Vcpip1 (valosin containing protein interacting protein 1) - Rat Genome Database

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Gene: Vcpip1 (valosin containing protein interacting protein 1) Rattus norvegicus
Analyze
Symbol: Vcpip1
Name: valosin containing protein interacting protein 1
RGD ID: 708520
Description: Enables cysteine-type deubiquitinase activity. Involved in Golgi reassembly; endoplasmic reticulum membrane fusion; and protein ubiquitination. Predicted to be located in cytoplasm and nucleus. Predicted to be active in synapse. Orthologous to human VCPIP1 (valosin containing protein interacting protein 1); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: deubiquitinating protein VCIP135; deubiquitinating protein VCPIP1; valosin containing protein (p97)/p47 complex interacting protein 1; valosin-containing protein (p97)/p47 complex-interacting protein 135; valosin-containing protein (p97)/p47 complex-interacting protein p135; valosin-containing protein p97/p47 complex-interacting protein 1; valosin-containing protein p97/p47 complex-interacting protein p135; Vcip135; VCP(p97)/p47-interacting protein
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
GRCr8514,317,083 - 14,343,724 (+)NCBIGRCr8
mRatBN7.259,534,247 - 9,560,889 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,534,129 - 9,562,040 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,687,600 - 11,714,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,319,317 - 13,345,988 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0513,022,278 - 13,049,213 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.059,231,180 - 9,257,821 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl59,230,984 - 9,257,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0514,031,258 - 14,057,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.459,088,295 - 9,114,936 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.159,088,236 - 9,116,073 (+)NCBI
Celera59,042,984 - 9,069,572 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
endoplasmic reticulum  (IEA)
Golgi stack  (IEA)
nucleus  (ISO,ISS)
synapse  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo. Uchiyama K, etal., J Cell Biol 2002 Dec 9;159(5):855-66. Epub 2002 Dec 9.
5. The localization and phosphorylation of p47 are important for Golgi disassembly-assembly during the cell cycle. Uchiyama K, etal., J Cell Biol 2003 Jun 23;161(6):1067-79. Epub 2003 Jun 16.
6. VCIP135 acts as a deubiquitinating enzyme during p97-p47-mediated reassembly of mitotic Golgi fragments. Wang Y, etal., J Cell Biol 2004 Mar 29;164(7):973-8. Epub 2004 Mar 22.
Additional References at PubMed
PMID:15328197   PMID:16452087   PMID:17550236   PMID:20871144   PMID:21811234   PMID:23827681  


Genomics

Comparative Map Data
Vcpip1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8514,317,083 - 14,343,724 (+)NCBIGRCr8
mRatBN7.259,534,247 - 9,560,889 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,534,129 - 9,562,040 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx511,687,600 - 11,714,534 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0513,319,317 - 13,345,988 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0513,022,278 - 13,049,213 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.059,231,180 - 9,257,821 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl59,230,984 - 9,257,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0514,031,258 - 14,057,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.459,088,295 - 9,114,936 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.159,088,236 - 9,116,073 (+)NCBI
Celera59,042,984 - 9,069,572 (+)NCBICelera
Cytogenetic Map5q11NCBI
VCPIP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38866,628,487 - 66,667,231 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl866,628,487 - 66,667,231 (-)EnsemblGRCh38hg38GRCh38
GRCh37867,540,722 - 67,579,466 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36867,705,042 - 67,742,006 (-)NCBINCBI36Build 36hg18NCBI36
Celera863,535,483 - 63,572,240 (-)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef863,032,538 - 63,071,315 (-)NCBIHuRef
CHM1_1867,597,370 - 67,634,328 (-)NCBICHM1_1
T2T-CHM13v2.0867,054,243 - 67,092,986 (-)NCBIT2T-CHM13v2.0
Vcpip1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3919,788,847 - 9,818,607 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl19,788,847 - 9,818,607 (-)EnsemblGRCm39 Ensembl
GRCm3819,718,622 - 9,748,382 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl19,718,622 - 9,748,382 (-)EnsemblGRCm38mm10GRCm38
MGSCv3719,713,273 - 9,738,463 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3619,708,406 - 9,733,596 (-)NCBIMGSCv36mm8
Celera19,697,685 - 9,724,194 (-)NCBICelera
Cytogenetic Map1A2NCBI
cM Map12.08NCBI
Vcpip1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544412,542,479 - 12,567,971 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544412,542,479 - 12,567,971 (+)NCBIChiLan1.0ChiLan1.0
VCPIP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2782,367,580 - 82,404,559 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1858,007,273 - 58,043,996 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0863,173,116 - 63,210,119 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1864,836,468 - 64,874,818 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl864,842,479 - 64,874,818 (-)Ensemblpanpan1.1panPan2
VCPIP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12916,204,932 - 16,235,893 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2916,209,353 - 16,235,586 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2916,520,420 - 16,552,129 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02916,284,665 - 16,316,409 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2916,285,422 - 16,316,353 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12916,316,618 - 16,348,345 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02916,416,266 - 16,447,999 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02916,672,097 - 16,703,810 (-)NCBIUU_Cfam_GSD_1.0
Vcpip1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530367,409,454 - 67,433,444 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364967,352,018 - 7,376,964 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364967,352,043 - 7,376,023 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCPIP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl468,073,447 - 68,110,621 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1468,073,403 - 68,109,221 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2474,259,695 - 74,274,272 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VCPIP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1862,506,541 - 62,546,238 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl862,510,808 - 62,546,229 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603978,961,467 - 79,002,860 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vcpip1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474424,664,636 - 24,700,416 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474424,664,833 - 24,700,416 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vcpip1
86 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:755
Count of miRNA genes:301
Interacting mature miRNAs:383
Transcripts:ENSRNOT00000009136
Prediction methods:Microtar, Miranda
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat

Markers in Region
D1Mit296  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.259,532,612 - 9,532,770 (+)MAPPERmRatBN7.2
Rnor_6.059,229,546 - 9,229,703NCBIRnor6.0
Rnor_5.0514,029,624 - 14,029,781UniSTSRnor5.0
RGSC_v3.459,086,661 - 9,086,818UniSTSRGSC3.4
Celera59,041,357 - 9,041,508UniSTS
Cytogenetic Map5q11UniSTS
RH142499  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.259,540,754 - 9,540,863 (+)MAPPERmRatBN7.2
Rnor_6.059,237,688 - 9,237,796NCBIRnor6.0
Rnor_5.0514,037,766 - 14,037,874UniSTSRnor5.0
RGSC_v3.459,094,803 - 9,094,911UniSTSRGSC3.4
Celera59,049,492 - 9,049,600UniSTS
RH 3.4 Map550.2UniSTS
Cytogenetic Map5q11UniSTS


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 29 48 32 19 32 7 7 74 34 41 11 7
Low 1 14 9 9 9 1 4 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009136   ⟹   ENSRNOP00000009136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl59,534,129 - 9,562,040 (+)Ensembl
Rnor_6.0 Ensembl59,230,984 - 9,257,934 (+)Ensembl
RefSeq Acc Id: NM_176857   ⟹   NP_789827
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8514,317,083 - 14,343,724 (+)NCBI
mRatBN7.259,534,247 - 9,560,889 (+)NCBI
Rnor_6.059,231,180 - 9,257,821 (+)NCBI
Rnor_5.0514,031,258 - 14,057,899 (+)NCBI
RGSC_v3.459,088,295 - 9,114,936 (+)RGD
Celera59,042,984 - 9,069,572 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_789827 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ14350 (Get FASTA)   NCBI Sequence Viewer  
  BAC44841 (Get FASTA)   NCBI Sequence Viewer  
  EDM11556 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009136
  ENSRNOP00000009136.3
  ENSRNOP00055023908
  ENSRNOP00060013594
  ENSRNOP00065024002
GenBank Protein Q8CF97 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_789827   ⟸   NM_176857
- UniProtKB: Q7TNK5 (UniProtKB/Swiss-Prot),   Q8CF97 (UniProtKB/Swiss-Prot),   A6JFG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009136   ⟸   ENSRNOT00000009136
Protein Domains
OTU

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CF97-F1-model_v2 AlphaFold Q8CF97 1-1221 view protein structure

Transcriptome

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

Promoters
RGD ID:13693536
Promoter ID:EPDNEW_R4061
Type:initiation region
Name:Vcpip1_1
Description:valosin containing protein interacting 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_6.059,231,058 - 9,231,118EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708520 AgrOrtholog
BioCyc Gene G2FUF-42198 BioCyc
Ensembl Genes ENSRNOG00000006980 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055017596 UniProtKB/Swiss-Prot
  ENSRNOG00060010354 UniProtKB/Swiss-Prot
  ENSRNOG00065018030 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009136 ENTREZGENE
  ENSRNOT00000009136.5 UniProtKB/Swiss-Prot
  ENSRNOT00055029773 UniProtKB/Swiss-Prot
  ENSRNOT00060017502 UniProtKB/Swiss-Prot
  ENSRNOT00065030211 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.70.80 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro OTU1_Ubl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OTU_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VCIP135 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VCPIP1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:286761 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 286761 ENTREZGENE
PANTHER DEUBIQUITINATING PROTEIN VCIP135 UniProtKB/TrEMBL
  DEUBIQUITINATING PROTEIN VCPIP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR14843 UniProtKB/Swiss-Prot
Pfam OTU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OTU1_UBXL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VCIP135_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vcpip1 PhenoGen
PROSITE OTU UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006980 RatGTEx
  ENSRNOG00055017596 RatGTEx
  ENSRNOG00060010354 RatGTEx
  ENSRNOG00065018030 RatGTEx
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6JFG0 ENTREZGENE, UniProtKB/TrEMBL
  Q7TNK5 ENTREZGENE
  Q8CF97 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q7TNK5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Vcpip1  valosin containing protein interacting protein 1  Vcpip1  valosin containing protein (p97)/p47 complex interacting protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Vcpip1  valosin containing protein (p97)/p47 complex interacting protein 1  Vcip135  valosin-containing protein (p97)/p47 complex-interacting protein 135  Symbol and Name updated 1299863 APPROVED
2005-07-08 Vcip135  valosin-containing protein (p97)/p47 complex-interacting protein 135    valosin-containing protein (p97)/p47 complex-interacting protein p135  Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference