Sytl4 (synaptotagmin-like 4) - Rat Genome Database
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Gene: Sytl4 (synaptotagmin-like 4) Rattus norvegicus
Analyze
Symbol: Sytl4
Name: synaptotagmin-like 4
RGD ID: 620204
Description: Predicted to have neurexin family protein binding activity and phospholipid binding activity. Predicted to be involved in several processes, including plasma membrane repair; regulation of plasma membrane repair; and regulation of secretion by cell. Localizes to apical plasma membrane and secretory granule membrane. Orthologous to human SYTL4 (synaptotagmin like 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: exophilin-2; granuphilin b; synaptotagmin-like 4 (granuphilin-a); synaptotagmin-like protein 4
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
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X104,763,961 - 104,814,152 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,473,414 - 121,499,134 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X121,546,846 - 121,572,567 (-)NCBI
CeleraX98,183,387 - 98,209,107 (-)NCBICelera
Cytogenetic MapXq32NCBI
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:2732579   PMID:10497219   PMID:11243866   PMID:12590134   PMID:16186111   PMID:16890542   PMID:18573236   PMID:19082571   PMID:19966785   PMID:22206666   PMID:25002582   PMID:27325790  


Genomics

Comparative Map Data
Sytl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X104,763,961 - 104,814,152 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,473,414 - 121,499,134 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X121,546,846 - 121,572,567 (-)NCBI
CeleraX98,183,387 - 98,209,107 (-)NCBICelera
Cytogenetic MapXq32NCBI
SYTL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX100,674,491 - 100,732,123 (-)EnsemblGRCh38hg38GRCh38
GRCh38X100,671,964 - 100,732,137 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X99,929,488 - 99,987,108 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,816,144 - 99,873,154 (-)NCBINCBI36hg18NCBI36
Build 34X99,735,633 - 99,792,643NCBI
CeleraX100,448,228 - 100,505,895 (-)NCBI
Cytogenetic MapXq22.1NCBI
HuRefX89,729,520 - 89,785,468 (-)NCBIHuRef
CHM1_1X99,822,386 - 99,880,040 (-)NCBICHM1_1
Sytl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X132,837,134 - 132,882,569 (-)NCBIGRCm39mm39
GRCm39 EnsemblX132,837,134 - 132,882,561 (-)Ensembl
GRCm38X133,936,385 - 133,981,821 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,936,385 - 133,981,812 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X130,470,924 - 130,516,322 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X129,282,735 - 129,328,133 (-)NCBImm8
CeleraX116,812,358 - 116,857,700 (-)NCBICelera
Cytogenetic MapXE3NCBI
Sytl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555036,821,236 - 6,899,983 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555036,821,263 - 6,899,983 (-)NCBIChiLan1.0ChiLan1.0
SYTL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X100,024,434 - 100,051,663 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX100,024,434 - 100,051,663 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X89,885,478 - 89,941,381 (-)NCBIMhudiblu_PPA_v0panPan3
SYTL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX74,539,183 - 74,565,753 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X74,537,937 - 74,617,580 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sytl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365845,882,428 - 5,945,514 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYTL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX82,367,549 - 82,437,404 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X82,367,546 - 82,437,439 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X90,208,955 - 90,310,119 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYTL4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X88,985,495 - 89,041,256 (-)NCBI
ChlSab1.1 EnsemblX88,987,016 - 89,041,194 (-)Ensembl
Sytl4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249021,876,608 - 1,945,728 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X101333032146333032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:123
Interacting mature miRNAs:138
Transcripts:ENSRNOT00000004909, ENSRNOT00000004921
Prediction methods:Microtar, Miranda, Pita, 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 1 8 7 11
Low 2 43 49 41 12 41 8 10 72 35 25 11 8
Below cutoff 1 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004909   ⟹   ENSRNOP00000004909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX104,765,294 - 104,814,145 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000004921   ⟹   ENSRNOP00000004921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX104,765,492 - 104,791,210 (-)Ensembl
RefSeq Acc Id: NM_080410   ⟹   NP_536335
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,137,031 - 97,162,754 (-)NCBI
Rnor_6.0X104,765,492 - 104,791,210 (-)NCBI
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBI
RGSC_v3.4X121,473,414 - 121,499,134 (-)RGD
CeleraX98,183,387 - 98,209,107 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257213   ⟹   XP_006257275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
Rnor_6.0X104,763,961 - 104,814,152 (-)NCBI
Rnor_5.0X104,598,207 - 104,648,029 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773387   ⟹   XP_008771609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
Rnor_6.0X104,765,486 - 104,814,151 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099429   ⟹   XP_038955357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
RefSeq Acc Id: XM_039099430   ⟹   XP_038955358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,437 (-)NCBI
RefSeq Acc Id: XM_039099431   ⟹   XP_038955359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,865 (-)NCBI
RefSeq Acc Id: XM_039099432   ⟹   XP_038955360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,135,500 - 97,185,867 (-)NCBI
RefSeq Acc Id: XM_039099433   ⟹   XP_038955361
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,137,037 - 97,185,867 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_536335   ⟸   NM_080410
- UniProtKB: Q8VHQ7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006257275   ⟸   XM_006257213
- Peptide Label: isoform X1
- UniProtKB: G3V6G6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771609   ⟸   XM_008773387
- Peptide Label: isoform X4
- UniProtKB: D3ZTZ2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004921   ⟸   ENSRNOT00000004921
RefSeq Acc Id: ENSRNOP00000004909   ⟸   ENSRNOT00000004909
RefSeq Acc Id: XP_038955360   ⟸   XM_039099432
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955357   ⟸   XM_039099429
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955359   ⟸   XM_039099431
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955358   ⟸   XM_039099430
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955361   ⟸   XM_039099433
- 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)
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)
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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 104609394 104609395 C A snv IS/Kyo (KyushuU), BN/SsNSlc (KyushuU)
X 104609399 104609400 T G snv IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620204 AgrOrtholog
BIND 134440
  134444
  134445
  134446
Ensembl Genes ENSRNOG00000003526 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004909 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000004921 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004909 UniProtKB/TrEMBL
  ENSRNOT00000004921 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
  FYVE_Slp4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rab_BD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SLP-4/5_C2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYTL1-5_C2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYTL4 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:140594 UniProtKB/Swiss-Prot
NCBI Gene 140594 ENTREZGENE
PANTHER PTHR45716:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FYVE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sytl4 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 D3ZTZ2 ENTREZGENE, UniProtKB/TrEMBL
  G3V6G6 ENTREZGENE, UniProtKB/TrEMBL
  Q8VHQ7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q8VHQ6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Sytl4  synaptotagmin-like 4    synaptotagmin-like 4 (granuphilin-a)  Name updated 1299863 APPROVED
2002-08-07 Sytl4  synaptotagmin-like 4 (granuphilin-a)      Symbol and Name status set to provisional 70820 PROVISIONAL