130,071,748 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242246   ⟹   XP_006242308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87122,336,758 - 122,362,381 (-)NCBI
mRatBN7.27120,456,800 - 120,482,741 (-)NCBI
Rnor_6.07130,360,511 - 130,386,461 (-)NCBI
Rnor_5.07130,045,693 - 130,071,748 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595121   ⟹   XP_017450610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87122,336,882 - 122,362,608 (-)NCBI
mRatBN7.27120,457,263 - 120,482,882 (-)NCBI
Rnor_6.07130,361,027 - 130,386,673 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001128725 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242306 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242308 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450610 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76568 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062544
  ENSRNOP00000062544.3
RefSeq Acc Id: NP_001128725   ⟸   NM_001135253
- UniProtKB: A6K7M5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242306   ⟸   XM_006242244
- Peptide Label: isoform X1
- UniProtKB: D3ZDD6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242308   ⟸   XM_006242246
- Peptide Label: isoform X3
- UniProtKB: A6K7M5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450610   ⟸   XM_017595121
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000062544   ⟸   ENSRNOT00000064328

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDD6-F1-model_v2 AlphaFold D3ZDD6 1-88 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:1586367 AgrOrtholog
BioCyc Gene G2FUF-32436 BioCyc
Ensembl Genes ENSRNOG00000042056 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064328 ENTREZGENE
  ENSRNOT00000064328.4 UniProtKB/TrEMBL
InterPro Synaptonemal_3 UniProtKB/TrEMBL
KEGG Report rno:689933 UniProtKB/TrEMBL
NCBI Gene 689933 ENTREZGENE
PANTHER PTHR36686 UniProtKB/TrEMBL
  SYNAPTONEMAL COMPLEX CENTRAL ELEMENT PROTEIN 3 UniProtKB/TrEMBL
Pfam Synaptonemal_3 UniProtKB/TrEMBL
PhenoGen Syce3 PhenoGen
RatGTEx ENSRNOG00000042056 RatGTEx
UniProt A6K7M5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZDD6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-18 Syce3  synaptonemal complex central element protein 3  LOC689933  hypothetical protein LOC689933  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC689933  hypothetical protein LOC689933      Symbol and Name status set to provisional 70820 PROVISIONAL