Lyst (lysosomal trafficking regulator) - Rat Genome Database

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Gene: Lyst (lysosomal trafficking regulator) Rattus norvegicus
Analyze
Symbol: Lyst (Ensembl: AABR07028902.1)
Name: lysosomal trafficking regulator
RGD ID: 621837
Description: Involved in pigmentation. Predicted to be located in 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; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21786,241,384 - 86,443,501 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1786,241,384 - 86,443,480 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1790,517,628 - 90,679,857 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01794,353,524 - 94,515,764 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01788,370,050 - 88,532,284 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01790,323,055 - 90,522,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01792,156,826 - 92,183,054 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01791,983,426 - 92,113,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41766,569,478 - 66,735,402 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Identification of mutations in two major mRNA isoforms of the Chediak-Higashi syndrome gene in human and mouse. Barbosa MD, etal., Hum Mol Genet 1997 Jul;6(7):1091-8.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. A new beige mutant rat ACI/N-Lystbg-Kyo. Mori M, etal., Exp Anim 2003 Jan;52(1):31-6.
5. Deletion in the beige gene of the beige rat owing to recombination between LINE1s. Mori M, etal., Mamm Genome 1999 Jul;10(7):692-5.
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
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 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1786,241,384 - 86,443,480 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1790,517,628 - 90,679,857 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01794,353,524 - 94,515,764 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01788,370,050 - 88,532,284 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01790,323,055 - 90,522,091 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01792,156,826 - 92,183,054 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01791,983,426 - 92,113,948 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41766,569,478 - 66,735,402 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381235,661,031 - 235,883,713 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1235,661,041 - 235,883,724 (-)EnsemblGRCh38hg38GRCh38
GRCh371235,824,331 - 236,047,013 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361233,890,966 - 234,096,843 (-)NCBINCBI36Build 36hg18NCBI36
Celera1209,067,680 - 209,273,532 (-)NCBICelera
Cytogenetic Map1q42.3NCBI
HuRef1206,276,078 - 206,498,442 (-)NCBIHuRef
CHM1_11237,097,073 - 237,319,731 (-)NCBICHM1_1
T2T-CHM13v2.01235,057,704 - 235,280,316 (-)NCBIT2T-CHM13v2.0
Lyst
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391313,764,896 - 13,953,388 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1313,764,982 - 13,953,388 (+)EnsemblGRCm39 Ensembl
GRCm381313,590,311 - 13,778,803 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1313,590,397 - 13,778,803 (+)EnsemblGRCm38mm10GRCm38
MGSCv371313,682,676 - 13,869,707 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361313,382,535 - 13,569,566 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1113,506,415 - 13,728,594 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01211,229,800 - 211,451,947 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11216,231,824 - 216,436,293 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1216,231,824 - 216,436,293 (-)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.044,128,097 - 4,317,357 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl44,128,101 - 4,316,523 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.144,140,014 - 4,329,208 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.044,257,740 - 4,446,788 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.044,478,809 - 4,668,078 (+)NCBIUU_Cfam_GSD_1.0
Lyst
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934440,585,775 - 40,750,794 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648416,763,511 - 16,916,022 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493648416,750,976 - 16,915,999 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYST
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1455,433,597 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12572,827,997 - 73,048,645 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2572,828,006 - 72,991,970 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605574,871,183 - 75,097,795 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lyst
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477514,705,693 - 14,898,660 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477514,670,498 - 14,900,501 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lyst
763 total Variants
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.


QTLs in Region (mRatBN7.2)
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)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat

Markers in Region
D17Rat132  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21786,278,804 - 86,279,167 (-)MAPPERmRatBN7.2
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


Related Rat Strains
The following Strains have been annotated to Lyst


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077767   ⟹   ENSRNOP00000073572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1786,241,384 - 86,443,480 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117614   ⟹   ENSRNOP00000096376
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1786,241,384 - 86,443,480 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000120081   ⟹   ENSRNOP00000076739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1786,241,384 - 86,443,480 (+)Ensembl
RefSeq Acc Id: NM_053518   ⟹   NP_445970
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,495 (+)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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096120   ⟹   XP_038952048
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,424 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096121   ⟹   XP_038952049
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,497 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096122   ⟹   XP_038952050
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,275,038 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096123   ⟹   XP_038952051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096124   ⟹   XP_038952052
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,443,501 (+)NCBI
RefSeq Acc Id: XM_039096126   ⟹   XP_038952054
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21786,241,384 - 86,422,158 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_445970   ⟸   NM_053518
- UniProtKB: A0A0G2K5V4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038952047   ⟸   XM_039096119
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952051   ⟸   XM_039096123
- Peptide Label: isoform X2
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952052   ⟸   XM_039096124
- Peptide Label: isoform X3
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952054   ⟸   XM_039096126
- Peptide Label: isoform X5
- UniProtKB: A6KTD2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952048   ⟸   XM_039096120
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952049   ⟸   XM_039096121
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952050   ⟸   XM_039096122
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B436 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000076739   ⟸   ENSRNOT00000120081
RefSeq Acc Id: ENSRNOP00000073572   ⟸   ENSRNOT00000077767
RefSeq Acc Id: ENSRNOP00000096376   ⟸   ENSRNOT00000117614
Protein Domains
BEACH   BEACH-type PH

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621837 AgrOrtholog
BioCyc Gene G2FUF-8451 BioCyc
Ensembl Genes ENSRNOG00000058094 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073572 ENTREZGENE
  ENSRNOP00000073572.2 UniProtKB/TrEMBL
  ENSRNOP00000076739.1 UniProtKB/TrEMBL
  ENSRNOP00000096376 ENTREZGENE
  ENSRNOP00000096376.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077767 ENTREZGENE
  ENSRNOT00000077767.2 UniProtKB/TrEMBL
  ENSRNOT00000117614 ENTREZGENE
  ENSRNOT00000117614.1 UniProtKB/TrEMBL
  ENSRNOT00000120081.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1540.10 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  BEACH_dom_sf UniProtKB/TrEMBL
  Beige_BEACH UniProtKB/TrEMBL
  PH-BEACH_dom UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:85419 UniProtKB/TrEMBL
NCBI Gene 85419 ENTREZGENE
PANTHER BEIGE/BEACH-RELATED UniProtKB/TrEMBL
  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
  PH domain-like UniProtKB/TrEMBL
  SSF48371 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt A0A0G2K5V4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5Y701_RAT UniProtKB/TrEMBL
  A0A8I6B436 ENTREZGENE, UniProtKB/TrEMBL
  A6KTD2 ENTREZGENE, UniProtKB/TrEMBL
  Q9Z2X9_RAT 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