Sycp2l (synaptonemal complex protein 2-like) - Rat Genome Database

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Gene: Sycp2l (synaptonemal complex protein 2-like) Rattus norvegicus
Analyze
Symbol: Sycp2l
Name: synaptonemal complex protein 2-like
RGD ID: 1564922
Description: Predicted to act upstream of or within negative regulation of programmed cell death. Predicted to be located in female germ cell nucleus. Predicted to be active in condensed chromosome, centromeric region and lateral element. Orthologous to human SYCP2L (synaptonemal complex protein 2 like); INTERACTS WITH bisphenol A; 4,4'-sulfonyldiphenol (ortholog); aflatoxin B1 (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: AABR07027258.1; LOC108348546; LOC364688; RGD1564922; similar to OTTHUMP00000039249; similar to Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein); uncharacterized LOC108348546
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
GRCr81723,798,424 - 23,851,017 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1723,798,649 - 23,854,050 (-)EnsemblGRCr8
mRatBN7.21723,589,217 - 23,645,273 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1723,592,899 - 23,648,306 (-)EnsemblmRatBN7.2
Rnor_6.01721,430,470 - 21,486,091 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1721,430,337 - 21,484,456 (-)NCBIrn6Rnor6.0
Rnor_5.01723,410,100 - 23,468,644 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41729,536,991 - 29,598,175 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1723,264,191 - 23,319,515 (-)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse:




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
chromosome  (IEA)
condensed chromosome, centromeric region  (IBA,IEA,ISO)
lateral element  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)

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:26362258  


Genomics

Comparative Map Data
Sycp2l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81723,798,424 - 23,851,017 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1723,798,649 - 23,854,050 (-)EnsemblGRCr8
mRatBN7.21723,589,217 - 23,645,273 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1723,592,899 - 23,648,306 (-)EnsemblmRatBN7.2
Rnor_6.01721,430,470 - 21,486,091 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1721,430,337 - 21,484,456 (-)NCBIrn6Rnor6.0
Rnor_5.01723,410,100 - 23,468,644 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41729,536,991 - 29,598,175 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1723,264,191 - 23,319,515 (-)NCBICelera
Cytogenetic Map17p12NCBI
SYCP2L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38610,887,052 - 10,974,309 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl610,886,831 - 10,979,320 (+)Ensemblhg38GRCh38
GRCh37610,887,285 - 10,974,542 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36610,995,050 - 11,082,528 (+)NCBIBuild 36Build 36hg18NCBI36
Celera612,115,512 - 12,202,979 (+)NCBICelera
Cytogenetic Map6p24.2NCBI
HuRef610,762,853 - 10,906,303 (+)NCBIHuRef
CHM1_1610,889,155 - 10,976,634 (+)NCBICHM1_1
T2T-CHM13v2.0610,754,685 - 10,841,961 (+)NCBIT2T-CHM13v2.0
Sycp2l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391341,267,895 - 41,327,827 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1341,267,783 - 41,327,827 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381341,114,419 - 41,174,351 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1341,114,307 - 41,174,351 (+)Ensemblmm10GRCm38
MGSCv371341,125,393 - 41,157,668 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361341,212,080 - 41,273,683 (+)NCBIMGSCv36mm8
Celera1342,207,007 - 42,245,168 (+)NCBICelera
Cytogenetic Map13A3.3NCBI
cM Map1320.32NCBI
Sycp2l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554653,440,106 - 3,518,840 (-)NCBIChiLan1.0ChiLan1.0
SYCP2L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2525,419,642 - 25,623,381 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1621,409,326 - 21,613,566 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0610,611,051 - 10,834,913 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1610,867,834 - 11,111,969 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl610,867,833 - 10,879,787 (+)EnsemblpanPan2panpan1.1
SYCP2L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13510,568,191 - 10,678,633 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3510,575,849 - 10,664,032 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3510,526,112 - 10,627,792 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03510,681,166 - 10,780,930 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.13510,501,597 - 10,611,681 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03510,557,122 - 10,659,960 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03511,878,598 - 11,981,589 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sycp2l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494613,755,355 - 13,876,426 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365342,024,341 - 2,131,241 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCP2L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl77,574,372 - 7,640,989 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.177,574,153 - 7,647,874 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.277,929,073 - 7,973,128 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SYCP2L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11761,166,225 - 61,244,576 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604410,924,953 - 11,000,623 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sycp2l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475614,996,868 - 15,084,285 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475614,999,209 - 15,084,967 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Sycp2l
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11460,109,857 - 60,162,851 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sycp2l
500 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:122
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000038180
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
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17143999106Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17926675540968173Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17436005727233623Rat
8552966Pigfal18Plasma insulin-like growth factor 1 level QTL 188.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)171286094257860942Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17212084342054133Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920650523859062Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)17622199858177198Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172266079955604694Rat
9589151Insul30Insulin level QTL 308.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)171286094257860942Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172149899450592236Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131706603Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17473353449733534Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172328632264246472Rat
9589057Scfw6Subcutaneous fat weight QTL 68.620.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)171286094257860942Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920650523859062Rat
9590154Scort9Serum corticosterone level QTL 923.570.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)171286094257860942Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172201970567019705Rat
9590088Insglur7Insulin/glucose ratio QTL 720.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)171286094257860942Rat
1331720Rf43Renal function QTL 432.881kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)171553702528637951Rat
2317053Aia25Adjuvant induced arthritis QTL 252.69joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)171060469455604694Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17136045694Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171553702560531414Rat
7411666Foco31Food consumption QTL 3111.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)171286094257860942Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17473353449733534Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17857434232199534Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138037084Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920650523859062Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17143999106Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17436005727233623Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17143999106Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat


Expression

RNA-SEQ Expression

ectoderm
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
5 3 2 2 4 1 2 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000038180   ⟹   ENSRNOP00000028936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1723,798,649 - 23,854,050 (-)Ensembl
mRatBN7.2 Ensembl1723,592,899 - 23,648,306 (-)Ensembl
RefSeq Acc Id: XM_039096438   ⟹   XP_038952366
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81723,798,424 - 23,851,017 (-)NCBI
mRatBN7.21723,589,217 - 23,645,273 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038952366 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000028936
  ENSRNOP00000028936.6
RefSeq Acc Id: XP_038952366   ⟸   XM_039096438
- UniProtKB: F1M2G0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000028936   ⟸   ENSRNOT00000038180
Protein Domains
Synaptonemal complex protein 2 armadillo-repeat-   Synaptonemal complex protein 2 Spt16M-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M2G0-F1-model_v2 AlphaFold F1M2G0 1-813 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:1564922 AgrOrtholog
BioCyc Gene G2FUF-9732 BioCyc
Ensembl Genes ENSRNOG00000023831 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038180 ENTREZGENE
  ENSRNOT00000038180.7 UniProtKB/TrEMBL
InterPro SYCP1/2 UniProtKB/TrEMBL
  SYCP2_ARLD UniProtKB/TrEMBL
  SYCP2_SLD UniProtKB/TrEMBL
NCBI Gene 364688 ENTREZGENE
PANTHER PTHR15607 UniProtKB/TrEMBL
  SYNAPTONEMAL COMPLEX PROTEIN 2-LIKE UniProtKB/TrEMBL
Pfam SYCP2_ARLD UniProtKB/TrEMBL
  SYCP2_SLD UniProtKB/TrEMBL
PhenoGen Sycp2l PhenoGen
RatGTEx ENSRNOG00000023831 RatGTEx
UniProt F1M2G0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Sycp2l  synaptonemal complex protein 2-like  AABR07027258.1    Data merged from RGD:15003573 737654 PROVISIONAL
2021-03-09 Sycp2l  synaptonemal complex protein 2-like  LOC108348546  uncharacterized LOC108348546  Data merged from RGD:11515493 737654 PROVISIONAL
2019-11-08 AABR07027258.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2016-08-02 LOC108348546  uncharacterized LOC108348546      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-05-24 Sycp2l  synaptonemal complex protein 2-like  LOC682504  similar to Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein)  Data merged from RGD:1597970 1643240 APPROVED
2008-03-07 Sycp2l  synaptonemal complex protein 2-like  RGD1564922_predicted  similar to OTTHUMP00000039249 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC682504  similar to Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1564922_predicted  similar to OTTHUMP00000039249 (predicted)  LOC364688  similar to OTTHUMP00000039249  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC364688  similar to OTTHUMP00000039249      Symbol and Name status set to provisional 70820 PROVISIONAL