Zup1 (zinc finger containing ubiquitin peptidase 1) - Rat Genome Database

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Gene: Zup1 (zinc finger containing ubiquitin peptidase 1) Rattus norvegicus
Analyze
Symbol: Zup1
Name: zinc finger containing ubiquitin peptidase 1
RGD ID: 1307672
Description: Predicted to enable cysteine-type deubiquitinase activity and metal ion binding activity. Predicted to be located in cytosol and nucleoplasm. Orthologous to human ZUP1 (zinc finger containing ubiquitin peptidase 1); INTERACTS WITH 3H-1,2-dithiole-3-thione; bisphenol A; decabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DUB; hypothetical LOC294390; LOC294390; lys-63-specific deubiquitinase ZUFSP; MGC94667; RGD1307672; ubiquitin carboxyl-terminal hydrolase ZUFSP; zinc finger with UFM1-specific peptidase domain; zinc finger with UFM1-specific peptidase domain protein; zinc finger-containing ubiquitin peptidase 1; Zufsp
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
GRCr82031,327,939 - 31,358,088 (-)NCBIGRCr8
mRatBN7.22030,785,226 - 30,815,377 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,785,227 - 30,815,306 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,796,148 - 31,826,237 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,187,068 - 31,217,157 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,923,787 - 31,953,877 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,471,670 - 32,501,693 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,471,672 - 32,501,722 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,255,576 - 34,285,599 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,096,106 - 30,126,201 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,109,906 - 30,140,001 (-)NCBI
Celera2032,202,226 - 32,232,242 (-)NCBICelera
Cytogenetic Map20q11NCBI
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

Cellular Component
cytoplasm  (IEA)
cytosol  (ISO)
nucleoplasm  (ISO)
nucleus  (IEA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Zup1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,327,939 - 31,358,088 (-)NCBIGRCr8
mRatBN7.22030,785,226 - 30,815,377 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,785,227 - 30,815,306 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,796,148 - 31,826,237 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,187,068 - 31,217,157 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,923,787 - 31,953,877 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,471,670 - 32,501,693 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,471,672 - 32,501,722 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,255,576 - 34,285,599 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,096,106 - 30,126,201 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,109,906 - 30,140,001 (-)NCBI
Celera2032,202,226 - 32,232,242 (-)NCBICelera
Cytogenetic Map20q11NCBI
ZUP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,635,618 - 116,668,766 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6116,635,618 - 116,668,794 (-)EnsemblGRCh38hg38GRCh38
GRCh376116,956,781 - 116,989,929 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,063,474 - 117,096,652 (-)NCBINCBI36Build 36hg18NCBI36
Build 346117,063,473 - 117,096,650NCBI
Celera6117,699,849 - 117,733,039 (-)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6114,536,357 - 114,569,549 (-)NCBIHuRef
CHM1_16117,220,405 - 117,253,587 (-)NCBICHM1_1
T2T-CHM13v2.06117,819,329 - 117,852,469 (-)NCBIT2T-CHM13v2.0
Zup1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391033,795,138 - 33,827,316 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1033,795,138 - 33,827,265 (-)EnsemblGRCm39 Ensembl
GRCm381033,919,142 - 33,951,294 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1033,919,142 - 33,951,269 (-)EnsemblGRCm38mm10GRCm38
MGSCv371033,646,742 - 33,671,018 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361033,616,352 - 33,648,207 (-)NCBIMGSCv36mm8
Celera1034,837,312 - 34,861,586 (-)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1018.85NCBI
Zup1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554362,057 - 33,251 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554361,001 - 28,469 (+)NCBIChiLan1.0ChiLan1.0
ZUP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25136,649,403 - 136,682,936 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16134,542,421 - 134,575,953 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06114,443,844 - 114,477,220 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16118,588,455 - 118,621,123 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6118,598,031 - 118,621,081 (-)Ensemblpanpan1.1panPan2
ZUP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,076,730 - 57,108,527 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,067,005 - 57,106,837 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha157,875,202 - 57,903,637 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,261,956 - 57,290,387 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,261,962 - 57,290,365 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1157,156,332 - 57,184,769 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0157,004,493 - 57,032,925 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0157,633,012 - 57,661,676 (-)NCBIUU_Cfam_GSD_1.0
Zup1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,802,407 - 107,823,359 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493706821,276 - 42,264 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493706821,312 - 42,266 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZUP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl144,939,951 - 44,961,145 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1144,939,914 - 45,013,764 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2150,212,885 - 50,235,181 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZUP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11357,146,150 - 57,172,473 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1357,146,172 - 57,177,127 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604029,480,575 - 29,506,919 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zup1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479812,991,865 - 13,021,268 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479812,992,315 - 13,021,450 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Zup1
259 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000000448
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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 3 30 34 18 19 18 1 1 74 32 38 11 1
Low 13 23 23 23 7 10 3 3 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000000448   ⟹   ENSRNOP00000000448
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2030,785,227 - 30,815,306 (-)Ensembl
Rnor_6.0 Ensembl2032,471,672 - 32,501,722 (-)Ensembl
RefSeq Acc Id: NM_001008308   ⟹   NP_001008309
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,327,939 - 31,358,023 (-)NCBI
mRatBN7.22030,785,226 - 30,815,306 (-)NCBI
Rnor_6.02032,471,670 - 32,501,693 (-)NCBI
Rnor_5.02034,255,576 - 34,285,599 (-)NCBI
RGSC_v3.42030,096,106 - 30,126,201 (-)RGD
Celera2032,202,226 - 32,232,242 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098589   ⟹   XP_038954517
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,327,939 - 31,356,017 (-)NCBI
mRatBN7.22030,785,226 - 30,813,297 (-)NCBI
RefSeq Acc Id: XM_039098590   ⟹   XP_038954518
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,327,939 - 31,353,063 (-)NCBI
mRatBN7.22030,785,226 - 30,813,177 (-)NCBI
RefSeq Acc Id: XM_039098591   ⟹   XP_038954519
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,339,658 - 31,358,086 (-)NCBI
mRatBN7.22030,796,983 - 30,815,377 (-)NCBI
RefSeq Acc Id: XM_039098592   ⟹   XP_038954520
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,327,939 - 31,345,738 (-)NCBI
mRatBN7.22030,785,226 - 30,803,384 (-)NCBI
RefSeq Acc Id: XM_063279066   ⟹   XP_063135136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,345,771 - 31,358,088 (-)NCBI
RefSeq Acc Id: XR_010060650
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,336,618 - 31,358,085 (-)NCBI
RefSeq Acc Id: NP_001008309   ⟸   NM_001008308
- UniProtKB: Q5U2S3 (UniProtKB/Swiss-Prot),   A6K470 (UniProtKB/TrEMBL),   A6K469 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000448   ⟸   ENSRNOT00000000448
RefSeq Acc Id: XP_038954517   ⟸   XM_039098589
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954518   ⟸   XM_039098590
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954520   ⟸   XM_039098592
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954519   ⟸   XM_039098591
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063135136   ⟸   XM_063279066
- Peptide Label: isoform X4
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U2S3-F1-model_v2 AlphaFold Q5U2S3 1-577 view protein structure

Transcriptome

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

Promoters
RGD ID:13701619
Promoter ID:EPDNEW_R12143
Type:multiple initiation site
Name:Zufsp_1
Description:zinc finger with UFM1-specific peptidase domain
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_6.02032,501,694 - 32,501,754EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307672 AgrOrtholog
BioCyc Gene G2FUF-3667 BioCyc
Ensembl Genes ENSRNOG00000000398 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055014858 UniProtKB/Swiss-Prot
  ENSRNOG00060007716 UniProtKB/Swiss-Prot
  ENSRNOG00065003412 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000448 ENTREZGENE
  ENSRNOT00000000448.6 UniProtKB/Swiss-Prot
  ENSRNOT00055025443 UniProtKB/Swiss-Prot
  ENSRNOT00060012728 UniProtKB/Swiss-Prot
  ENSRNOT00065004848 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.70.130 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7192192 IMAGE-MGC_LOAD
InterPro Papain-like_cys_pep_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C78_UfSP1/2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294390 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94667 IMAGE-MGC_LOAD
NCBI Gene 294390 ENTREZGENE
PANTHER ZINC FINGER PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC FINGER-CONTAINING UBIQUITIN PEPTIDASE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Peptidase_C78 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zup1 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000398 RatGTEx
  ENSRNOG00055014858 RatGTEx
  ENSRNOG00060007716 RatGTEx
  ENSRNOG00065003412 RatGTEx
SMART ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Cysteine proteinases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6K469 ENTREZGENE, UniProtKB/TrEMBL
  A6K470 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2S3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-02-28 Zup1  zinc finger containing ubiquitin peptidase 1  Zufsp  zinc finger with UFM1-specific peptidase domain  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-31 Zufsp  zinc finger with UFM1-specific peptidase domain  RGD1307672  hypothetical LOC294390  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1307672  hypothetical LOC294390  RGD1307672_predicted  hypothetical LOC294390 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307672_predicted  hypothetical LOC294390 (predicted)  LOC294390_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC294390_predicted  hypothetical LOC294390 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL