Vps28 (VPS28 subunit of ESCRT-I) - Rat Genome Database

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Gene: Vps28 (VPS28 subunit of ESCRT-I) Rattus norvegicus
Analyze
Symbol: Vps28
Name: VPS28 subunit of ESCRT-I
RGD ID: 1306537
Description: Predicted to enable ubiquitin binding activity. Predicted to be involved in positive regulation of ubiquitin-dependent endocytosis; protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; and regulation of protein metabolic process. Located in cytosol. Orthologous to human VPS28 (VPS28 subunit of ESCRT-I); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC300052; MGC188842; vacuolar protein sorting 28 (yeast); vacuolar protein sorting 28 homolog; vacuolar protein sorting 28 homolog (S. cerevisiae); vacuolar protein sorting-associated protein 28 homolog; VPS28, ESCRT-I subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87110,222,638 - 110,226,486 (-)NCBIGRCr8
mRatBN7.27108,341,989 - 108,345,837 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7108,341,989 - 108,345,837 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7110,083,851 - 110,087,699 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07112,307,425 - 112,311,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07112,268,254 - 112,272,102 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07117,684,339 - 117,688,187 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,684,339 - 117,688,187 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,672,422 - 117,676,270 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,670,491 - 114,674,339 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17114,704,722 - 114,708,565 (-)NCBI
Celera7104,692,151 - 104,695,999 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Vps28RatBrown-Vialetto-Van Laere syndrome 2  ISOVPS28 (Homo sapiens)8554872ClinVar Annotator: match by term: Brown-Vialetto-van Laere syndrome 2ClinVarPMID:20301336 more ...
Vps28Ratepidermolysis bullosa simplex with muscular dystrophy  ISOVPS28 (Homo sapiens)8554872ClinVar Annotator: match by term: Epidermolysis bullosa simplex 5B and with muscular dystrophyClinVarPMID:20301336 more ...
Vps28Ratholoprosencephaly  ISOVPS28 (Homo sapiens)8554872ClinVar Annotator: match by term: Holoprosencephaly sequenceClinVarPMID:28492532
Vps28RatRecombinant Chromosome 8 Syndrome  ISOVPS28 (Homo sapiens)8554872ClinVar Annotator: match by term: Recombinant 8 syndromeClinVarPMID:31690835

1 to 20 of 46 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Vps28Rat(S)-nicotine multiple interactionsISOVps28 (Mus musculus)6480464[Nicotine co-treated with 1-Methyl-4-phenyl-1 more ...CTDPMID:20230807
Vps28Rat1,2-dimethylhydrazine decreases expressionISOVps28 (Mus musculus)64804641 and 2-Dimethylhydrazine results in decreased expression of VPS28 mRNACTDPMID:22206623
Vps28Rat1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine decreases expressionISOVps28 (Mus musculus)64804641-Methyl-4-phenyl-1 more ...CTDPMID:20230807
Vps28Rat1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine multiple interactionsISOVps28 (Mus musculus)6480464[Nicotine co-treated with 1-Methyl-4-phenyl-1 more ...CTDPMID:20230807
Vps28Rat17alpha-ethynylestradiol multiple interactionsISOVps28 (Mus musculus)6480464[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of VPS28 mRNACTDPMID:17942748
Vps28Rat17alpha-ethynylestradiol decreases expressionISOVps28 (Mus musculus)6480464Ethinyl Estradiol results in decreased expression of VPS28 mRNACTDPMID:17555576
Vps28Rat17beta-estradiol increases expressionISOVps28 (Mus musculus)6480464Estradiol results in increased expression of VPS28 mRNACTDPMID:39298647
Vps28Rat2,2',4,4'-Tetrabromodiphenyl ether affects expressionISOVps28 (Mus musculus)64804642 more ...CTDPMID:30294300
Vps28Rat2,3,7,8-tetrachlorodibenzodioxine multiple interactionsISOVps28 (Mus musculus)6480464[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of VPS28 mRNACTDPMID:17942748
Vps28Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionEXP 6480464Tetrachlorodibenzodioxin results in increased expression of VPS28 mRNACTDPMID:33387578
Vps28Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionISOVps28 (Mus musculus)6480464Tetrachlorodibenzodioxin affects the expression of VPS28 mRNACTDPMID:21570461
Vps28Rat4,4'-diaminodiphenylmethane increases expressionISOVps28 (Mus musculus)64804644 and 4'-diaminodiphenylmethane results in increased expression of VPS28 mRNACTDPMID:18648102
Vps28Rat4,4'-sulfonyldiphenol increases expressionISOVps28 (Mus musculus)6480464bisphenol S results in increased expression of VPS28 mRNACTDPMID:39298647
Vps28Ratacrolein multiple interactionsISOVPS28 (Homo sapiens)6480464[Acrolein co-treated with methacrylaldehyde co-treated with alpha-pinene co-treated with Ozone] results in increased expression of and results in increased oxidation of VPS28 mRNA and [Air Pollutants results in increased abundance of [Acrolein co-treated with methacrylaldehyde co-treated with alpha-pinene co-treated with Ozone]] which results in increased expression of and results in increased oxidation of VPS28 mRNACTDPMID:32699268
Vps28Rataflatoxin B1 increases methylationISOVPS28 (Homo sapiens)6480464Aflatoxin B1 results in increased methylation of VPS28 geneCTDPMID:27153756
Vps28Ratall-trans-retinoic acid increases expressionISOVPS28 (Homo sapiens)6480464Tretinoin results in increased expression of VPS28 mRNACTDPMID:33167477
Vps28Ratalpha-pinene multiple interactionsISOVPS28 (Homo sapiens)6480464[Acrolein co-treated with methacrylaldehyde co-treated with alpha-pinene co-treated with Ozone] results in increased expression of and results in increased oxidation of VPS28 mRNA and [Air Pollutants results in increased abundance of [Acrolein co-treated with methacrylaldehyde co-treated with alpha-pinene co-treated with Ozone]] which results in increased expression of and results in increased oxidation of VPS28 mRNACTDPMID:32699268
Vps28Ratbenzo[a]pyrene increases expressionISOVps28 (Mus musculus)6480464Benzo(a)pyrene results in increased expression of VPS28 mRNACTDPMID:22228805
Vps28Ratbenzo[a]pyrene affects methylationISOVPS28 (Homo sapiens)6480464Benzo(a)pyrene affects the methylation of VPS28 promoterCTDPMID:27901495
Vps28Ratbenzo[a]pyrene decreases methylationISOVPS28 (Homo sapiens)6480464Benzo(a)pyrene results in decreased methylation of VPS28 3' UTRCTDPMID:27901495

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Biological Process
1 to 14 of 14 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Vps28Ratendosome transport via multivesicular body sorting pathway involved_inIEAInterPro:IPR0071431600115GO_REF:0000002InterProGO_REF:0000002
Vps28Ratnegative regulation of protein ubiquitination involved_inISSUniProtKB:Q9UK411600115GO_REF:0000024UniProtGO_REF:0000024
Vps28Ratnegative regulation of protein ubiquitination involved_inISOVPS28 (Homo sapiens)1624291 PMID:18077552RGDPMID:18077552
Vps28Ratnegative regulation of protein ubiquitination involved_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratpositive regulation of protein catabolic process involved_inISOVPS28 (Homo sapiens)1624291 PMID:11916981RGDPMID:11916981
Vps28Ratpositive regulation of protein catabolic process involved_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratpositive regulation of ubiquitin-dependent endocytosis involved_inISOVPS28 (Homo sapiens)1624291 PMID:11916981RGDPMID:11916981
Vps28Ratpositive regulation of ubiquitin-dependent endocytosis involved_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratprotein transport involved_inIEAUniRule:UR0004002801600115GO_REF:0000104UniProtGO_REF:0000104
Vps28Ratprotein transport involved_inIEAUniProtKB-KW:KW-06531600115GO_REF:0000043UniProtGO_REF:0000043
Vps28Ratprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway involved_inIBAPANTHER:PTN000309785 and PomBase:SPAC1B3.07c1600115GO_REF:0000033GO_CentralGO_REF:0000033
Vps28Ratubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway involved_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway involved_inISOVPS28 (Homo sapiens)1624291 PMID:21757351RGDPMID:21757351
Vps28Ratubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway involved_inISSUniProtKB:Q9UK411600115GO_REF:0000024UniProtGO_REF:0000024
1 to 14 of 14 rows

Cellular Component
1 to 20 of 27 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Vps28Ratcytoplasm located_inISOVPS28 (Homo sapiens)1624291 PMID:18077552RGDPMID:18077552
Vps28Ratcytoplasm located_inIEAUniProtKB-SubCell:SL-00861600115GO_REF:0000044UniProtGO_REF:0000044
Vps28Ratcytoplasm located_inIEAUniProtKB-KW:KW-09631600115GO_REF:0000043UniProtGO_REF:0000043
Vps28Ratcytoplasm located_inISSUniProtKB:Q9UK411600115GO_REF:0000024UniProtGO_REF:0000024
Vps28Ratcytoplasm located_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratcytosol located_inISOVPS28 (Homo sapiens)1624291 PMID:11134028RGDPMID:11134028
Vps28Ratcytosol located_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratcytosol located_inIDA 10047383PMID:11134028UniProt 
Vps28Ratearly endosome located_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratearly endosome located_inISOVPS28 (Homo sapiens)1624291 PMID:11916981RGDPMID:11916981
Vps28Ratendosome located_inISOVPS28 (Homo sapiens)1624291 PMID:11134028 and PMID:17940959RGDPMID:11134028 and PMID:17940959
Vps28Ratendosome located_inIEAUniProtKB-SubCell:SL-01011600115GO_REF:0000044UniProtGO_REF:0000044
Vps28Ratendosome located_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28Ratendosome located_inIEAUniProtKB-KW:KW-09671600115GO_REF:0000043UniProtGO_REF:0000043
Vps28Ratendosome membrane located_inISOVPS28 (Homo sapiens)1624291 PMID:11134028RGDPMID:11134028
Vps28Ratendosome membrane located_inIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28RatESCRT I complex part_ofISOVPS28 (Homo sapiens)1624291 PMID:18005716 more ...RGDPMID:18005716 more ...
Vps28RatESCRT I complex part_ofIEAUniProtKB:Q9UK41 and ensembl:ENSP000002925101600115GO_REF:0000107EnsemblGO_REF:0000107
Vps28RatESCRT I complex part_ofIBAFB:FBgn0021814 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Vps28RatESCRT I complex part_ofIEAInterPro:IPR0071431600115GO_REF:0000002InterProGO_REF:0000002
1 to 20 of 27 rows

Molecular Function

  

Imported Annotations - KEGG (archival)

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Vps28Ratendocytosis pathway  IEA 6907045 KEGGrno:04144

#
Reference Title
Reference Citation
1. TSG101/mammalian VPS23 and mammalian VPS28 interact directly and are recruited to VPS4-induced endosomes. Bishop N and Woodman P, J Biol Chem. 2001 Apr 13;276(15):11735-42. Epub 2000 Dec 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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:11916981   PMID:12477932   PMID:17940959   PMID:18005716   PMID:18077552   PMID:19056867   PMID:19199708   PMID:20458337   PMID:20654576   PMID:21757351   PMID:22232651   PMID:23376485  
PMID:23533145  



Vps28
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87110,222,638 - 110,226,486 (-)NCBIGRCr8
mRatBN7.27108,341,989 - 108,345,837 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7108,341,989 - 108,345,837 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7110,083,851 - 110,087,699 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07112,307,425 - 112,311,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07112,268,254 - 112,272,102 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07117,684,339 - 117,688,187 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,684,339 - 117,688,187 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,672,422 - 117,676,270 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,670,491 - 114,674,339 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17114,704,722 - 114,708,565 (-)NCBI
Celera7104,692,151 - 104,695,999 (-)NCBICelera
Cytogenetic Map7q34NCBI
VPS28
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388144,423,617 - 144,428,548 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8144,423,601 - 144,428,563 (-)EnsemblGRCh38hg38GRCh38
GRCh378145,649,000 - 145,653,931 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,619,808 - 145,624,735 (-)NCBINCBI36Build 36hg18NCBI36
Build 348145,619,807 - 145,624,735NCBI
Celera8141,823,433 - 141,828,362 (-)NCBICelera
Cytogenetic Map8q24.3NCBI
HuRef8140,762,216 - 140,767,180 (-)NCBIHuRef
CHM1_18145,687,291 - 145,692,187 (-)NCBICHM1_1
T2T-CHM13v2.08145,593,428 - 145,598,361 (-)NCBIT2T-CHM13v2.0
Vps28
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,506,286 - 76,510,284 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1576,506,287 - 76,510,286 (-)EnsemblGRCm39 Ensembl
GRCm381576,622,086 - 76,626,084 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,622,087 - 76,626,086 (-)EnsemblGRCm38mm10GRCm38
MGSCv371576,452,518 - 76,456,457 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361576,449,343 - 76,453,282 (-)NCBIMGSCv36mm8
Celera1578,115,695 - 78,119,634 (-)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1536.17NCBI
Vps28
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554543,048,042 - 3,054,361 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554543,049,977 - 3,054,078 (-)NCBIChiLan1.0ChiLan1.0
VPS28
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27161,914,393 - 161,919,947 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan18137,443,401 - 137,449,013 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v08141,189,967 - 141,195,482 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.18144,180,081 - 144,185,173 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8144,180,081 - 144,185,175 (-)Ensemblpanpan1.1panPan2
VPS28
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11337,841,524 - 37,845,954 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1337,841,518 - 37,846,339 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1337,802,903 - 37,806,996 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01338,315,868 - 38,319,961 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1338,314,749 - 38,319,956 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11338,007,669 - 38,011,758 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01338,116,303 - 38,120,391 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01338,592,696 - 38,596,782 (-)NCBIUU_Cfam_GSD_1.0
Vps28
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303403,032 - 407,134 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364707,830,114 - 7,833,047 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364707,829,207 - 7,833,213 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS28
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4362,912 - 370,588 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14362,902 - 368,038 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24453,488 - 458,638 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS28
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18138,636,092 - 138,641,011 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660391,215,277 - 1,220,217 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps28
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473512,426,543 - 12,430,698 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473512,426,687 - 12,430,698 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in Vps28
13 total Variants

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:74
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000019707
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.


1 to 10 of 35 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat

1 to 10 of 35 rows
RH131182  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27108,346,114 - 108,346,265 (+)MAPPERmRatBN7.2
Rnor_6.07117,688,465 - 117,688,615NCBIRnor6.0
Rnor_5.07117,676,548 - 117,676,698UniSTSRnor5.0
RGSC_v3.47114,674,617 - 114,674,767UniSTSRGSC3.4
Celera7104,696,277 - 104,696,427UniSTS
RH 3.4 Map7793.2UniSTS
Cytogenetic Map7q34UniSTS




alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31



Ensembl Acc Id: ENSRNOT00000019707   ⟹   ENSRNOP00000019707
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,341,989 - 108,345,837 (-)Ensembl
Rnor_6.0 Ensembl7117,684,339 - 117,688,187 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103642   ⟹   ENSRNOP00000081278
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,341,994 - 108,345,780 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108573   ⟹   ENSRNOP00000088292
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,341,991 - 108,345,790 (-)Ensembl
RefSeq Acc Id: NM_001130492   ⟹   NP_001123964
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87110,222,638 - 110,226,486 (-)NCBI
mRatBN7.27108,341,989 - 108,345,837 (-)NCBI
Rnor_6.07117,684,339 - 117,688,187 (-)NCBI
Rnor_5.07117,672,422 - 117,676,270 (-)NCBI
RGSC_v3.47114,670,491 - 114,674,339 (-)RGD
Celera7104,692,151 - 104,695,999 (-)RGD
Sequence:
Protein RefSeqs NP_001123964 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68742 (Get FASTA)   NCBI Sequence Viewer  
  B5DEN9 (Get FASTA)   NCBI Sequence Viewer  
  EDM15954 (Get FASTA)   NCBI Sequence Viewer  
  EDM15955 (Get FASTA)   NCBI Sequence Viewer  
  EDM15956 (Get FASTA)   NCBI Sequence Viewer  
  EDM15957 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019707
RefSeq Acc Id: NP_001123964   ⟸   NM_001130492
- UniProtKB: B5DEN9 (UniProtKB/Swiss-Prot),   A0A0H2UHM0 (UniProtKB/TrEMBL),   A6HSB6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019707   ⟸   ENSRNOT00000019707
Ensembl Acc Id: ENSRNOP00000088292   ⟸   ENSRNOT00000108573
Ensembl Acc Id: ENSRNOP00000081278   ⟸   ENSRNOT00000103642
VPS28 C-terminal   VPS28 N-terminal

Name Modeler Protein Id AA Range Protein Structure
AF-B5DEN9-F1-model_v2 AlphaFold B5DEN9 1-228 view protein structure


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

RGD ID:13695429
Promoter ID:EPDNEW_R5954
Type:initiation region
Name:Vps28_1
Description:VPS28, ESCRT-I subunit
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_6.07117,688,142 - 117,688,202EPDNEW


1 to 27 of 27 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-32916 BioCyc
Ensembl Genes ENSRNOG00000014633 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000019707 ENTREZGENE
Gene3D-CATH 1.20.120.1130 UniProtKB/Swiss-Prot
  1.20.1440.200 UniProtKB/Swiss-Prot
InterPro ESCRT_assembly_dom UniProtKB/Swiss-Prot
  Vps28 UniProtKB/Swiss-Prot
  VPS28_C UniProtKB/Swiss-Prot
  VPS28_C_sf UniProtKB/Swiss-Prot
  VPS28_N UniProtKB/Swiss-Prot
  VPS28_N_sf UniProtKB/Swiss-Prot
NCBI Gene 300052 ENTREZGENE
PANTHER PTHR12937 UniProtKB/Swiss-Prot
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG UniProtKB/Swiss-Prot
Pfam VPS28 UniProtKB/Swiss-Prot
PhenoGen Vps28 PhenoGen
PIRSF VPS28 UniProtKB/Swiss-Prot
PROSITE VPS28_C UniProtKB/Swiss-Prot
  VPS28_N UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014633 RatGTEx
Superfamily-SCOP SSF140111 UniProtKB/Swiss-Prot
  SSF140427 UniProtKB/Swiss-Prot
UniProt A0A0H2UHM0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZS68_RAT UniProtKB/TrEMBL
  A0A8I6AAI1_RAT UniProtKB/TrEMBL
  A6HSB6 ENTREZGENE, UniProtKB/TrEMBL
  B5DEN9 ENTREZGENE, UniProtKB/Swiss-Prot
1 to 27 of 27 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Vps28  VPS28 subunit of ESCRT-I  Vps28  VPS28, ESCRT-I subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-08 Vps28  VPS28, ESCRT-I subunit  Vps28  vacuolar protein sorting 28 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps28  vacuolar protein sorting 28 homolog (S. cerevisiae)  Vps28  vacuolar protein sorting 28 (yeast)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Vps28  vacuolar protein sorting 28 (yeast)   Vps28_predicted  vacuolar protein sorting 28 (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Vps28_predicted  vacuolar protein sorting 28 (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED