Sytl5 (synaptotagmin-like 5) - Rat Genome Database

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Gene: Sytl5 (synaptotagmin-like 5) Rattus norvegicus
Analyze
Symbol: Sytl5
Name: synaptotagmin-like 5
RGD ID: 631342
Description: Predicted to have neurexin family protein binding activity. Predicted to be involved in exocytosis. Predicted to localize to exocytic vesicle and plasma membrane. Orthologous to human SYTL5 (synaptotagmin like 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: synaptotagmin 15; synaptotagmin-like protein 5
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
mRatBN7.2X12,775,529 - 13,030,134 (-)NCBI
Rnor_6.0 EnsemblX14,019,961 - 14,109,568 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X14,642,886 - 14,891,896 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X24,945,436 - 25,034,025 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X25,059,892 - 25,087,494 (-)NCBI
CeleraX13,398,414 - 13,486,944 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12590134  


Genomics

Comparative Map Data
Sytl5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X12,775,529 - 13,030,134 (-)NCBI
Rnor_6.0 EnsemblX14,019,961 - 14,109,568 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X14,642,886 - 14,891,896 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X24,945,436 - 25,034,025 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X25,059,892 - 25,087,494 (-)NCBI
CeleraX13,398,414 - 13,486,944 (-)NCBICelera
Cytogenetic MapXq12NCBI
SYTL5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX38,006,553 - 38,128,819 (+)EnsemblGRCh38hg38GRCh38
GRCh38X37,888,915 - 38,128,820 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X37,865,806 - 37,988,073 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X37,778,087 - 37,870,927 (+)NCBINCBI36hg18NCBI36
Build 34X37,649,359 - 37,742,200NCBI
CeleraX42,003,495 - 42,125,714 (+)NCBI
Cytogenetic MapXp11.4NCBI
HuRefX35,611,538 - 35,733,083 (+)NCBIHuRef
CHM1_1X37,896,717 - 38,019,127 (+)NCBICHM1_1
Sytl5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X9,613,851 - 9,871,268 (+)NCBIGRCm39mm39
GRCm39 EnsemblX9,751,861 - 9,860,782 (+)Ensembl
GRCm38X9,747,622 - 9,998,864 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX9,885,622 - 9,994,543 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X9,462,748 - 9,571,669 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X9,042,581 - 9,151,502 (+)NCBImm8
CeleraX7,598,989 - 7,706,928 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
Sytl5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495560176,647 - 210,208 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495560176,647 - 210,198 (+)NCBIChiLan1.0ChiLan1.0
SYTL5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X38,164,569 - 38,286,366 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX38,164,308 - 38,288,628 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X30,355,289 - 30,578,052 (+)NCBIMhudiblu_PPA_v0panPan3
SYTL5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X32,652,389 - 32,886,793 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX32,651,968 - 32,879,525 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX20,001,349 - 20,232,716 (+)NCBI
ROS_Cfam_1.0X32,699,069 - 32,931,470 (+)NCBI
UMICH_Zoey_3.1X32,780,480 - 33,012,485 (+)NCBI
UNSW_CanFamBas_1.0X32,744,381 - 32,984,277 (+)NCBI
UU_Cfam_GSD_1.0X32,904,116 - 33,023,381 (+)NCBI
Sytl5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X24,909,573 - 25,149,712 (+)NCBI
SpeTri2.0NW_0049365024,873,750 - 4,987,742 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYTL5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX33,687,031 - 34,036,269 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X33,798,296 - 34,066,127 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X37,773,056 - 37,854,459 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103247463
(Chlorocebus sabaeus - African green monkey)
No map positions available.
Sytl5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476217,401,304 - 17,659,757 (-)NCBI

Position Markers
ha2932  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X88,206,089 - 88,206,554 (+)MAPPER
Rnor_6.0X94,919,050 - 94,919,514NCBIRnor6.0
Rnor_5.0X94,807,178 - 94,807,642UniSTSRnor5.0
CeleraX13,417,319 - 13,418,573UniSTS
CeleraX89,371,262 - 89,371,726UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:40
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000004785
Prediction methods: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 3
Low 2 23 10 7 10 58 31 30 11
Below cutoff 1 30 25 22 10 22 8 8 16 4 8 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_178333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB098162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC133223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC133696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004785   ⟹   ENSRNOP00000004785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX14,019,961 - 14,109,568 (+)Ensembl
RefSeq Acc Id: NM_178333   ⟹   NP_848016
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,788,959 - 12,877,756 (-)NCBI
Rnor_6.0X14,020,157 - 14,108,951 (+)NCBI
Rnor_5.0X14,642,886 - 14,891,896 (+)NCBI
RGSC_v3.4X24,945,436 - 25,034,025 (-)RGD
CeleraX13,398,414 - 13,486,944 (-)RGD
Sequence:
RefSeq Acc Id: XM_008773069   ⟹   XP_008771291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 13,030,134 (-)NCBI
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773070   ⟹   XP_008771292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 12,957,585 (-)NCBI
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601977   ⟹   XP_017457466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,904,075 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601978   ⟹   XP_017457467
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601979   ⟹   XP_017457468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601980   ⟹   XP_017457469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601981   ⟹   XP_017457470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601982   ⟹   XP_017457471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601983   ⟹   XP_017457472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601984   ⟹   XP_017457473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601985   ⟹   XP_017457474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,914,433 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601986   ⟹   XP_017457475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601988   ⟹   XP_017457477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601989   ⟹   XP_017457478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601990   ⟹   XP_017457479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601991   ⟹   XP_017457480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 12,957,585 (-)NCBI
Rnor_6.0X13,938,796 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601992   ⟹   XP_017457481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X13,857,669 - 14,109,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099626   ⟹   XP_038955554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 12,957,585 (-)NCBI
RefSeq Acc Id: XM_039099627   ⟹   XP_038955555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 12,957,585 (-)NCBI
RefSeq Acc Id: XM_039099628   ⟹   XP_038955556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X12,775,529 - 12,957,585 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_848016   ⟸   NM_178333
- UniProtKB: Q812E4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771291   ⟸   XM_008773069
- Peptide Label: isoform X1
- UniProtKB: G3V6F7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771292   ⟸   XM_008773070
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457468   ⟸   XM_017601979
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457481   ⟸   XM_017601992
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457470   ⟸   XM_017601981
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457467   ⟸   XM_017601978
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457473   ⟸   XM_017601984
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457475   ⟸   XM_017601986
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457479   ⟸   XM_017601990
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457472   ⟸   XM_017601983
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457469   ⟸   XM_017601980
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457477   ⟸   XM_017601988
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457478   ⟸   XM_017601989
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457471   ⟸   XM_017601982
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457466   ⟸   XM_017601977
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457474   ⟸   XM_017601985
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457480   ⟸   XM_017601991
- Peptide Label: isoform X1
- UniProtKB: G3V6F7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004785   ⟸   ENSRNOT00000004785
RefSeq Acc Id: XP_038955555   ⟸   XM_039099627
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955554   ⟸   XM_039099626
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955556   ⟸   XM_039099628
- Peptide Label: isoform X3
Protein Domains
C2   RabBD

Transcriptome

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


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)
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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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
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
X 14031293 14031294 A C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631342 AgrOrtholog
Ensembl Genes ENSRNOG00000003585 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004785 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004785 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C2_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C2_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FYVE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rab_BD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SLP-4/5_C2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Slp5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYTL1-5_C2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYTL5_FYVE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:302538 UniProtKB/Swiss-Prot
NCBI Gene 302538 ENTREZGENE
PANTHER PTHR45716:SF6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FYVE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sytl5 PhenoGen
PROSITE PS50004 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RABBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6F7 ENTREZGENE, UniProtKB/TrEMBL
  Q812E4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Sytl5  synaptotagmin-like 5    synaptotagmin 15  Name updated 1299863 APPROVED
2004-02-11 Slc1a7  synaptotagmin 15  Sytl5  synaptotagmin-like 5  Name updated to reflect Human and Mouse nomenclature 625702 APPROVED