Lyst (lysosomal trafficking regulator) - Rat Genome Database

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Gene: Lyst (lysosomal trafficking regulator) Rattus norvegicus
Analyze
Symbol: Lyst
Name: lysosomal trafficking regulator
RGD ID: 621837
Description: Involved in pigmentation. Predicted to localize to cytosol and microtubule cytoskeleton. Used to study Chediak-Higashi syndrome. Human ortholog(s) of this gene implicated in Chediak-Higashi syndrome. Orthologous to human LYST (lysosomal trafficking regulator); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Beige; LOC360289; lysosomal-trafficking regulator
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   DA.Cg-Foxn1rnu Lystbg/Slc  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
Rnor_6.01790,323,055 - 90,522,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01791,983,426 - 92,113,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01792,156,826 - 92,183,054 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41766,569,478 - 66,735,402 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11766,580,310 - 66,746,235NCBI
Celera1785,172,435 - 85,333,653 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:187062   PMID:580786   PMID:624833   PMID:1113502   PMID:1278263   PMID:2513223   PMID:4031470   PMID:4589319   PMID:4601767   PMID:4634048   PMID:4697831   PMID:6154765  
PMID:6170520   PMID:6218091   PMID:6272291   PMID:6696991   PMID:6977094   PMID:7089489   PMID:7988496   PMID:9368050   PMID:9606205   PMID:10648412   PMID:10803361   PMID:12638244  
PMID:13943454   PMID:16210783   PMID:16518687  


Genomics

Comparative Map Data
Lyst
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
Rnor_6.01790,323,055 - 90,522,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01791,983,426 - 92,113,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01792,156,826 - 92,183,054 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41766,569,478 - 66,735,402 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11766,580,310 - 66,746,235NCBI
Celera1785,172,435 - 85,333,653 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
LYST
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1235,661,041 - 235,883,640 (-)EnsemblGRCh38hg38GRCh38
GRCh381235,661,031 - 235,883,713 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371235,824,331 - 236,047,013 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361233,890,966 - 234,096,843 (-)NCBINCBI36hg18NCBI36
Celera1209,067,680 - 209,273,532 (-)NCBI
Cytogenetic Map1q42.3NCBI
HuRef1206,276,078 - 206,498,442 (-)NCBIHuRef
CHM1_11237,097,073 - 237,319,731 (-)NCBICHM1_1
Lyst
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391313,764,896 - 13,953,388 (+)NCBIGRCm39mm39
GRCm39 Ensembl1313,764,982 - 13,953,388 (+)Ensembl
GRCm381313,590,311 - 13,778,803 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1313,590,397 - 13,778,803 (+)EnsemblGRCm38mm10GRCm38
MGSCv371313,682,676 - 13,869,707 (+)NCBIGRCm37mm9NCBIm37
MGSCv361313,382,535 - 13,569,566 (+)NCBImm8
Celera1313,893,712 - 14,083,127 (+)NCBICelera
Cytogenetic Map13A1NCBI
cM Map135.28NCBI
Lyst
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554924,209,749 - 4,369,762 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554924,161,976 - 4,371,637 (+)NCBIChiLan1.0ChiLan1.0
LYST
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11216,231,824 - 216,436,293 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1216,231,824 - 216,436,293 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01211,229,800 - 211,451,947 (-)NCBIMhudiblu_PPA_v0panPan3
LYST
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.144,106,869 - 4,296,042 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl44,089,837 - 4,294,593 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha44,153,555 - 4,342,677 (+)NCBI
ROS_Cfam_1.044,128,097 - 4,317,357 (+)NCBI
UMICH_Zoey_3.144,140,014 - 4,329,208 (+)NCBI
UNSW_CanFamBas_1.044,257,740 - 4,446,788 (+)NCBI
UU_Cfam_GSD_1.044,478,809 - 4,668,078 (+)NCBI
Lyst
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934440,585,775 - 40,750,794 (+)NCBI
SpeTri2.0NW_00493648416,750,976 - 16,915,999 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYST
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1455,433,018 - 55,633,484 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11455,433,163 - 55,634,011 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21459,508,449 - 59,679,488 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LYST
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12572,827,997 - 73,048,645 (-)NCBI
ChlSab1.1 Ensembl2572,828,006 - 72,991,970 (-)Ensembl
Lyst
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477514,670,498 - 14,900,501 (+)NCBI

Position Markers
D17Rat132  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01790,522,442 - 90,522,804NCBIRnor6.0
Rnor_5.01792,183,405 - 92,183,767UniSTSRnor5.0
RGSC_v3.41766,735,752 - 66,736,115RGDRGSC3.4
RGSC_v3.41766,735,753 - 66,736,115UniSTSRGSC3.4
RGSC_v3.11766,746,492 - 66,747,055RGD
Celera1785,334,004 - 85,334,366UniSTS
SHRSP x BN Map1747.5399UniSTS
SHRSP x BN Map1747.5399RGD
Cytogenetic Map17q12.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat


Related Rat Strains
The following Strains have been annotated to Lyst

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:412
Count of miRNA genes:239
Interacting mature miRNAs:275
Transcripts:ENSRNOT00000017270, ENSRNOT00000058790
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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


Sequence


Reference Sequences
RefSeq Acc Id: NM_053518   ⟹   NP_445970
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,279,519 - 86,441,780 (+)NCBI
Rnor_6.01790,323,055 - 90,522,091 (-)NCBI
Rnor_5.01791,983,426 - 92,113,948 (-)NCBI
Rnor_5.01792,156,826 - 92,183,054 (-)NCBI
RGSC_v3.41766,569,478 - 66,735,402 (-)RGD
Celera1785,172,435 - 85,333,653 (-)RGD
Sequence:
RefSeq Acc Id: XM_039096119   ⟹   XP_038952047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096120   ⟹   XP_038952048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,424 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096121   ⟹   XP_038952049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,497 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096122   ⟹   XP_038952050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,275,038 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096123   ⟹   XP_038952051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096124   ⟹   XP_038952052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096125   ⟹   XP_038952053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096126   ⟹   XP_038952054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,422,158 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445970   ⟸   NM_053518
- UniProtKB: Q9Z2X9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038952047   ⟸   XM_039096119
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952053   ⟸   XM_039096125
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952051   ⟸   XM_039096123
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952052   ⟸   XM_039096124
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038952054   ⟸   XM_039096126
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038952048   ⟸   XM_039096120
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952049   ⟸   XM_039096121
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952050   ⟸   XM_039096122
- Peptide Label: isoform X1
Protein Domains
BEACH   BEACH-type PH   WD_REPEATS_REGION


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621837 AgrOrtholog
Gene3D-CATH 1.10.1540.10 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  BEACH_dom_sf UniProtKB/TrEMBL
  Beige_BEACH UniProtKB/TrEMBL
  LYST UniProtKB/TrEMBL
  PH-BEACH_dom UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:85419 UniProtKB/TrEMBL
NCBI Gene 85419 ENTREZGENE
PANTHER PTHR13743:SF86 UniProtKB/TrEMBL
Pfam Beach UniProtKB/TrEMBL
  PH_BEACH UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
PhenoGen Lyst PhenoGen
PROSITE BEACH UniProtKB/TrEMBL
  PH_BEACH UniProtKB/TrEMBL
  WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
SMART Beach UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
Superfamily-SCOP Beige_BEACH UniProtKB/TrEMBL
  SSF48371 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt Q9Z2X9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-02-23 Lyst  lysosomal trafficking regulator  Lyst_predicted  lysosomal trafficking regulator (predicted)  Data Merged 737654 APPROVED
2005-01-20 Lyst  lysosomal trafficking regulator      Symbol and Name status set to approved 1299863 APPROVED
2005-01-12 Lyst_predicted  lysosomal trafficking regulator (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-08-07 Lyst  lysosomal trafficking regulator      Symbol and Name status set to provisional 70820 PROVISIONAL