Usp49 (ubiquitin specific peptidase 49) - Rat Genome Database

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Gene: Usp49 (ubiquitin specific peptidase 49) Rattus norvegicus
Analyze
Symbol: Usp49
Name: ubiquitin specific peptidase 49
RGD ID: 1310513
Description: Predicted to enable histone binding activity and peptidase activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be active in cytoplasm. Orthologous to human USP49 (ubiquitin specific peptidase 49); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC316211; RGD1310513; similar to hypothetical protein MGC20741; ubiquitin carboxyl-terminal hydrolase 49; ubiquitin thioesterase 49
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
GRCr8920,803,177 - 20,867,681 (-)NCBIGRCr8
mRatBN7.2913,305,640 - 13,366,132 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl913,308,178 - 13,366,132 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx921,888,201 - 21,945,900 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,952,281 - 27,010,031 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0925,251,607 - 25,309,304 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0915,314,875 - 15,375,365 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,317,413 - 15,375,365 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,239,085 - 14,299,667 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,774,333 - 8,832,285 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.198,778,351 - 8,786,793 (-)NCBI
Celera911,060,638 - 11,117,551 (-)NCBICelera
Cytogenetic Map9q12NCBI
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  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14715245   PMID:15632090   PMID:23824326  


Genomics

Comparative Map Data
Usp49
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8920,803,177 - 20,867,681 (-)NCBIGRCr8
mRatBN7.2913,305,640 - 13,366,132 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl913,308,178 - 13,366,132 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx921,888,201 - 21,945,900 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,952,281 - 27,010,031 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0925,251,607 - 25,309,304 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0915,314,875 - 15,375,365 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,317,413 - 15,375,365 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,239,085 - 14,299,667 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.498,774,333 - 8,832,285 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.198,778,351 - 8,786,793 (-)NCBI
Celera911,060,638 - 11,117,551 (-)NCBICelera
Cytogenetic Map9q12NCBI
USP49
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38641,789,896 - 41,895,375 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl641,789,896 - 41,895,375 (-)EnsemblGRCh38hg38GRCh38
GRCh37641,757,634 - 41,863,113 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,873,361 - 41,971,077 (-)NCBINCBI36Build 36hg18NCBI36
Celera643,318,714 - 43,416,439 (-)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef641,484,106 - 41,581,878 (-)NCBIHuRef
CHM1_1641,768,743 - 41,866,405 (-)NCBICHM1_1
T2T-CHM13v2.0641,618,461 - 41,723,935 (-)NCBIT2T-CHM13v2.0
Usp49
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,941,615 - 47,997,664 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1747,941,615 - 47,997,663 (+)EnsemblGRCm39 Ensembl
GRCm381747,630,690 - 47,686,739 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1747,630,690 - 47,686,738 (+)EnsemblGRCm38mm10GRCm38
MGSCv371747,767,639 - 47,821,016 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361747,093,881 - 47,147,258 (+)NCBIMGSCv36mm8
Celera1751,067,647 - 51,120,972 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1723.72NCBI
Usp49
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,191,236 - 8,198,809 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,187,118 - 8,237,910 (-)NCBIChiLan1.0ChiLan1.0
USP49
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2556,282,907 - 56,389,693 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1652,152,885 - 52,256,921 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0641,375,083 - 41,479,143 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1642,678,680 - 42,781,748 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl642,683,149 - 42,695,707 (-)Ensemblpanpan1.1panPan2
USP49
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11210,474,873 - 10,556,900 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1210,479,733 - 10,577,918 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1210,504,358 - 10,589,769 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01210,955,129 - 11,041,174 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1210,955,164 - 11,051,627 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11210,485,701 - 10,567,699 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01210,569,381 - 10,654,952 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01210,663,097 - 10,748,867 (-)NCBIUU_Cfam_GSD_1.0
Usp49
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494645,957,669 - 46,049,495 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647617,991,688 - 18,000,794 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647617,946,875 - 18,002,081 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP49
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl736,981,383 - 37,052,568 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1736,978,291 - 37,054,027 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2742,393,547 - 42,458,617 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USP49
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11730,265,322 - 30,373,547 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1730,356,698 - 30,366,940 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604441,783,918 - 41,895,090 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Usp49
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475417,266,561 - 17,274,926 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475417,226,723 - 17,281,206 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Usp49
279 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:656
Count of miRNA genes:293
Interacting mature miRNAs:357
Transcripts:ENSRNOT00000018550
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
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat


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 43 8
Low 3 43 57 41 19 41 8 11 31 35 33 11 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000018550   ⟹   ENSRNOP00000018550
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl913,308,178 - 13,366,132 (-)Ensembl
Rnor_6.0 Ensembl915,317,413 - 15,375,365 (-)Ensembl
RefSeq Acc Id: NM_001136470   ⟹   NP_001129942
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,805,715 - 20,863,667 (-)NCBI
mRatBN7.2913,308,178 - 13,366,132 (-)NCBI
Rnor_6.0915,317,413 - 15,375,365 (-)NCBI
Rnor_5.0914,239,085 - 14,299,667 (-)NCBI
RGSC_v3.498,774,333 - 8,832,285 (-)RGD
Celera911,060,638 - 11,117,551 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244435   ⟹   XP_006244497
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,803,177 - 20,826,448 (-)NCBI
mRatBN7.2913,305,640 - 13,323,918 (-)NCBI
Rnor_6.0915,314,875 - 15,333,131 (-)NCBI
Rnor_5.0914,239,085 - 14,299,667 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596410   ⟹   XP_017451899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,803,177 - 20,863,303 (-)NCBI
mRatBN7.2913,305,640 - 13,365,484 (-)NCBI
Rnor_6.0915,314,875 - 15,374,664 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596411   ⟹   XP_017451900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,803,177 - 20,862,630 (-)NCBI
mRatBN7.2913,305,640 - 13,365,041 (-)NCBI
Rnor_6.0915,314,875 - 15,374,185 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083485   ⟹   XP_038939413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,803,177 - 20,862,751 (-)NCBI
mRatBN7.2913,305,640 - 13,365,194 (-)NCBI
RefSeq Acc Id: XM_063267083   ⟹   XP_063123153
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,803,177 - 20,867,681 (-)NCBI
RefSeq Acc Id: NP_001129942   ⟸   NM_001136470
- UniProtKB: D3ZJ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244497   ⟸   XM_006244435
- Peptide Label: isoform X1
- UniProtKB: D3ZJ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451899   ⟸   XM_017596410
- Peptide Label: isoform X1
- UniProtKB: D3ZJ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451900   ⟸   XM_017596411
- Peptide Label: isoform X1
- UniProtKB: D3ZJ49 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018550   ⟸   ENSRNOT00000018550
RefSeq Acc Id: XP_038939413   ⟸   XM_039083485
- Peptide Label: isoform X1
- UniProtKB: D3ZJ49 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063123153   ⟸   XM_063267083
- Peptide Label: isoform X2
Protein Domains
UBP-type   USP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJ49-F1-model_v2 AlphaFold D3ZJ49 1-685 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310513 AgrOrtholog
BioCyc Gene G2FUF-28276 BioCyc
Ensembl Genes ENSRNOG00000013866 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018550 ENTREZGENE
  ENSRNOT00000018550.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/TrEMBL
InterPro Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Pept_C19ubi-hydrolase_C_CS UniProtKB/TrEMBL
  Peptidase_C19 UniProtKB/TrEMBL
  UCH/PAN2 UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_UBP UniProtKB/TrEMBL
KEGG Report rno:316211 UniProtKB/TrEMBL
NCBI Gene 316211 ENTREZGENE
PANTHER UBIQUITIN CARBOXYL-TERMINAL HYDROLASE UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 49 UniProtKB/TrEMBL
Pfam UCH UniProtKB/TrEMBL
  zf-UBP UniProtKB/TrEMBL
PhenoGen Usp49 PhenoGen
PROSITE UCH_2_1 UniProtKB/TrEMBL
  UCH_2_2 UniProtKB/TrEMBL
  UCH_2_3 UniProtKB/TrEMBL
  ZF_UBP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013866 RatGTEx
SMART ZnF_UBP UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
  SSF54001 UniProtKB/TrEMBL
UniProt D3ZJ49 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Usp49  ubiquitin specific peptidase 49   Usp49_predicted  ubiquitin specific peptidase 49 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Usp49_predicted  ubiquitin specific peptidase 49 (predicted)  RGD1310513_predicted  similar to hypothetical protein MGC20741 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1310513_predicted  similar to hypothetical protein MGC20741 (predicted)  LOC316211_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316211_predicted  similar to hypothetical protein MGC20741 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL