Usp39 (ubiquitin specific peptidase 39) - Rat Genome Database
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Gene: Usp39 (ubiquitin specific peptidase 39) Mus musculus
Analyze
Symbol: Usp39
Name: ubiquitin specific peptidase 39
RGD ID: 1317683
MGI Page MGI
Description: Is expressed in cerebral cortex; early conceptus; and genitourinary system. Orthologous to human USP39 (ubiquitin specific peptidase 39); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: AA408960; AI894154; CGI-2; CGI-21; D6Wsu157; D6Wsu157e; inactive ubiquitin-specific peptidase 39; SA; SAD1; SnRNP assembly defective 1 homolog; U4/U6.U5 tri-snRNP-associated protein 2; ubiquitin specific protease 39
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39672,295,659 - 72,322,190 (-)NCBIGRCm39mm39
GRCm39 Ensembl672,295,661 - 72,322,167 (-)Ensembl
GRCm38672,318,676 - 72,345,208 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl672,318,678 - 72,345,184 (-)EnsemblGRCm38mm10GRCm38
MGSCv37672,268,670 - 72,295,169 (-)NCBIGRCm37mm9NCBIm37
MGSCv36672,248,185 - 72,274,684 (-)NCBImm8
Celera674,408,796 - 74,435,299 (-)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:8889548   PMID:9383293   PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11350945   PMID:12477932   PMID:12520002   PMID:12904583   PMID:15489334  
PMID:15761153   PMID:15782199   PMID:16141072   PMID:16141073   PMID:16325481   PMID:18287559   PMID:19129515   PMID:19334288   PMID:19521500   PMID:26167872   PMID:27626380   PMID:28447728  
PMID:31040226  


Genomics

Comparative Map Data
Usp39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39672,295,659 - 72,322,190 (-)NCBIGRCm39mm39
GRCm39 Ensembl672,295,661 - 72,322,167 (-)Ensembl
GRCm38672,318,676 - 72,345,208 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl672,318,678 - 72,345,184 (-)EnsemblGRCm38mm10GRCm38
MGSCv37672,268,670 - 72,295,169 (-)NCBIGRCm37mm9NCBIm37
MGSCv36672,248,185 - 72,274,684 (-)NCBImm8
Celera674,408,796 - 74,435,299 (-)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.27NCBI
USP39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl285,602,856 - 85,649,283 (+)EnsemblGRCh38hg38GRCh38
GRCh38285,602,843 - 85,649,283 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37285,829,984 - 85,876,406 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36285,696,794 - 85,729,917 (+)NCBINCBI36hg18NCBI36
Build 34285,754,940 - 85,788,063NCBI
Celera285,671,566 - 85,704,705 (+)NCBI
Cytogenetic Map2p11.2NCBI
HuRef285,727,104 - 85,773,387 (+)NCBIHuRef
CHM1_1285,759,771 - 85,806,166 (+)NCBICHM1_1
Usp39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24104,373,908 - 104,406,413 (-)NCBI
Rnor_6.0 Ensembl4100,181,455 - 100,213,858 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04100,181,408 - 100,211,425 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04164,952,169 - 164,982,100 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44105,623,922 - 105,650,275 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14105,868,446 - 105,900,853 (-)NCBI
Celera493,527,956 - 93,554,280 (-)NCBICelera
Cytogenetic Map4q31NCBI
Usp39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554241,867,850 - 1,894,157 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554241,867,910 - 1,893,338 (-)NCBIChiLan1.0ChiLan1.0
USP39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A87,219,121 - 87,251,931 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A87,215,366 - 87,251,931 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A85,655,633 - 85,701,775 (+)NCBIMhudiblu_PPA_v0panPan3
USP39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1739,438,329 - 39,470,549 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11739,437,908 - 39,470,579 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Usp39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367121,625,429 - 1,661,561 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USP39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl359,121,048 - 59,156,442 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1359,121,381 - 59,156,597 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2362,195,078 - 62,215,382 (-)NCBISscrofa10.2Sscrofa10.2susScr3
USP39
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11421,507,666 - 21,554,819 (-)NCBI
ChlSab1.1 Ensembl1421,508,104 - 21,541,553 (-)Ensembl
Usp39
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474917,500,781 - 17,526,755 (-)NCBI

Position Markers
AI894154  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38672,319,108 - 72,319,190UniSTSGRCm38
MGSCv37672,269,102 - 72,269,184UniSTSGRCm37
Celera674,409,228 - 74,409,310UniSTS
Cytogenetic Map6C1UniSTS
cM Map631.5UniSTS
Whitehead/MRC_RH6721.48UniSTS
RH124797  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38672,318,973 - 72,319,114UniSTSGRCm38
MGSCv37672,268,967 - 72,269,108UniSTSGRCm37
Celera674,409,093 - 74,409,234UniSTS
Cytogenetic Map6C1UniSTS
cM Map631.5UniSTS
D6Wsu157e  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38672,318,774 - 72,318,932UniSTSGRCm38
MGSCv37672,268,768 - 72,268,926UniSTSGRCm37
Celera674,408,894 - 74,409,052UniSTS
Cytogenetic Map6C1UniSTS
cM Map631.5UniSTS
Usp39  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38672,319,107 - 72,319,808UniSTSGRCm38
Celera674,409,227 - 74,409,928UniSTS
Cytogenetic Map6C1UniSTS
cM Map631.5UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487426034Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080600000Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414873387692Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62500000080000000Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3285065078238974Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
12880424V25Dq4_mvitamin D inactive form serum level QTL 4 (mouse)64160000075600000Mouse
1301266Lmr4_mleishmaniasis resistance 4 (mouse)Not determined64211637376116515Mouse
11040600Lmr4c_mleishmaniasis resistance 4c (mouse)64211637376116515Mouse
11040601Lmr4a_mleishmaniasis resistance 4a (mouse)64211637376116515Mouse
11533915Mts4_mmammary tumor susceptibility 4 (mouse)64211637376116515Mouse
12910785Pwgrq16_mpost-weaning growth rate QTL 16 (mouse)64382681377811523Mouse
12910798Pwgrq5_mpre-weaning growth rate QTL 5 (mouse)64382681377811523Mouse
12910802Pwbwq12_mpost-weaning body weight QTL 12 (mouse)64382681377811523Mouse
12910807Pwbwq11_mpost-weaning body weight QTL 11 (mouse)64382681377811523Mouse
12910809Pwbwq10_mpost-weaning body weight QTL 10 (mouse)64382681377811523Mouse
12910820Ogrq3_moverall growth rate QTL 3 (mouse)64382681377811523Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64531405987426034Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
4140983Srilp_msleep response to influenza, light phase (mouse)Not determined4872655675447710Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65117915085179300Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5437342788379171Mouse
15039373Adip28_madiposity 28 (mouse)65630821190308211Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65630821190308211Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
4141990Etax6_methanol induced ataxia 6 (mouse)Not determined7132262186275719Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:366
Count of miRNA genes:300
Interacting mature miRNAs:329
Transcripts:ENSMUST00000070345, ENSMUST00000154799
Prediction methods: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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006506216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017321609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC116115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK010443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK018595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK033105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK045062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK088354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK165625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK167668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK168003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK182709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK184796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK191104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK201881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK202971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK206422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK211034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK211359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK211395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK216737 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC026983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000070345   ⟹   ENSMUSP00000064515
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl672,318,678 - 72,345,184 (-)Ensembl
RefSeq Acc Id: ENSMUST00000154799
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl672,321,300 - 72,333,368 (-)Ensembl
RefSeq Acc Id: ENSMUST00000206262   ⟹   ENSMUSP00000145792
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl672,336,260 - 72,342,968 (-)Ensembl
RefSeq Acc Id: NM_138592   ⟹   NP_613058
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39672,295,659 - 72,322,158 (-)NCBI
GRCm38672,318,676 - 72,345,175 (-)NCBI
MGSCv37672,268,670 - 72,295,169 (-)RGD
Celera674,408,796 - 74,435,299 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506216   ⟹   XP_006506279
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39672,295,749 - 72,322,190 (-)NCBI
GRCm38672,318,766 - 72,345,208 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017321609   ⟹   XP_017177098
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39672,295,749 - 72,322,171 (-)NCBI
GRCm38672,318,766 - 72,345,190 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_613058   ⟸   NM_138592
- UniProtKB: Q3TIX9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006506279   ⟸   XM_006506216
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017177098   ⟸   XM_017321609
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000064515   ⟸   ENSMUST00000070345
RefSeq Acc Id: ENSMUSP00000145792   ⟸   ENSMUST00000206262
Protein Domains
USP

Promoters
RGD ID:6840138
Promoter ID:MM_KWN:46451
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:OTTMUST00000057291
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36672,295,001 - 72,295,501 (-)MPROMDB
RGD ID:6890006
Promoter ID:EPDNEW_M8454
Type:initiation region
Name:Usp39_1
Description:Mus musculus ubiquitin specific peptidase 39 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38672,345,163 - 72,345,223EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:107622 AgrOrtholog
Ensembl Genes ENSMUSG00000056305 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSMUSG00000104250 UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000064515 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000141203 UniProtKB/Swiss-Prot
  ENSMUSP00000145792 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000070345 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000193449 UniProtKB/Swiss-Prot
  ENSMUST00000206262 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Papain-like_cys_pep_sf UniProtKB/Swiss-Prot
  Peptidase_C19_UCH UniProtKB/Swiss-Prot
  USP39 UniProtKB/Swiss-Prot
  USP_dom UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_UBP UniProtKB/Swiss-Prot
KEGG Report mmu:28035 UniProtKB/Swiss-Prot
MGD MGI:107622 ENTREZGENE
NCBI Gene 28035 ENTREZGENE
PANTHER PTHR21646:SF16 UniProtKB/Swiss-Prot
Pfam UCH UniProtKB/Swiss-Prot
  zf-UBP UniProtKB/Swiss-Prot
PhenoGen Usp39 PhenoGen
PROSITE USP_3 UniProtKB/Swiss-Prot
  ZF_UBP UniProtKB/Swiss-Prot
SMART ZnF_UBP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54001 UniProtKB/Swiss-Prot
UniProt A0A0U1RP18_MOUSE UniProtKB/TrEMBL
  Q3TIX9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3TI55 UniProtKB/Swiss-Prot
  Q8BLI5 UniProtKB/Swiss-Prot
  Q8BZZ5 UniProtKB/Swiss-Prot
  Q9CQR1 UniProtKB/Swiss-Prot