SYCP1 (synaptonemal complex protein 1) - Rat Genome Database

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Gene: SYCP1 (synaptonemal complex protein 1) Canis lupus familiaris
Analyze
Symbol: SYCP1
Name: synaptonemal complex protein 1
RGD ID: 12100756
Description: ENCODES a protein that exhibits double-stranded DNA binding (inferred); INVOLVED IN chiasma assembly (ortholog); lateral element assembly (ortholog); meiotic DNA repair synthesis (ortholog); ASSOCIATED WITH adenocarcinoma (ortholog); genetic disease (ortholog); hereditary spastic paraplegia 47 (ortholog); FOUND IN synaptonemal complex (ortholog); transverse filament (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11752,538,909 - 52,681,495 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1752,539,615 - 52,648,133 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1752,185,713 - 52,295,690 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01753,416,396 - 53,526,463 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1753,417,228 - 53,526,125 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11752,450,471 - 52,560,463 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01752,492,758 - 52,603,152 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01753,066,281 - 53,176,061 (+)NCBIUU_Cfam_GSD_1.0
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SYCP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11752,538,909 - 52,681,495 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1752,539,615 - 52,648,133 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1752,185,713 - 52,295,690 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01753,416,396 - 53,526,463 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1753,417,228 - 53,526,125 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11752,450,471 - 52,560,463 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01752,492,758 - 52,603,152 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01753,066,281 - 53,176,061 (+)NCBIUU_Cfam_GSD_1.0
SYCP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381114,854,088 - 114,995,370 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1114,854,863 - 114,995,370 (+)EnsemblGRCh38hg38GRCh38
GRCh371115,397,484 - 115,537,991 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361115,198,978 - 115,339,514 (+)NCBINCBI36Build 36hg18NCBI36
Build 341115,109,496 - 115,250,030NCBI
Celera1113,626,675 - 113,767,206 (+)NCBICelera
Cytogenetic Map1p13.2NCBI
HuRef1113,255,798 - 113,396,257 (+)NCBIHuRef
CHM1_11115,512,661 - 115,653,225 (+)NCBICHM1_1
T2T-CHM13v2.01114,865,527 - 115,006,795 (+)NCBIT2T-CHM13v2.0
Sycp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393102,725,815 - 102,843,416 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3102,725,815 - 102,843,416 (-)EnsemblGRCm39 Ensembl
GRCm383102,818,499 - 102,936,100 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3102,818,499 - 102,936,100 (-)EnsemblGRCm38mm10GRCm38
MGSCv373102,622,422 - 102,740,023 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363102,947,711 - 103,065,145 (-)NCBIMGSCv36mm8
Celera3105,025,122 - 105,140,873 (-)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map345.25NCBI
Sycp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82192,985,164 - 193,145,234 (-)NCBIGRCr8
mRatBN7.22190,296,688 - 190,456,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2190,296,954 - 190,456,737 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2197,911,191 - 198,053,355 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02195,771,767 - 195,913,691 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02190,600,884 - 190,743,044 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02205,274,766 - 205,426,869 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2205,274,769 - 205,426,869 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02224,746,025 - 224,857,015 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02224,707,701 - 224,725,381 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42197,989,614 - 198,164,611 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12197,952,370 - 198,127,365 (-)NCBI
Celera2182,717,279 - 182,930,195 (-)NCBICelera
Cytogenetic Map2q34NCBI
Sycp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543518,157,173 - 18,291,732 (+)NCBIChiLan1.0ChiLan1.0
SYCP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21107,508,119 - 107,651,051 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11107,102,971 - 107,250,205 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0187,565,888 - 87,701,530 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11122,614,169 - 122,754,797 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1122,614,520 - 122,754,137 (-)Ensemblpanpan1.1panPan2
Sycp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505814,123,922 - 14,250,235 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936627239,232 - 365,062 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4105,591,743 - 105,730,398 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14105,592,354 - 105,730,413 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24115,731,010 - 115,869,676 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYCP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12018,712,236 - 18,827,120 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2018,712,587 - 18,823,277 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603821,463,980 - 21,577,606 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sycp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477210,525,203 - 10,699,560 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477210,524,656 - 10,699,894 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SYCP1
1693 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 8
Low 5 5 5 1
Below cutoff 4 5 16 1 6 1 5 5 12 9 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000015417   ⟹   ENSCAFP00000014266
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1752,539,615 - 52,648,133 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000046783   ⟹   ENSCAFP00000037843
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1752,539,615 - 52,648,133 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845048537   ⟹   ENSCAFP00845038073
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1753,417,228 - 53,526,125 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845048687   ⟹   ENSCAFP00845038195
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1753,417,228 - 53,526,125 (+)Ensembl
RefSeq Acc Id: XM_014120721   ⟹   XP_013976196
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11752,538,915 - 52,648,471 (+)NCBI
Dog10K_Boxer_Tasha1752,185,713 - 52,295,690 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038499289   ⟹   XP_038355217
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11752,450,471 - 52,560,463 (+)NCBI
RefSeq Acc Id: XM_038561854   ⟹   XP_038417782
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01753,066,281 - 53,176,061 (+)NCBI
RefSeq Acc Id: XM_038625925   ⟹   XP_038481853
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01752,492,758 - 52,603,152 (+)NCBI
RefSeq Acc Id: XM_038691858   ⟹   XP_038547786
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01753,416,396 - 53,526,463 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_013976196   ⟸   XM_014120721
- UniProtKB: A0A8C0MAT0 (UniProtKB/TrEMBL),   A0A8I3PY77 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000014266   ⟸   ENSCAFT00000015417
RefSeq Acc Id: ENSCAFP00000037843   ⟸   ENSCAFT00000046783
RefSeq Acc Id: XP_038355217   ⟸   XM_038499289
RefSeq Acc Id: XP_038481853   ⟸   XM_038625925
RefSeq Acc Id: XP_038547786   ⟸   XM_038691858
- UniProtKB: A0A8C0MAT0 (UniProtKB/TrEMBL),   A0A8I3PY77 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038417782   ⟸   XM_038561854
- UniProtKB: A0A8C0MAT0 (UniProtKB/TrEMBL),   A0A8I3PY77 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845038195   ⟸   ENSCAFT00845048687
RefSeq Acc Id: ENSCAFP00845038073   ⟸   ENSCAFT00845048537


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000009705 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030003928 UniProtKB/TrEMBL
  ENSCAFG00040010343 UniProtKB/TrEMBL
  ENSCAFG00845027397 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000015417.6 UniProtKB/TrEMBL
  ENSCAFT00000046783.4 UniProtKB/TrEMBL
  ENSCAFT00030007763.1 UniProtKB/TrEMBL
  ENSCAFT00030007890.1 UniProtKB/TrEMBL
  ENSCAFT00040019919.1 UniProtKB/TrEMBL
  ENSCAFT00040019994.1 UniProtKB/TrEMBL
  ENSCAFT00845048537 ENTREZGENE
  ENSCAFT00845048537.1 UniProtKB/TrEMBL
  ENSCAFT00845048687.1 UniProtKB/TrEMBL
InterPro SYCP1 UniProtKB/TrEMBL
NCBI Gene SYCP1 ENTREZGENE
PANTHER PTHR46918 UniProtKB/TrEMBL
  SYNAPTONEMAL COMPLEX PROTEIN 1 UniProtKB/TrEMBL
Pfam SCP-1 UniProtKB/TrEMBL
UniProt A0A8C0M9W3_CANLF UniProtKB/TrEMBL
  A0A8C0MAT0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PY77 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PYA6_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:47018 ENTREZGENE