Hps3 (HPS3, biogenesis of lysosomal organelles complex 2 subunit 1) - Rat Genome Database

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Gene: Hps3 (HPS3, biogenesis of lysosomal organelles complex 2 subunit 1) Rattus norvegicus
Analyze
Symbol: Hps3
Name: HPS3, biogenesis of lysosomal organelles complex 2 subunit 1
RGD ID: 1310548
Description: Predicted to be involved in organelle organization. Predicted to act upstream of or within pigmentation. Predicted to be part of BLOC-2 complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome and Hermansky-Pudlak syndrome 3. Orthologous to human HPS3 (HPS3 biogenesis of lysosomal organelles complex 2 subunit 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BLOC-2 complex member HPS3; Hermansky-Pudlak syndrome 3; Hermansky-Pudlak syndrome 3 homolog; Hermansky-Pudlak syndrome 3 homolog (human); LOC310288
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82104,413,618 - 104,455,091 (-)NCBIGRCr8
mRatBN7.22102,484,574 - 102,527,580 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2102,484,574 - 102,526,047 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2108,997,846 - 109,039,436 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02107,118,992 - 107,160,587 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02102,081,972 - 102,123,431 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02104,789,423 - 104,832,964 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2104,789,423 - 104,830,898 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02124,510,727 - 124,551,506 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42105,135,644 - 105,177,925 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12105,081,437 - 105,122,835 (-)NCBI
Celera297,855,105 - 97,896,551 (-)NCBICelera
Cytogenetic Map2q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
BLOC-2 complex  (IBA,ISO)
cytoplasm  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mutation of a new gene causes a unique form of Hermansky-Pudlak syndrome in a genetic isolate of central Puerto Rico. Anikster Y, etal., Nat Genet. 2001 Aug;28(4):376-80.
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. Hermansky-Pudlak syndrome type 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency. Huizing M, etal., Am J Hum Genet. 2001 Nov;69(5):1022-32. Epub 2001 Oct 3.
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
Additional References at PubMed
PMID:2379821   PMID:11707070   PMID:15030569  


Genomics

Comparative Map Data
Hps3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82104,413,618 - 104,455,091 (-)NCBIGRCr8
mRatBN7.22102,484,574 - 102,527,580 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2102,484,574 - 102,526,047 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2108,997,846 - 109,039,436 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02107,118,992 - 107,160,587 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02102,081,972 - 102,123,431 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02104,789,423 - 104,832,964 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2104,789,423 - 104,830,898 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02124,510,727 - 124,551,506 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42105,135,644 - 105,177,925 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12105,081,437 - 105,122,835 (-)NCBI
Celera297,855,105 - 97,896,551 (-)NCBICelera
Cytogenetic Map2q24NCBI
HPS3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383149,129,638 - 149,173,732 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3149,129,638 - 149,173,732 (+)EnsemblGRCh38hg38GRCh38
GRCh373148,847,425 - 148,891,519 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363150,330,061 - 150,373,995 (+)NCBINCBI36Build 36hg18NCBI36
Build 343150,330,068 - 150,374,003NCBI
Celera3147,257,896 - 147,301,827 (+)NCBICelera
Cytogenetic Map3q24NCBI
HuRef3146,218,659 - 146,262,596 (+)NCBIHuRef
CHM1_13148,810,445 - 148,854,378 (+)NCBICHM1_1
T2T-CHM13v2.03151,880,375 - 151,924,479 (+)NCBIT2T-CHM13v2.0
Hps3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39320,050,109 - 20,089,478 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl320,050,109 - 20,089,479 (-)EnsemblGRCm39 Ensembl
GRCm38319,995,945 - 20,035,334 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl319,995,945 - 20,035,315 (-)EnsemblGRCm38mm10GRCm38
MGSCv37319,895,945 - 19,935,310 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36320,188,102 - 20,227,431 (-)NCBIMGSCv36mm8
Celera319,985,203 - 20,024,665 (-)NCBICelera
Cytogenetic Map3A2NCBI
cM Map36.12NCBI
Hps3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955448438,152 - 465,955 (+)NCBIChiLan1.0ChiLan1.0
HPS3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22147,018,683 - 147,062,333 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13147,023,393 - 147,067,063 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03146,147,140 - 146,190,793 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13153,725,008 - 153,769,060 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3153,725,008 - 153,769,060 (+)Ensemblpanpan1.1panPan2
HPS3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12343,939,829 - 43,979,446 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2343,939,824 - 43,988,555 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2343,804,492 - 43,843,689 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02344,566,353 - 44,606,057 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2344,566,394 - 44,607,003 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12344,155,109 - 44,194,768 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02344,203,599 - 44,242,773 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02344,457,634 - 44,496,845 (+)NCBIUU_Cfam_GSD_1.0
Hps3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560283,229,063 - 83,263,915 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365196,466,212 - 6,499,101 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365196,470,077 - 6,530,897 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HPS3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1389,360,874 - 89,410,525 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11389,360,829 - 89,409,502 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21397,352,753 - 97,401,807 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HPS3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11541,537,122 - 41,581,994 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1541,537,837 - 41,581,929 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604114,379,184 - 14,424,269 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hps3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473026,426,578 - 26,469,777 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473026,426,495 - 26,469,744 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hps3
203 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:63
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000050440
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
5684990Bmd82Bone mineral density QTL 822.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)259324377103795077Rat
5684996Bmd85Bone mineral density QTL 854.70.024tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)259324377103795077Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
631500Bp99Blood pressure QTL 992.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)259324719102755241Rat
1578777Stresp15Stress response QTL 1520.05blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)259846005104846005Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)264366971109366971Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)267942638112942638Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)276539322102785628Rat
61465Bp13Blood pressure QTL 133.3blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)276539322102785628Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)288862519133862519Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)292337601137337601Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)292337601137337601Rat

Markers in Region
RH137941  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22102,486,358 - 102,486,494 (+)MAPPERmRatBN7.2
Rnor_6.02104,791,208 - 104,791,343NCBIRnor6.0
Rnor_5.02124,512,512 - 124,512,647UniSTSRnor5.0
RGSC_v3.42105,137,429 - 105,137,564UniSTSRGSC3.4
Celera297,856,890 - 97,857,025UniSTS
RH 3.4 Map21126.5UniSTS
Cytogenetic Map2q24UniSTS
BE101680  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22102,519,250 - 102,519,434 (+)MAPPERmRatBN7.2
Rnor_6.02104,824,100 - 104,824,283NCBIRnor6.0
Rnor_5.02124,544,708 - 124,544,891UniSTSRnor5.0
RGSC_v3.42105,171,133 - 105,171,316UniSTSRGSC3.4
Celera297,889,758 - 97,889,941UniSTS
RH 3.4 Map2730.1UniSTS
Cytogenetic Map2q24UniSTS
RH141500  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22102,497,797 - 102,497,979 (+)MAPPERmRatBN7.2
Rnor_6.02104,802,647 - 104,802,828NCBIRnor6.0
Rnor_5.02124,523,753 - 124,523,934UniSTSRnor5.0
RGSC_v3.42105,148,654 - 105,148,835UniSTSRGSC3.4
Celera297,868,327 - 97,868,508UniSTS
RH 3.4 Map2620.9UniSTS
Cytogenetic Map2q24UniSTS


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 2 22 7 19 7 43 23 14 11
Low 1 43 35 34 34 8 11 31 12 27 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050440   ⟹   ENSRNOP00000050238
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2102,484,574 - 102,526,047 (-)Ensembl
Rnor_6.0 Ensembl2104,789,423 - 104,830,898 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102644   ⟹   ENSRNOP00000081948
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2102,484,639 - 102,526,047 (-)Ensembl
RefSeq Acc Id: NM_001107664   ⟹   NP_001101134
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,413,618 - 104,455,091 (-)NCBI
mRatBN7.22102,484,574 - 102,526,047 (-)NCBI
Rnor_6.02104,789,423 - 104,830,898 (-)NCBI
Rnor_5.02124,510,727 - 124,551,506 (-)NCBI
RGSC_v3.42105,135,644 - 105,177,925 (-)RGD
Celera297,855,105 - 97,896,551 (-)RGD
Sequence:
RefSeq Acc Id: XM_008760868   ⟹   XP_008759090
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,413,683 - 104,455,039 (-)NCBI
mRatBN7.22102,484,639 - 102,527,580 (-)NCBI
Rnor_6.02104,789,488 - 104,832,964 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102237   ⟹   XP_038958165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,413,683 - 104,443,633 (-)NCBI
mRatBN7.22102,484,639 - 102,514,589 (-)NCBI
RefSeq Acc Id: XM_063281769   ⟹   XP_063137839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,413,683 - 104,450,427 (-)NCBI
RefSeq Acc Id: XR_005500284
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,414,504 - 104,455,039 (-)NCBI
mRatBN7.22102,485,458 - 102,527,580 (-)NCBI
RefSeq Acc Id: XR_590973
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82104,414,440 - 104,455,039 (-)NCBI
mRatBN7.22102,485,398 - 102,527,580 (-)NCBI
Rnor_6.02104,790,298 - 104,832,964 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001101134   ⟸   NM_001107664
- UniProtKB: D3ZGG8 (UniProtKB/TrEMBL),   A6IHC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759090   ⟸   XM_008760868
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZU61 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050238   ⟸   ENSRNOT00000050440
RefSeq Acc Id: XP_038958165   ⟸   XM_039102237
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000081948   ⟸   ENSRNOT00000102644
RefSeq Acc Id: XP_063137839   ⟸   XM_063281769
- Peptide Label: isoform X2
Protein Domains
BLOC-2 complex member HPS3 C-terminal   BLOC-2 complex member HPS3 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGG8-F1-model_v2 AlphaFold D3ZGG8 1-1002 view protein structure

Transcriptome

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

Promoters
RGD ID:13691258
Promoter ID:EPDNEW_R1781
Type:multiple initiation site
Name:Hps3_1
Description:HPS3, biogenesis of lysosomal organelles complex 2 subunit 1
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_6.02104,830,874 - 104,830,934EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310548 AgrOrtholog
BioCyc Gene G2FUF-53607 BioCyc
Ensembl Genes ENSRNOG00000031406 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050440 ENTREZGENE
  ENSRNOT00000050440.6 UniProtKB/TrEMBL
  ENSRNOT00000102644.1 UniProtKB/TrEMBL
InterPro HPS3 UniProtKB/TrEMBL
  HPS3_C UniProtKB/TrEMBL
  HPS3_N UniProtKB/TrEMBL
KEGG Report rno:310288 UniProtKB/TrEMBL
NCBI Gene 310288 ENTREZGENE
PANTHER HERMANSKY-PUDLAK SYNDROME 3 PROTEIN UniProtKB/TrEMBL
  PTHR28633 UniProtKB/TrEMBL
Pfam HPS3_C UniProtKB/TrEMBL
  HPS3_N UniProtKB/TrEMBL
PhenoGen Hps3 PhenoGen
PIRSF BLOC-2_complex_Hps3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031406 RatGTEx
UniProt A0A8I5ZU61 ENTREZGENE, UniProtKB/TrEMBL
  A6IHC6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZGG8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-07 Hps3  HPS3, biogenesis of lysosomal organelles complex 2 subunit 1  Hps3  Hermansky-Pudlak syndrome 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-02 Hps3  Hermansky-Pudlak syndrome 3  Hps3  Hermansky-Pudlak syndrome 3 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Hps3  Hermansky-Pudlak syndrome 3 homolog (human)   Hps3_predicted  Hermansky-Pudlak syndrome 3 homolog (human) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Hps3_predicted  Hermansky-Pudlak syndrome 3 homolog (human) (predicted)    Hermansky-Pudlak syndrome 3 (predicted)  Name updated 1299863 APPROVED
2005-01-12 Hps3_predicted  Hermansky-Pudlak syndrome 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED