Ushbp1 (USH1 protein network component harmonin binding protein 1) - Rat Genome Database

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Gene: Ushbp1 (USH1 protein network component harmonin binding protein 1) Rattus norvegicus
Analyze
Symbol: Ushbp1
Name: USH1 protein network component harmonin binding protein 1
RGD ID: 1310859
Description: Predicted to enable PDZ domain binding activity. Orthologous to human USHBP1 (USH1 protein network component harmonin binding protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: harmonin-binding protein USHBP1; LOC290629; MGC124707; USH1C-binding protein 1; Usher syndrome 1C binding protein 1; usher syndrome type-1C protein-binding protein 1
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
GRCr81618,091,311 - 18,101,927 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1618,091,316 - 18,101,867 (-)EnsemblGRCr8
mRatBN7.21618,057,321 - 18,067,933 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,057,326 - 18,067,877 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1618,108,949 - 18,119,545 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,241,512 - 19,252,096 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,161,870 - 18,172,466 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,781,276 - 19,791,832 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,781,279 - 19,791,832 (-)Ensemblrn6Rnor6.0
Rnor_5.01619,641,397 - 19,651,953 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41618,546,489 - 18,557,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1618,262,900 - 18,273,456 (-)NCBICelera
RGSC_v3.11618,546,486 - 18,555,536 (-)NCBI
Cytogenetic Map16p14NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11311560   PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Ushbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,091,311 - 18,101,927 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1618,091,316 - 18,101,867 (-)EnsemblGRCr8
mRatBN7.21618,057,321 - 18,067,933 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,057,326 - 18,067,877 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1618,108,949 - 18,119,545 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01619,241,512 - 19,252,096 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01618,161,870 - 18,172,466 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,781,276 - 19,791,832 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,781,279 - 19,791,832 (-)Ensemblrn6Rnor6.0
Rnor_5.01619,641,397 - 19,651,953 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41618,546,489 - 18,557,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1618,262,900 - 18,273,456 (-)NCBICelera
RGSC_v3.11618,546,486 - 18,555,536 (-)NCBI
Cytogenetic Map16p14NCBI
USHBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381917,249,171 - 17,264,745 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1917,249,171 - 17,282,786 (-)Ensemblhg38GRCh38
GRCh371917,359,980 - 17,375,554 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361917,221,849 - 17,236,544 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341917,221,848 - 17,236,544NCBI
Celera1917,262,392 - 17,277,301 (-)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1916,927,891 - 16,942,605 (-)NCBIHuRef
CHM1_11917,360,331 - 17,375,018 (-)NCBICHM1_1
T2T-CHM13v2.01917,384,049 - 17,399,626 (-)NCBIT2T-CHM13v2.0
Ushbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39871,836,918 - 71,848,480 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl871,836,916 - 71,848,446 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38871,384,274 - 71,395,834 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl871,384,272 - 71,395,802 (-)Ensemblmm10GRCm38
MGSCv37873,908,173 - 73,919,700 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36874,314,358 - 74,324,774 (-)NCBIMGSCv36mm8
Celera873,908,945 - 73,920,510 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.43NCBI
Ushbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955524946,561 - 957,029 (+)Ensembl
ChiLan1.0NW_004955524945,044 - 954,424 (+)NCBIChiLan1.0ChiLan1.0
USHBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22022,119,365 - 22,135,998 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11921,125,938 - 21,142,572 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01916,737,813 - 16,752,891 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11917,711,987 - 17,726,576 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1917,711,987 - 17,726,524 (-)EnsemblpanPan2panpan1.1
USHBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12045,477,070 - 45,486,552 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2045,477,592 - 45,486,510 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2045,390,394 - 45,399,904 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02045,963,233 - 45,972,744 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2045,962,145 - 45,972,731 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12045,199,878 - 45,209,379 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02045,609,695 - 45,619,255 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02045,885,552 - 45,895,064 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ushbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118204,035,715 - 204,044,346 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365963,584,879 - 3,593,496 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365963,584,890 - 3,593,481 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USHBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl260,411,629 - 60,422,554 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1260,411,629 - 60,422,577 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
USHBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1615,758,962 - 15,772,737 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl615,758,777 - 15,772,471 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660743,669,606 - 3,683,305 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ushbp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624908662,451 - 670,191 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624908661,663 - 670,226 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ushbp1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11313,605,883 - 13,616,251 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ushbp1
37 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:117
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000040393
Prediction methods:Microtar, Miranda, Rnahybrid
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
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161574800625801629Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)161627818427244292Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338679026128267Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161773081872536785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)161590580260905802Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat

Markers in Region
BM387488  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,061,190 - 18,061,369 (+)MAPPERmRatBN7.2
Rnor_6.01619,785,146 - 19,785,324NCBIRnor6.0
Rnor_5.01619,645,267 - 19,645,445UniSTSRnor5.0
RGSC_v3.41618,550,359 - 18,550,537UniSTSRGSC3.4
Celera1618,266,770 - 18,266,948UniSTS
RH 3.4 Map16181.21UniSTS
Cytogenetic Map16p14UniSTS


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 67 157 91 90 59 50 59 6 314 150 11 131 81 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000040393   ⟹   ENSRNOP00000042639
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1618,091,316 - 18,101,867 (-)Ensembl
mRatBN7.2 Ensembl1618,057,326 - 18,067,877 (-)Ensembl
Rnor_6.0 Ensembl1619,781,279 - 19,791,832 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000131258   ⟹   ENSRNOP00000101326
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1618,091,316 - 18,101,867 (-)Ensembl
RefSeq Acc Id: NM_001033687   ⟹   NP_001028859
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,091,311 - 18,101,867 (-)NCBI
mRatBN7.21618,057,321 - 18,067,877 (-)NCBI
Rnor_6.01619,781,276 - 19,791,832 (-)NCBI
Rnor_5.01619,641,397 - 19,651,953 (-)NCBI
RGSC_v3.41618,546,489 - 18,557,045 (-)RGD
Celera1618,262,900 - 18,273,456 (-)RGD
Sequence:
RefSeq Acc Id: XM_039094294   ⟹   XP_038950222
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,091,311 - 18,101,927 (-)NCBI
mRatBN7.21618,057,321 - 18,067,933 (-)NCBI
RefSeq Acc Id: XM_039094295   ⟹   XP_038950223
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,093,447 - 18,101,927 (-)NCBI
mRatBN7.21618,059,447 - 18,067,933 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001028859 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950222 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950223 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI01906 (Get FASTA)   NCBI Sequence Viewer  
  EDL90806 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000042639
  ENSRNOP00000042639.3
  ENSRNOP00000101326
GenBank Protein Q3T1I3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001028859   ⟸   NM_001033687
- UniProtKB: Q3T1I3 (UniProtKB/Swiss-Prot),   A6K9T1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000042639   ⟸   ENSRNOT00000040393
RefSeq Acc Id: XP_038950222   ⟸   XM_039094294
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038950223   ⟸   XM_039094295
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000101326   ⟸   ENSRNOT00000131258
Protein Domains
Harmonin-binding protein USHBP1 PDZ-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3T1I3-F1-model_v2 AlphaFold Q3T1I3 1-680 view protein structure

Transcriptome

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

Promoters
RGD ID:13699996
Promoter ID:EPDNEW_R10520
Type:single initiation site
Name:Ushbp1_1
Description:USH1 protein network component harmonin binding protein 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_6.01619,791,844 - 19,791,904EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310859 AgrOrtholog
BioCyc Gene G2FUF-11855 BioCyc
Ensembl Genes ENSRNOG00000023485 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000040393 ENTREZGENE
  ENSRNOT00000040393.5 UniProtKB/Swiss-Prot
  ENSRNOT00000131258 ENTREZGENE
IMAGE_CLONE IMAGE:7934347 IMAGE-MGC_LOAD
InterPro USBP1-like UniProtKB/Swiss-Prot
  USH1C-bd_PDZ_domain UniProtKB/Swiss-Prot
KEGG Report rno:290629 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124707 IMAGE-MGC_LOAD
NCBI Gene 290629 ENTREZGENE
PANTHER PTHR23347 UniProtKB/Swiss-Prot
  USHER SYNDROME TYPE-1C PROTEIN-BINDING PROTEIN 1 UniProtKB/Swiss-Prot
Pfam MCC-bdg_PDZ UniProtKB/Swiss-Prot
PhenoGen Ushbp1 PhenoGen
RatGTEx ENSRNOG00000023485 RatGTEx
UniProt A0ABK0L0I1_RAT UniProtKB/TrEMBL
  A6K9T1 ENTREZGENE, UniProtKB/TrEMBL
  Q3T1I3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Ushbp1  USH1 protein network component harmonin binding protein 1  Ushbp1  Usher syndrome 1C binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ushbp1  Usher syndrome 1C binding protein 1  Ushbp1_predicted  Usher syndrome 1C binding protein 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ushbp1_predicted  Usher syndrome 1C binding protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED