Hps6 (HPS6, biogenesis of lysosomal organelles complex 2 subunit 3) - Rat Genome Database

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Gene: Hps6 (HPS6, biogenesis of lysosomal organelles complex 2 subunit 3) Mus musculus
Analyze
Symbol: Hps6
Name: HPS6, biogenesis of lysosomal organelles complex 2 subunit 3
RGD ID: 1619246
MGI Page MGI
Description: Predicted to enable GTP-dependent protein binding activity and small GTPase binding activity. Involved in lysosome localization. Acts upstream of or within blood coagulation; organelle organization; and pigmentation. Predicted to be located in several cellular components, including endoplasmic reticulum; endosome; and lysosome. Predicted to be part of BLOC-2 complex. Predicted to be active in lysosomal membrane. Used to study Hermansky-Pudlak syndrome 6. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome and Hermansky-Pudlak syndrome 6. Orthologous to human HPS6 (HPS6 biogenesis of lysosomal organelles complex 2 subunit 3).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5330434M19Rik; BLOC; BLOC-2 complex member HPS6; BLOC2; Hermansky-Pudlak syndrome 6; Hermansky-Pudlak syndrome 6 protein homolog; MGC31055; r; ru; ruby eye; ruby-eye protein
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391945,991,917 - 45,994,612 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1945,991,947 - 45,994,612 (+)EnsemblGRCm39 Ensembl
GRCm381946,003,478 - 46,006,173 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1946,003,508 - 46,006,173 (+)EnsemblGRCm38mm10GRCm38
MGSCv371946,077,968 - 46,080,663 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361946,056,819 - 46,059,464 (+)NCBIMGSCv36mm8
Celera1946,765,544 - 46,768,239 (+)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1938.75NCBI
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

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Clinical and cellular characterisation of Hermansky-Pudlak syndrome type 6. Huizing M, etal., J Med Genet. 2009 Dec;46(12):803-10. doi: 10.1136/jmg.2008.065961. Epub 2009 Oct 20.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. Mouse MP Annotation Import Pipeline RGD automated import pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:102659   PMID:273256   PMID:1319776   PMID:1322500   PMID:1855483   PMID:2013688   PMID:2369371   PMID:2379821   PMID:3516713   PMID:3998439   PMID:4436535   PMID:4634048  
PMID:5279341   PMID:5902512   PMID:6031677   PMID:6067640   PMID:6696991   PMID:6776948   PMID:6971254   PMID:7274657   PMID:7828830   PMID:7835879   PMID:8043950   PMID:8962054  
PMID:9107690   PMID:9256466   PMID:9714600   PMID:10193444   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11256068   PMID:12445206   PMID:12466851   PMID:12477932  
PMID:12548288   PMID:13943454   PMID:14718540   PMID:15265785   PMID:15489334   PMID:15702992   PMID:15782199   PMID:16141072   PMID:16141073   PMID:16578176   PMID:17247639   PMID:18230650  
PMID:18629000   PMID:18890162   PMID:19010779   PMID:19395672   PMID:21045126   PMID:21392365   PMID:21677750   PMID:21873635   PMID:22203954   PMID:22984402   PMID:23247405   PMID:23364476  
PMID:25189619   PMID:25593336   PMID:26008744   PMID:27889498   PMID:29074498   PMID:30710063   PMID:32614949   PMID:33513603  


Genomics

Comparative Map Data
Hps6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391945,991,917 - 45,994,612 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1945,991,947 - 45,994,612 (+)EnsemblGRCm39 Ensembl
GRCm381946,003,478 - 46,006,173 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1946,003,508 - 46,006,173 (+)EnsemblGRCm38mm10GRCm38
MGSCv371946,077,968 - 46,080,663 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361946,056,819 - 46,059,464 (+)NCBIMGSCv36mm8
Celera1946,765,544 - 46,768,239 (+)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1938.75NCBI
HPS6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810102,065,349 - 102,068,036 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl10102,065,349 - 102,068,036 (+)EnsemblGRCh38hg38GRCh38
GRCh3710103,825,106 - 103,827,793 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610103,815,137 - 103,817,783 (+)NCBINCBI36Build 36hg18NCBI36
Build 3410103,815,136 - 103,817,782NCBI
Celera1097,566,095 - 97,568,741 (+)NCBICelera
Cytogenetic Map10q24.32NCBI
HuRef1097,457,379 - 97,460,050 (+)NCBIHuRef
CHM1_110104,108,713 - 104,111,384 (+)NCBICHM1_1
T2T-CHM13v2.010102,950,361 - 102,953,048 (+)NCBIT2T-CHM13v2.0
Hps6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21244,853,256 - 244,855,865 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,853,194 - 244,855,883 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1252,997,503 - 253,000,100 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01259,692,504 - 259,695,101 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01252,344,660 - 252,347,269 (+)NCBIRnor_WKY
Rnor_6.01265,761,818 - 265,764,427 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1265,761,738 - 265,764,437 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01273,191,755 - 273,194,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,226,344 - 251,228,953 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11251,486,912 - 251,489,521 (+)NCBI
Celera1240,659,828 - 240,662,437 (+)NCBICelera
Cytogenetic Map1q54NCBI
Hps6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554858,271,134 - 8,273,056 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554858,270,997 - 8,273,060 (-)NCBIChiLan1.0ChiLan1.0
HPS6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan110113,959,666 - 113,962,681 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01098,670,168 - 98,672,896 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110102,139,235 - 102,142,002 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10102,139,439 - 102,141,766 (+)Ensemblpanpan1.1panPan2
HPS6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12814,614,434 - 14,617,138 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2814,614,584 - 14,653,629 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2814,784,970 - 14,787,714 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02815,085,684 - 15,088,428 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2815,085,678 - 15,088,389 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12814,631,368 - 14,634,112 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02814,670,512 - 14,673,256 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02814,802,944 - 14,805,688 (+)NCBIUU_Cfam_GSD_1.0
Hps6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721332,151,099 - 32,153,873 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366003,754,460 - 3,756,880 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366003,754,324 - 3,757,048 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HPS6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14113,081,981 - 113,084,534 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114113,081,981 - 113,084,534 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214122,933,891 - 122,936,445 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HPS6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1995,098,879 - 95,101,643 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl995,099,095 - 95,101,422 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604856,190,439 - 56,193,197 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hps6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248311,524,330 - 1,526,711 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248311,524,329 - 1,526,826 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hps6
141 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:71
Interacting mature miRNAs:73
Transcripts:ENSMUST00000099393
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10413881Moe2_mmodifier of epilepsy 2 (mouse)191492301648923138Mouse
1301336Alcp23_malcohol preference locus 23 (mouse)Not determined191591260749912719Mouse
1301633Alcp24_malcohol preference locus 24 (mouse)Not determined191591260749912719Mouse
1302063Eae19_mexperimental allergic encephalomyelitis 19 (mouse)Not determined191829516252295381Mouse
1302004Lfp2_mlong free running period 2 (mouse)Not determined191829516252295381Mouse
4142343Moen2_mmodifier of engrailed QTL 2 (mouse)Not determined192023431454234461Mouse
10412251Mnp_mmodifier of Niemann Pick type C1 (mouse)Not determined192023431454234461Mouse
4141659Pbwg20_mpostnatal body weight growth 20 (mouse)Not determined192137870555378928Mouse
1558876W3q14_mweight 3 weeks QTL 14 (mouse)Not determined192231332653911504Mouse
12790634Ebm1_mEpidermolysis Bullosa modifier 1 (mouse)192498843958988439Mouse
1301451Ath16_matherosclerosis 16 (mouse)Not determined192542691759427005Mouse
13506250Renmq1_mrenal mercury accumulation QTL 1 (mouse)192738559461385705Mouse
4141138Femwf11_mfemur work to failure 11 (mouse)Not determined2814034861420004Mouse
1300683Fembm7_mfemoral bone morphometry 7 (mouse)Not determined193014122461420004Mouse
1301942Pas13_mpulmonary adenoma susceptibility 13 (mouse)Not determined193014123161420004Mouse
1301410Cd8mts6_mCD8 memory T cell subset 6 (mouse)Not determined193014123161420004Mouse
1300856Nobq2_mNew Zealand obese QTL 2 (mouse)Not determined193089788061420004Mouse
1301741Lith2_mlithogenic gene 2 (mouse)Not determined193299215861420004Mouse
1301639Stnn_mstriatal neuron number (mouse)Not determined193395195261420004Mouse
4141019Tgq29_mtriglyceride QTL 29 (mouse)Not determined3459678661420004Mouse
1301479Sluc1_msusceptibility to lung cancer 1 (mouse)Not determined193601694446761521Mouse
1302170Tanidd1_mtally ho associated non-insulin dependednt diabetes mellitus 1 (mouse)Not determined193675259761420004Mouse
4141650Chldq9_mcholesterol and HDL QTL 9 (mouse)Not determined193788298261420004Mouse
1301466T2dm2_mtype 2 diabetes mellitus 2 (mouse)Not determined193837605061420004Mouse
1302104Lfp1_mlong free running period 1 (mouse)Not determined193918406461420004Mouse
10043896Bw21_mbody weight QTL 21 (mouse)Not determined193959606661420004Mouse
1300585Pgia12_mproteoglycan induced arthritis 12 (mouse)Not determined194258685961420004Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000099393   ⟹   ENSMUSP00000096991
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1945,991,947 - 45,994,612 (+)Ensembl
GRCm38.p6 Ensembl1946,003,508 - 46,006,173 (+)Ensembl
RefSeq Acc Id: NM_176785   ⟹   NP_789742
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391945,991,917 - 45,994,612 (+)NCBI
GRCm381946,003,478 - 46,006,173 (+)ENTREZGENE
MGSCv371946,077,968 - 46,080,663 (+)RGD
Celera1946,765,544 - 46,768,239 (+)RGD
cM Map19 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_789742   ⟸   NM_176785
- UniProtKB: Q8CIA3 (UniProtKB/Swiss-Prot),   Q8BLY7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000096991   ⟸   ENSMUST00000099393

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BLY7-F1-model_v2 AlphaFold Q8BLY7 1-805 view protein structure

Promoters
RGD ID:13679652
Promoter ID:EPDNEW_M23975
Type:initiation region
Name:Hps6_1
Description:Mus musculus HPS6, biogenesis of lysosomal organelles complex2 subunit 3 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381946,003,513 - 46,003,573EPDNEW
RGD ID:6830122
Promoter ID:MM_KWN:27208
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_176785
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361946,077,824 - 46,078,324 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2181763 AgrOrtholog
Ensembl Genes ENSMUSG00000074811 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000096991 ENTREZGENE
  ENSMUSP00000096991.3 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000099393 ENTREZGENE
  ENSMUST00000099393.4 UniProtKB/Swiss-Prot
InterPro BLOC-2_complex_Hps6_subunit UniProtKB/Swiss-Prot
  HPS6_C UniProtKB/Swiss-Prot
  HPS6_N UniProtKB/Swiss-Prot
KEGG Report mmu:20170 UniProtKB/Swiss-Prot
MGD MGI:2181763 ENTREZGENE
NCBI Gene 20170 ENTREZGENE
PANTHER HERMANSKY-PUDLAK SYNDROME 6 PROTEIN UniProtKB/Swiss-Prot
  PTHR14696 UniProtKB/Swiss-Prot
Pfam HPS6 UniProtKB/Swiss-Prot
  HPS6_C UniProtKB/Swiss-Prot
PhenoGen Hps6 PhenoGen
PIRSF BLOC-2_complex_Hps6 UniProtKB/Swiss-Prot
UniProt HPS6_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8CIA3 ENTREZGENE
UniProt Secondary Q3TWQ8 UniProtKB/Swiss-Prot
  Q8BML5 UniProtKB/Swiss-Prot
  Q8CIA3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Hps6  HPS6, biogenesis of lysosomal organelles complex 2 subunit 3    Hermansky-Pudlak syndrome 6  Symbol and/or name change 5135510 APPROVED