Human Gene USP38 (uc003ijb.3) Description and Page Index
  Description: Homo sapiens ubiquitin specific peptidase 38 (USP38), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:144,106,070-144,143,141 Size: 37,072 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr4:144,106,604-144,141,609 Size: 35,006 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:144,106,070-144,143,141)mRNA (may differ from genome)Protein (1042 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: UBP38_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 38; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 38; AltName: Full=HP43.8KD; AltName: Full=Ubiquitin thioesterase 38; AltName: Full=Ubiquitin-specific-processing protease 38;
FUNCTION: Deubiquitinating enzyme exhibiting a preference towards 'Lys-63'-linked Ubiquitin chains.
CATALYTIC ACTIVITY: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C- terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
TISSUE SPECIFICITY: Highly expressed in skeletal muscle. Expressed in adrenal gland.
SIMILARITY: Belongs to the peptidase C19 family.
SEQUENCE CAUTION: Sequence=AAK26248.1; Type=Erroneous initiation; Sequence=BAB71627.1; Type=Erroneous initiation; Sequence=BAC03730.1; Type=Miscellaneous discrepancy; Note=The absence of the residues from Tyr-840 to Ser-871 is not the result of an alternative splicing;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): USP38
CDC HuGE Published Literature: USP38
Positive Disease Associations: Iron
Related Studies:
  1. Iron
    , , . [PubMed 0]
  2. Iron
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.77 RPKM in Muscle - Skeletal
Total median expression: 157.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -278.10534-0.521 Picture PostScript Text
3' UTR -341.111532-0.223 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018200 - Pept_C19ubi-hydrolase_C_CS
IPR001394 - Peptidase_C19

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF13423 - Ubiquitin carboxyl-terminal hydrolase

SCOP Domains:
54001 - Cysteine proteinases

ModBase Predicted Comparative 3D Structure on Q8NB14
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity

Biological Process:
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016579 protein deubiquitination


-  Descriptions from all associated GenBank mRNAs
  LF208165 - JP 2014500723-A/15668: Polycomb-Associated Non-Coding RNAs.
BC039115 - Homo sapiens ubiquitin specific peptidase 38, mRNA (cDNA clone MGC:43052 IMAGE:5258804), complete cds.
JD164402 - Sequence 145426 from Patent EP1572962.
AL833976 - Homo sapiens mRNA; cDNA DKFZp434D2311 (from clone DKFZp434D2311).
AK126943 - Homo sapiens cDNA FLJ44996 fis, clone BRAWH3010657, highly similar to Ubiquitin carboxyl-terminal hydrolase 38 (EC 3.1.2.15).
BC068975 - Homo sapiens ubiquitin specific peptidase 38, mRNA (cDNA clone MGC:70375 IMAGE:6067501), complete cds.
JD106370 - Sequence 87394 from Patent EP1572962.
JD435537 - Sequence 416561 from Patent EP1572962.
JD256376 - Sequence 237400 from Patent EP1572962.
JD458988 - Sequence 440012 from Patent EP1572962.
JD197244 - Sequence 178268 from Patent EP1572962.
JD126153 - Sequence 107177 from Patent EP1572962.
JD227725 - Sequence 208749 from Patent EP1572962.
JD521382 - Sequence 502406 from Patent EP1572962.
HQ257971 - Synthetic construct Homo sapiens clone IMAGE:100072280 ubiquitin specific peptidase 38 (USP38) gene, encodes complete protein.
KJ899815 - Synthetic construct Homo sapiens clone ccsbBroadEn_09209 USP38 gene, encodes complete protein.
AK093754 - Homo sapiens cDNA FLJ36435 fis, clone THYMU2012024.
AX748288 - Sequence 1813 from Patent EP1308459.
AB067478 - Homo sapiens mRNA for KIAA1891 protein, partial cds.
AK057992 - Homo sapiens cDNA FLJ25263 fis, clone STM05053.
LF373164 - JP 2014500723-A/180667: Polycomb-Associated Non-Coding RNAs.
AK091712 - Homo sapiens cDNA FLJ34393 fis, clone HCHON2000271.
AX747143 - Sequence 668 from Patent EP1308459.
LF373159 - JP 2014500723-A/180662: Polycomb-Associated Non-Coding RNAs.
AF211481 - Homo sapiens HP43.8KD mRNA, complete cds.
LF373157 - JP 2014500723-A/180660: Polycomb-Associated Non-Coding RNAs.
AK093289 - Homo sapiens cDNA FLJ35970 fis, clone TESTI2013231, highly similar to Ubiquitin carboxyl-terminal hydrolase 38 (EC3.1.2.15).
AX748035 - Sequence 1560 from Patent EP1308459.
LF373155 - JP 2014500723-A/180658: Polycomb-Associated Non-Coding RNAs.
JD429909 - Sequence 410933 from Patent EP1572962.
LF373154 - JP 2014500723-A/180657: Polycomb-Associated Non-Coding RNAs.
JD509879 - Sequence 490903 from Patent EP1572962.
JD224038 - Sequence 205062 from Patent EP1572962.
LF373153 - JP 2014500723-A/180656: Polycomb-Associated Non-Coding RNAs.
MA608741 - JP 2018138019-A/180667: Polycomb-Associated Non-Coding RNAs.
MA608736 - JP 2018138019-A/180662: Polycomb-Associated Non-Coding RNAs.
MA608734 - JP 2018138019-A/180660: Polycomb-Associated Non-Coding RNAs.
MA608732 - JP 2018138019-A/180658: Polycomb-Associated Non-Coding RNAs.
MA608731 - JP 2018138019-A/180657: Polycomb-Associated Non-Coding RNAs.
MA608730 - JP 2018138019-A/180656: Polycomb-Associated Non-Coding RNAs.
MA443742 - JP 2018138019-A/15668: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KX93, KIAA1891, NM_032557, NP_115946, Q8NB14, Q8NDF5, Q96DK6, Q96PZ6, Q9BY55, UBP38_HUMAN
UCSC ID: uc003ijb.3
RefSeq Accession: NM_032557
Protein: Q8NB14 (aka UBP38_HUMAN or UB38_HUMAN)
CCDS: CCDS3758.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032557.5
exon count: 10CDS single in 3' UTR: no RNA size: 5195
ORF size: 3129CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6316.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.