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[189727_at] ubiquitin protease

Description F09D1.1 /REP_DB=WormBase Gene ID /WP=CE20660 /TR=O44787 /GB=AAD34652.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=ubiquitin protease
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 48      4grp_highest_8_8 > 32      4grp_high_8_8 > 51      6grp_highest_nonorm > 84      6grp_total > 48      4grp_total > 61      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 443
1 2 3 4 range
A 689.4
(3)
P 		662
(2.4)
P 		622.4
(1.7)
P 		391.1
(-3)
P 		298
B 675.7
(3)
P 		616.9
(2)
P 		584.5
(1.4)
P 		328.2
(-3)
P 		348
C 716.9
(2.8)
P 		731.6
(3)
P 		649.8
(1.9)
P 		288.7
(-3)
P 		443
avr 694
(3) 		670.2
(2.6) 		618.9
(1.7) 		336
(-3) 		358

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 319
1 2 3 4 5 6 range
A 678.1
(3)
P 		522.7
(-0.7)
P 		462.9
(-2.2)
P 		428.1
(-3)
P 		584.8
(0.8)
P 		655.9
(2.5)
P 		250
B 747
(3)
P 		585.2
(-2.4)
P 		589.8
(-2.2)
P 		566
(-3)
P 		607.5
(-1.6)
P 		706.9
(1.7)
P 		181
C 670.1
(0.6)
P 		638.9
(-0.7)
P 		614.4
(-1.7)
P 		616.6
(-1.7)
P 		584.1
(-3)
P 		728.9
(3)
P 		145
avr 698.4
(3) 		582.3
(-1.3) 		555.7
(-2.3) 		536.9
(-3) 		592.1
(-0.9) 		697.2
(3) 		162
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 202
1 2 3 4 range
A 251
(3)
P 		143.7
(-0.3)
P 		162.7
(0.3)
P 		57.2
(-3)
P 		194
B 215.5
(3)
P 		152.4
(0.4)
P 		135.5
(-0.3)
P 		69.9
(-3)
P 		146
C 237.3
(3)
P 		210.3
(2.1)
P 		226.5
(2.7)
P 		48.7
(-3)
P 		189
avr 234.6
(3) 		168.8
(0.8) 		174.9
(1) 		58.6
(-3) 		176

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 125
(-1.3)
P 		185.9
(3)
P 		100.8
(-3)
P 		108.6
(-2.5)
P 		176.5
(2.3)
P 		159.7
(1.2)
P 		85
B 259.9
(2.8)
P 		194.8
(-0.4)
P 		143.2
(-3)
P 		149.9
(-2.7)
P 		246.8
(2.2)
P 		263.6
(3)
P 		120
C 248.4
(3)
P 		195
(0.4)
P 		156.4
(-1.4)
P 		124
(-3)
P 		189
(0.1)
P 		244
(2.8)
P 		124
avr 211.1
(2.3) 		191.9
(1.1) 		133.5
(-2.6) 		127.5
(-3) 		204.1
(1.8) 		222.4
(3) 		95
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189727_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4259
Sequence Type Exemplar sequence
Representative Public ID F09D1.1 NCBI
Target Description F09D1.1 /REP_DB=WormBase Gene ID /WP=CE20660 /TR=O44787 /GB=AAD34652.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=ubiquitin protease
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_061897(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061897 NCBI Caenorhabditis elegans F09D1.1 (F09D1.1) mRNA, complete cds. 11/11 None
F09D1.1 ENSEMBL cdna:known chromosome:CEL140:II:2565276:2575904:1 gene:F09D1.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000001656 8/11 Cross Hyb Matching Probes None
GENEFINDER00000001668 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:2565275-2575807(+) 100.0 100.0
Public Domain and Genome References
Gene Title ubiquitin protease
Ensembl F09D1.1
Entrez Gene 173606 Entrez gene
SwissProt O44787 EMBL-EBI
WormBase CE20660 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:19185_S_AT ubiquitin carboxyl-terminal hydrolase family protein at
ATH1-121501:254353_S_AT ubiquitin carboxyl-terminal hydrolase family protein at
CANINE_2:CFA.2594.1.A1_AT similar to ubiquitin specific protease 39 cfa
CANINE_2:CFAAFFX.12360.1.S1_AT similar to ubiquitin specific protease 39 cfa
DROSOPHILA_2:1636587_AT dm
DROSGENOME1:151702_R_AT dm
DROSGENOME1:151701_S_AT dm
HG-U133_PLUS_2:217829_S_AT ubiquitin specific peptidase 39 hs
HG-U133A:217829_S_AT ubiquitin specific peptidase 39 hs
HG-FOCUS:217829_S_AT ubiquitin specific peptidase 39 hs
HG-U133A_2:217829_S_AT ubiquitin specific peptidase 39 hs
HU35KSUBA:AA007264_AT ubiquitin specific peptidase 39 hs
HU35KSUBA:RC_AA598988_AT ubiquitin specific peptidase 39 hs
U133_X3P:G5730024_3P_A_AT ubiquitin specific peptidase 39 hs
HG-U95C:48911_AT ubiquitin specific peptidase 39 hs
HG-U95D:67297_AT ubiquitin specific peptidase 39 hs
MU11KSUBA:AA271181_S_AT ubiquitin specific peptidase 39 mm
MG-U74AV2:96646_AT ubiquitin specific peptidase 39 mm
MG-U74AV2:161242_F_AT ubiquitin specific peptidase 39 mm
MOE430A:1460209_AT ubiquitin specific peptidase 39 mm
MOUSE430A_2:1460209_AT ubiquitin specific peptidase 39 mm
MOUSE430_2:1460209_AT ubiquitin specific peptidase 39 mm
MOE430A:1437007_X_AT ubiquitin specific peptidase 39 mm
MOUSE430A_2:1437007_X_AT ubiquitin specific peptidase 39 mm
MOUSE430_2:1437007_X_AT ubiquitin specific peptidase 39 mm
MU19KSUBB:TC31363_AT Ubiquitin specific peptidase 39 (Usp39), mRNA mm
MU19KSUBC:TC37572_AT Ubiquitin specific peptidase 39 (Usp39), mRNA mm
RG-U34B:RC_AI012467_AT ubiquitin specific protease 39 (predicted) rn
RG-U34B:RC_AI044269_AT ubiquitin specific protease 39 (predicted) rn
RAE230A:1389344_AT ubiquitin specific protease 39 (predicted) rn
RAT230_2:1389344_AT ubiquitin specific protease 39 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6511 ubiquitin-dependent protein catabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4197 cysteine-type endopeptidase activity inferred from electronic annotation QuickGO AmiGO
4221 ubiquitin thiolesterase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAD34652 Hypothetical protein F09D1.1 [Caenorhabditis elegans] ref|NP_494298.1| F09D1.1 [Caenorhabditis elegans] 0.0
blast CAE60688 Hypothetical protein CBG04341 [Caenorhabditis briggsae] 0.0
blast NP_006581 ubiquitin specific protease 39 [Homo sapiens] gb|AAH67273.1| USP39 protein [Homo sapiens] 1.0E-174
Protein Domains
Database ID Description E-Value
Pfam IPR001607 EMBL-EBI Zn-finger in ubiquitin thiolesterase 1.2E-13
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-17
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 4.2E-10
Sequence
Target Sequence 
>C. ELEGANS:189727_AT
ttgtacctaactctggatcttccatcggctccactctatcgtgatgttcaactgcagaac
attattccacaagtaccactgagcactttattggagaaatttgatggaaaaactgagaag
gaatacccaacgtacaacgacaataatatcatgaaacgcttcgaattgctacaactaccc
gattttctcataatcacctacaaaagattccagaaaaatcagtggttcgtcgaaaaaaac
ccgactatcgtcaattttcccattgcgaacgttgatttttacgattgcctggctaaggat
gcccgtgctaatcataaatacactacgtatgatcttgtggcaaatgtcgtacacgaagga
acttttaaagatggaaattatcgaattcagattgttcatgagggctccggaaaatggttt
gaactcgaggatttgcacgtgaaggaccttttgccgcagatgattgtgctcgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGTACCTAACTCTGGATCTTCCAT 691 699 1267 Antisense
GGCTCCACTCTATCGTGATGTTCAA 367 539 1293 Antisense
TATTCCACAAGTACCACTGAGCACT 515 665 1329 Antisense
GAAACGCTTCGAATTGCTACAACTA 220 359 1419 Antisense
CTACAACTACCCGATTTTCTCATAA 275 227 1435 Antisense
ACCCGACTATCGTCAATTTTCCCAT 93 91 1505 Antisense
AATTTTCCCATTGCGAACGTTGATT 212 175 1519 Antisense
GATTTTTACGATTGCCTGGCTAAGG 250 427 1540 Antisense
GCTAAGGATGCCCGTGCTAATCATA 197 303 1558 Antisense
GAAGGACCTTTTGCCGCAGATGATT 461 333 1707 Antisense
TTTGCCGCAGATGATTGTGCTCGCC 278 669 1716 Antisense
Sequence Source Affymetrix Proprietary Database