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

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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 melanosome assembly; positive regulation of protein targeting to mitochondrion; 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81249,924,444 - 49,955,201 (-)NCBIGRCr8
mRatBN7.21244,264,037 - 44,294,791 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,264,037 - 44,294,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1245,433,082 - 45,462,177 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,043,292 - 46,072,462 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,103,830 - 45,133,000 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,285,239 - 50,315,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01252,043,358 - 52,072,939 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41914,326,654 - 14,355,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11914,345,603 - 14,357,741 (+)NCBI
Celera1245,847,642 - 45,876,371 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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 (-)NCBIGRCr8
mRatBN7.21244,264,037 - 44,294,791 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,264,037 - 44,294,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1245,433,082 - 45,462,177 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,043,292 - 46,072,462 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,103,830 - 45,133,000 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,285,239 - 50,315,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01252,043,358 - 52,072,939 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41914,326,654 - 14,355,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11914,345,603 - 14,357,741 (+)NCBI
Celera1245,847,642 - 45,876,371 (-)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
GRCh372226,839,075 - 26,879,829 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362225,177,446 - 25,209,820 (-)NCBINCBI36Build 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 Ensembl
GRCm385112,342,983 - 112,378,424 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5112,343,083 - 112,378,414 (+)EnsemblGRCm38mm10GRCm38
MGSCv375112,772,115 - 112,807,444 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2619,995,923 - 20,023,346 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02620,495,535 - 20,522,930 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247473,004,370 - 3,033,692 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hps4
142 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat

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
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 10 8 7 4 7 66 27 38 3
Low 1 33 49 34 15 34 8 11 8 8 3 8 8
Below cutoff

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

RefSeq Acc Id: ENSRNOT00000000824   ⟹   ENSRNOP00000000824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1244,264,037 - 44,291,248 (-)Ensembl
Rnor_6.0 Ensembl1250,285,294 - 50,313,976 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079256   ⟹   ENSRNOP00000071892
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1244,264,081 - 44,294,632 (-)Ensembl
Rnor_6.0 Ensembl1250,285,278 - 50,314,406 (-)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:
RefSeq Acc Id: ENSRNOP00000071892   ⟸   ENSRNOT00000079256
RefSeq 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)
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 ENTREZGENE
  ENSRNOT00000000824.5 UniProtKB/TrEMBL
  ENSRNOT00000079256.2 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
  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