Sycp2 (synaptonemal complex protein 2) - Rat Genome Database
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Gene: Sycp2 (synaptonemal complex protein 2) Rattus norvegicus
Analyze
Symbol: Sycp2
Name: synaptonemal complex protein 2
RGD ID: 69429
Description: Predicted to have DNA binding activity. Predicted to be involved in several processes, including male genitalia morphogenesis; meiotic nuclear division; and mitotic G1 phase. Localizes to lateral element. Human ortholog(s) of this gene implicated in spermatogenic failure 1. Orthologous to human SYCP2 (synaptonemal complex protein 2); INTERACTS WITH 2-ethoxyethanol; 2-methoxyethanol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: rnSCP2; SCP-2; synaptonemal complex lateral element protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.0 Ensembl3173,884,287 - 173,947,018 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03173,884,559 - 173,948,304 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03183,144,181 - 183,206,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43167,437,522 - 167,502,083 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13167,343,557 - 167,408,119 (-)NCBI
Celera3167,063,122 - 167,125,089 (+)NCBICelera
Cytogenetic Map3q43NCBI
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

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10341103   PMID:10652260   PMID:16717126   PMID:18283110   PMID:18316482   PMID:19034475   PMID:22011390   PMID:22164254   PMID:22711701   PMID:23133398   PMID:26362258  


Genomics

Comparative Map Data
Sycp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.0 Ensembl3173,884,287 - 173,947,018 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03173,884,559 - 173,948,304 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03183,144,181 - 183,206,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43167,437,522 - 167,502,083 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13167,343,557 - 167,408,119 (-)NCBI
Celera3167,063,122 - 167,125,089 (+)NCBICelera
Cytogenetic Map3q43NCBI
SYCP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2059,863,564 - 59,933,655 (-)EnsemblGRCh38hg38GRCh38
GRCh382059,863,277 - 59,933,700 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372058,438,626 - 58,508,692 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372058,438,612 - 58,508,704 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362057,872,013 - 57,940,604 (-)NCBINCBI36hg18NCBI36
Build 342057,872,013 - 57,940,604NCBI
Celera2055,179,316 - 55,247,887 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2055,225,354 - 55,294,509 (-)NCBIHuRef
CHM1_12058,339,670 - 58,409,780 (-)NCBICHM1_1
Sycp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392177,987,088 - 178,051,580 (-)NCBIGRCm39mm39
GRCm382178,345,295 - 178,407,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2178,345,293 - 178,407,685 (-)EnsemblGRCm38mm10GRCm38
MGSCv372178,080,000 - 178,142,363 (-)NCBIGRCm37mm9NCBIm37
MGSCv362178,274,701 - 178,333,233 (-)NCBImm8
Celera2182,431,695 - 182,494,066 (-)NCBICelera
Cytogenetic Map2H4NCBI
Sycp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555283,809,438 - 3,886,312 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555283,809,438 - 3,887,055 (+)NCBIChiLan1.0ChiLan1.0
SYCP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12057,571,625 - 57,639,701 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2057,571,935 - 57,629,016 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02056,219,579 - 56,289,382 (-)NCBIMhudiblu_PPA_v0panPan3
SYCP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2444,471,828 - 44,546,495 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12444,471,516 - 44,546,501 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sycp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365148,264,628 - 8,331,577 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1759,877,505 - 59,955,209 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11759,875,992 - 59,962,314 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21767,296,749 - 67,373,790 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYCP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.124,214,713 - 4,283,451 (+)NCBI
ChlSab1.1 Ensembl24,226,063 - 4,282,751 (+)Ensembl
Sycp2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474126,108,446 - 26,208,184 (-)NCBI

Position Markers
D3Got171  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03173,891,353 - 173,891,573NCBIRnor6.0
Rnor_5.03183,199,638 - 183,199,858UniSTSRnor5.0
RGSC_v3.43167,444,313 - 167,444,534RGDRGSC3.4
RGSC_v3.43167,444,314 - 167,444,534UniSTSRGSC3.4
RGSC_v3.13167,350,350 - 167,350,570RGD
Celera3167,118,093 - 167,118,313UniSTS
RH 3.4 Map31501.1RGD
RH 3.4 Map31501.1UniSTS
RH 2.0 Map31020.4RGD
Cytogenetic Map3q43UniSTS
G65197  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03173,913,084 - 173,913,656NCBIRnor6.0
Rnor_5.03183,177,702 - 183,178,274UniSTSRnor5.0
RGSC_v3.43167,467,481 - 167,468,053UniSTSRGSC3.4
Celera3167,096,464 - 167,097,036UniSTS
Cytogenetic Map3q43UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3170428815177699992Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:80
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000006038
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


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 14
Low 40 7 3 11 3 5 5 42 12 22 8 5
Below cutoff 3 3 38 26 8 26 3 3 32 23 5 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078047   ⟹   ENSRNOP00000070540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3173,884,561 - 173,947,018 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079019   ⟹   ENSRNOP00000075596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3173,884,287 - 173,944,396 (-)Ensembl
RefSeq Acc Id: NM_130735   ⟹   NP_570091
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,436,331 - 165,498,789 (-)NCBI
Rnor_6.03173,884,561 - 173,947,018 (-)NCBI
Rnor_5.03183,144,181 - 183,206,650 (+)NCBI
RGSC_v3.43167,437,522 - 167,502,083 (-)RGD
Celera3167,063,122 - 167,125,089 (+)RGD
Sequence:
RefSeq Acc Id: XM_008762547   ⟹   XP_008760769
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03173,884,559 - 173,948,304 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592073   ⟹   XP_017447562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.03173,884,559 - 173,946,894 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592074   ⟹   XP_017447563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.03173,884,559 - 173,946,894 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592075   ⟹   XP_017447564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.03173,884,559 - 173,947,223 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592076   ⟹   XP_017447565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.03173,884,559 - 173,947,223 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105967   ⟹   XP_038961895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
RefSeq Acc Id: XM_039105969   ⟹   XP_038961897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
RefSeq Acc Id: XM_039105970   ⟹   XP_038961898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23165,431,715 - 165,486,745 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_570091   ⟸   NM_130735
- UniProtKB: O70608 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008760769   ⟸   XM_008762547
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447564   ⟸   XM_017592075
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017447565   ⟸   XM_017592076
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447562   ⟸   XM_017592073
- Peptide Label: isoform X1
- UniProtKB: O70608 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447563   ⟸   XM_017592074
- Peptide Label: isoform X1
- UniProtKB: O70608 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075596   ⟸   ENSRNOT00000079019
RefSeq Acc Id: ENSRNOP00000070540   ⟸   ENSRNOT00000078047
RefSeq Acc Id: XP_038961895   ⟸   XM_039105967
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961897   ⟸   XM_039105969
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961898   ⟸   XM_039105970
- Peptide Label: isoform X4

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692727
Promoter ID:EPDNEW_R3251
Type:multiple initiation site
Name:Sycp2_1
Description:synaptonemal complex protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03173,946,986 - 173,947,046EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 173916264 173916265 G T snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69429 AgrOrtholog
Ensembl Genes ENSRNOG00000061690 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000070540 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075596 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000078047 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000079019 UniProtKB/Swiss-Prot
InterPro ARM-type_fold UniProtKB/Swiss-Prot
  SYCP1/2 UniProtKB/Swiss-Prot
  SYCP2 UniProtKB/Swiss-Prot
  SYCP2_ARLD UniProtKB/Swiss-Prot
  SYCP2_SLD UniProtKB/Swiss-Prot
KEGG Report rno:83820 UniProtKB/Swiss-Prot
NCBI Gene 83820 ENTREZGENE
PANTHER PTHR15607 UniProtKB/Swiss-Prot
  PTHR15607:SF12 UniProtKB/Swiss-Prot
Pfam SYCP2_ARLD UniProtKB/Swiss-Prot
  SYCP2_SLD UniProtKB/Swiss-Prot
PhenoGen Sycp2 PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
TIGR TC210568
UniProt O70608 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Sycp2  synaptonemal complex protein 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed specifically in the testis, in meiotic prophase cells 69387
gene_function may be a DNA-binding protein 69387
gene_protein molecular mass of 173 kDa 69387