Hps4 (HPS4, biogenesis of lysosomal organelles complex 3 subunit 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Hps4 (HPS4, biogenesis of lysosomal organelles complex 3 subunit 2) Rattus norvegicus
Analyze
Symbol: Hps4
Name: HPS4, biogenesis of lysosomal organelles complex 3 subunit 2
RGD ID: 1308070
Description: Predicted to enable protein homodimerization activity and small GTPase binding activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including lysosome organization; melanosome assembly; and protein stabilization. Predicted to act upstream of or within blood coagulation and melanocyte differentiation. Predicted to be located in cytoplasmic vesicle; lysosome; and membrane. Predicted to be part of BLOC-3 complex. Predicted to be active in cytoplasmic vesicle and lysosomal membrane. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome; Hermansky-Pudlak syndrome 4; and schizophrenia. Orthologous to human HPS4 (HPS4 biogenesis of lysosomal organelles complex 3 subunit 2); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BLOC-3 complex member HPS4; Hermansky-Pudlak syndrome 4; Hermansky-Pudlak syndrome 4 homolog; Hermansky-Pudlak syndrome 4 homolog (human); LOC304555
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81249,924,444 - 49,955,201 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1249,924,444 - 49,953,613 (-)EnsemblGRCr8
mRatBN7.21244,264,037 - 44,294,791 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,264,037 - 44,294,632 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1245,433,082 - 45,462,177 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,043,292 - 46,072,462 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,103,830 - 45,133,000 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,285,239 - 50,315,893 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)Ensemblrn6Rnor6.0
Rnor_5.01252,043,358 - 52,072,939 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41914,326,654 - 14,355,770 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1245,847,642 - 45,876,371 (-)NCBICelera
RGSC_v3.11914,345,603 - 14,357,741 (+)NCBI
Cytogenetic Map12q16NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
BLOC-3 complex  (IBA,IEA,ISO)
cytoplasm  (IEA,ISO)
cytoplasmic vesicle  (IBA,ISO)
lysosomal membrane  (IBA)
lysosome  (IEA,ISO)
melanosome  (IEA,ISO)
membrane  (IEA,ISO)
platelet dense granule  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Hermansky-Pudlak syndrome type 4 (HPS-4): clinical and molecular characteristics. Anderson PD, etal., Hum Genet. 2003 Jul;113(1):10-7. Epub 2003 Mar 27.
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 GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. An association study of the Hermansky-Pudlak syndrome type 4 gene in schizophrenic patients. Saito A, etal., Psychiatr Genet. 2013 Aug;23(4):163-73. doi: 10.1097/YPG.0b013e32836130a9.
10. Hermansky-Pudlak syndrome is caused by mutations in HPS4, the human homolog of the mouse light-ear gene. Suzuki T, etal., Nat Genet. 2002 Mar;30(3):321-4. Epub 2002 Feb 11.
Additional References at PubMed
PMID:6696991   PMID:12477932   PMID:12663659   PMID:12756248   PMID:20048159   PMID:23084991   PMID:24270810   PMID:26620560  


Genomics

Comparative Map Data
Hps4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81249,924,444 - 49,955,201 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1249,924,444 - 49,953,613 (-)EnsemblGRCr8
mRatBN7.21244,264,037 - 44,294,791 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,264,037 - 44,294,632 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1245,433,082 - 45,462,177 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,043,292 - 46,072,462 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,103,830 - 45,133,000 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,285,239 - 50,315,893 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)Ensemblrn6Rnor6.0
Rnor_5.01252,043,358 - 52,072,939 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41914,326,654 - 14,355,770 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1245,847,642 - 45,876,371 (-)NCBICelera
RGSC_v3.11914,345,603 - 14,357,741 (+)NCBI
Cytogenetic Map12q16NCBI
HPS4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382226,443,109 - 26,483,863 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2226,443,107 - 26,483,931 (-)Ensemblhg38GRCh38
GRCh372226,839,075 - 26,879,829 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362225,177,446 - 25,209,820 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342225,171,999 - 25,204,374NCBI
Celera2210,651,342 - 10,683,694 (-)NCBICelera
Cytogenetic Map22q12.1NCBI
HuRef229,794,422 - 9,827,382 (-)NCBIHuRef
CHM1_12226,806,304 - 26,839,247 (-)NCBICHM1_1
T2T-CHM13v2.02226,905,547 - 26,946,273 (-)NCBIT2T-CHM13v2.0
Hps4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395112,490,849 - 112,526,290 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5112,490,949 - 112,526,280 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm385112,342,983 - 112,378,424 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5112,343,083 - 112,378,414 (+)Ensemblmm10GRCm38
MGSCv375112,772,115 - 112,807,444 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv365112,585,083 - 112,618,716 (+)NCBIMGSCv36mm8
Celera5109,463,044 - 109,498,400 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map554.69NCBI
Hps4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554551,049,992 - 1,073,950 (-)Ensembl
ChiLan1.0NW_0049554551,048,946 - 1,076,097 (-)NCBIChiLan1.0ChiLan1.0
HPS4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22336,457,072 - 36,489,470 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12239,156,253 - 39,188,641 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0227,513,397 - 7,545,782 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12225,235,761 - 25,268,699 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2225,236,360 - 25,268,699 (-)EnsemblpanPan2panpan1.1
HPS4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12620,131,658 - 20,157,532 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2619,933,281 - 20,157,058 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2619,995,923 - 20,023,346 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02620,495,535 - 20,522,930 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2620,486,803 - 20,522,957 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12620,212,135 - 20,239,523 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02620,468,000 - 20,495,466 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02620,537,450 - 20,564,852 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hps4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118114,766,390 - 114,795,406 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366571,075,261 - 1,103,055 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366571,075,300 - 1,104,328 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HPS4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1444,049,707 - 44,073,621 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11444,041,684 - 44,073,661 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21446,929,530 - 46,953,466 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HPS4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1199,356,868 - 9,387,847 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl199,356,145 - 9,386,254 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666045116,717,018 - 116,748,362 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hps4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247473,005,509 - 3,032,037 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247473,004,370 - 3,033,692 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Hps4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11641,601,675 - 41,631,955 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:281
Count of miRNA genes:154
Interacting mature miRNAs:173
Transcripts:ENSRNOT00000000824
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122480502252308831Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121613502952308831Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743851213550Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122871771850386405Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122598935552308831Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123776414551558799Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121847304152308831Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121847304152308831Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121526424852308831Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049752308831Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121613502952308831Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123370043251558799Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121618743852308831Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)124413955852308831Rat

Markers in Region
BI274486  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21244,264,116 - 44,264,273 (+)MAPPERmRatBN7.2
Rnor_6.01250,285,319 - 50,285,475NCBIRnor6.0
Rnor_5.01252,043,384 - 52,043,540UniSTSRnor5.0
RGSC_v3.41914,355,588 - 14,355,744UniSTSRGSC3.4
Celera1245,847,722 - 45,847,878UniSTS
RH 3.4 Map19158.0UniSTS
Cytogenetic Map19p11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089506 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063271362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063271363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063271364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_358770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC123358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000000824   ⟹   ENSRNOP00000000824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1249,924,444 - 49,951,654 (-)Ensembl
mRatBN7.2 Ensembl1244,264,037 - 44,291,248 (-)Ensembl
Rnor_6.0 Ensembl1250,285,294 - 50,313,976 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000079256   ⟹   ENSRNOP00000071892
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1249,924,444 - 49,953,613 (-)Ensembl
mRatBN7.2 Ensembl1244,264,081 - 44,294,632 (-)Ensembl
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000135478   ⟹   ENSRNOP00000107830
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1249,926,386 - 49,953,613 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000156275   ⟹   ENSRNOP00000111201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1249,924,444 - 49,952,126 (-)Ensembl
RefSeq Acc Id: NM_001107148   ⟹   NP_001100618
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,444 - 49,953,613 (-)NCBI
mRatBN7.21244,264,037 - 44,293,207 (-)NCBI
Rnor_6.01250,285,239 - 50,314,408 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
RGSC_v3.41914,326,654 - 14,355,770 (+)RGD
Celera1245,847,642 - 45,876,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249542   ⟹   XP_006249604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,161 (-)NCBI
mRatBN7.21244,264,091 - 44,294,698 (-)NCBI
Rnor_6.01250,285,293 - 50,315,874 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249543   ⟹   XP_006249605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,027 (-)NCBI
mRatBN7.21244,264,091 - 44,294,578 (-)NCBI
Rnor_6.01250,285,293 - 50,315,781 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249544   ⟹   XP_006249606
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,168 (-)NCBI
mRatBN7.21244,264,091 - 44,294,749 (-)NCBI
Rnor_6.01250,285,293 - 50,315,893 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249546   ⟹   XP_006249608
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,113 (-)NCBI
mRatBN7.21244,266,306 - 44,294,699 (-)NCBI
Rnor_6.01250,288,201 - 50,315,874 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089506   ⟹   XP_038945434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,201 (-)NCBI
mRatBN7.21244,264,091 - 44,294,791 (-)NCBI
RefSeq Acc Id: XM_039089507   ⟹   XP_038945435
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,113 (-)NCBI
mRatBN7.21244,267,166 - 44,294,699 (-)NCBI
RefSeq Acc Id: XM_063271362   ⟹   XP_063127432
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,954,975 (-)NCBI
RefSeq Acc Id: XM_063271363   ⟹   XP_063127433
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,954,689 (-)NCBI
RefSeq Acc Id: XM_063271364   ⟹   XP_063127434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,505 - 49,955,113 (-)NCBI
RefSeq Acc Id: XR_358770
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81249,924,896 - 49,955,113 (-)NCBI
mRatBN7.21244,264,489 - 44,294,699 (-)NCBI
Rnor_6.01250,285,740 - 50,315,874 (-)NCBI
Rnor_5.01252,043,358 - 52,072,939 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001100618   ⟸   NM_001107148
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249604   ⟸   XM_006249542
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249606   ⟸   XM_006249544
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249605   ⟸   XM_006249543
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249608   ⟸   XM_006249546
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K1L6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071892   ⟸   ENSRNOT00000079256
Ensembl Acc Id: ENSRNOP00000000824   ⟸   ENSRNOT00000000824
RefSeq Acc Id: XP_038945434   ⟸   XM_039089506
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038945435   ⟸   XM_039089507
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K1L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063127434   ⟸   XM_063271364
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K1L6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063127432   ⟸   XM_063271362
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063127433   ⟸   XM_063271363
- Peptide Label: isoform X1
- UniProtKB: A0A8J8YPH6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107830   ⟸   ENSRNOT00000135478
Ensembl Acc Id: ENSRNOP00000111201   ⟸   ENSRNOT00000156275
Protein Domains
CCZ1/INTU/HPS4 third Longin   CCZ1/INTU/HSP4 first Longin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K1L6-F1-model_v2 AlphaFold A0A0G2K1L6 1-700 view protein structure

Transcriptome

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

Promoters
RGD ID:13698731
Promoter ID:EPDNEW_R9251
Type:single initiation site
Name:Hps4_1
Description:HPS4, biogenesis of lysosomal organelles complex 3 subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01250,314,353 - 50,314,413EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308070 AgrOrtholog
BioCyc Gene G2FUF-18869 BioCyc
Ensembl Genes ENSRNOG00000000661 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000824.6 UniProtKB/TrEMBL
  ENSRNOT00000079256 ENTREZGENE
  ENSRNOT00000079256.3 UniProtKB/TrEMBL
  ENSRNOT00000135478.1 UniProtKB/TrEMBL
  ENSRNOT00000156275.1 UniProtKB/TrEMBL
InterPro CCZ1/INTU/HSP4_longin_1 UniProtKB/TrEMBL
  CCZ1/INTU/HSP4_longin_3 UniProtKB/TrEMBL
  HPS4 UniProtKB/TrEMBL
KEGG Report rno:304555 UniProtKB/TrEMBL
NCBI Gene 304555 ENTREZGENE
PANTHER HERMANSKY-PUDLAK SYNDROME 4 PROTEIN UniProtKB/TrEMBL
  PTHR14407 UniProtKB/TrEMBL
Pfam Intu_longin_1 UniProtKB/TrEMBL
  Intu_longin_3 UniProtKB/TrEMBL
PhenoGen Hps4 PhenoGen
RatGTEx ENSRNOG00000000661 RatGTEx
UniProt A0A0G2K1L6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8YPH6 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LZ62_RAT UniProtKB/TrEMBL
  A0ABK0M6A8_RAT UniProtKB/TrEMBL
  B5DF28_RAT UniProtKB/TrEMBL
UniProt Secondary F1LMB3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-07 Hps4  HPS4, biogenesis of lysosomal organelles complex 3 subunit 2  Hps4  Hermansky-Pudlak syndrome 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-15 Hps4  Hermansky-Pudlak syndrome 4  Hps4  Hermansky-Pudlak syndrome 4 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Hps4  Hermansky-Pudlak syndrome 4 homolog (human)   Hps4_predicted  Hermansky-Pudlak syndrome 4 homolog (human) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Hps4_predicted  Hermansky-Pudlak syndrome 4 homolog (human) (predicted)    Hermansky-Pudlak syndrome 4 (predicted)  Name updated 1299863 APPROVED
2005-01-12 Hps4_predicted  Hermansky-Pudlak syndrome 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED