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[193706_s_at] Ubiquitin carboxyl-terminal hydrolases family 2

Description Y106G6H.12 /REP_DB=WormBase Gene ID /WP=CE20421 /TR=Q9U2Z6 /GB=CAB63341.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Ubiquitin carboxyl-terminal hydrolases family 2
Cluster 6grp_highest_10_10 > 57      6grp_high1_10_10 > 75      4grp_highest_8_8 > 61      4grp_high_8_8 > 17      6grp_highest_nonorm > 72      6grp_total > 75      4grp_total > 31      6grp_cgc > 66      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 247
1 2 3 4 range
A 452.6
(3)
P 		346.1
(-0.3)
P 		258
(-3)
P 		428.2
(2.2)
P 		195
B 454.6
(3)
P 		341.6
(-1.8)
P 		345
(-1.6)
P 		312.1
(-3)
P 		143
C 413.1
(3)
P 		233.4
(-2.2)
P 		207.7
(-3)
P 		328.3
(0.5)
P 		205
avr 440.1
(3) 		307
(-1.7) 		270.2
(-3) 		356.2
(0) 		170

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 278
1 2 3 4 5 6 range
A 361.4
(-2.9)
P 		476.1
(-0.2)
P 		357.3
(-3)
P 		535.1
(1.3)
P 		408.9
(-1.8)
P 		607.8
(3)
P 		251
B 397.6
(-0.9)
P 		394.5
(-1)
P 		524.8
(3)
P 		450.6
(0.7)
P 		330.2
(-3)
P 		511.6
(2.6)
P 		195
C 399.1
(-3)
P 		456.4
(-0.8)
P 		476.7
(-0)
P 		554.9
(3)
P 		476.9
(-0)
P 		474
(-0.1)
P 		156
avr 386
(-3) 		442.3
(-0.7) 		452.9
(-0.2) 		513.5
(2.3) 		405.3
(-2.2) 		531.1
(3) 		145
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 164.8
(3)
P 		75.1
(-2.3)
P 		67.5
(-2.7)
P 		62.7
(-3)
P 		102
B 145
(3)
P 		84.4
(-1.6)
P 		79.9
(-2)
P 		66.5
(-3)
P 		79
C 136.8
(3)
P 		67.1
(-2.1)
P 		72.4
(-1.7)
P 		55.4
(-3)
P 		81
avr 148.9
(3) 		75.5
(-2) 		73.3
(-2.2) 		61.5
(-3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 124
1 2 3 4 5 6 range
A 66.6
(-3)
P 		169.3
(3)
P 		77.8
(-2.3)
P 		135.7
(1)
P 		123.4
(0.3)
P 		148
(1.8)
P 		103
B 138.3
(-1.4)
P 		131.3
(-2)
P 		127.4
(-2.3)
P 		119.3
(-3)
P 		134.2
(-1.7)
P 		190.8
(3)
P 		72
C 147.9
(1.6)
P 		139.3
(0.5)
P 		121.3
(-1.8)
P 		111.6
(-3)
P 		154.3
(2.4)
P 		158.7
(3)
P 		47
avr 117.6
(-2.1) 		146.6
(1) 		108.8
(-3) 		122.2
(-1.6) 		137.3
(0) 		165.8
(3) 		57
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193706_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1821
Sequence Type Exemplar sequence
Representative Public ID Y106G6H.12 NCBI
Target Description Y106G6H.12 /REP_DB=WormBase Gene ID /WP=CE20421 /TR=Q9U2Z6 /GB=CAB63341.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Ubiquitin carboxyl-terminal hydrolases family 2
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_060335(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060335 NCBI Caenorhabditis elegans Deubiquitylating with USP/UBP and OTU domains family member (duo-3) (duo-3) mRNA, complete cds. 11/11 None
SNAP00000001708 ENSEMBL cdna:SNAP chromosome:CEL140:I:10472720:10476602:-1 11/11 None
GENEFINDER00000001718 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10472720:10479179:-1 11/11 None
Y106G6H.12 ENSEMBL cdna:known chromosome:CEL140:I:10472453:10479179:-1 gene:Y106G6H.12 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:10472650-10479050(-) 100.0 100.0
Public Domain and Genome References
Gene Title Ubiquitin carboxyl-terminal hydrolases family 2
Gene Symbol duo-3
Ensembl Y106G6H.12
Entrez Gene 172925 Entrez gene
SwissProt Q9U2Z6 EMBL-EBI
WormBase CE20421 Wormbase
Functional Annotations
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 CAB63341 Hypothetical protein Y106G6H.12 [Caenorhabditis elegans] ref|NP_492736.1| Deubiquitylating with USP/UBP and OTU domains family member (duo-3) [Caenorhabditis elegans] 0.0
blast T21950 hypothetical protein F38B7.5 - Caenorhabditis elegans 3.0E-78
blast CAA98471 Hypothetical protein F38B7.5 [Caenorhabditis elegans] ref|NP_505931.2| Deubiquitylating with USP/UBP and OTU domains family member (duo-1) [Caenorhabditis elegans] dbj|BAC22611.1| ubiquitin-specific protease [Caenorhabditis elegans] 5.0E-75
blast CAE58947 Hypothetical protein CBG02215 [Caenorhabditis briggsae] 1.0E-74
blast CAE58947 Hypothetical protein CBG02215 [Caenorhabditis briggsae] 1.0E-72
Protein Domains
Database ID Description E-Value
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 5.0E-35
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-20
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 5.0E-35
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 5.8E-13
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-20
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 5.0E-35
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-15
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-20
Sequence
Target Sequence 
>C. ELEGANS:193706_S_AT
tacacatttctatcggatggctggatatgcacatcacctcaaaatagttcaacatctcgc
agtggatcattttatcttgaaaataaggattgccactatgaaccagttctcagtttgaag
aaagatgattcgttgagaagccgaaaaagaagaaacacagatactgaatatacggatgac
aatgaaggcggtggttttaagaaaagaaagcccgatgatgatgcttcacgtaaaccaaga
aatttatcagagtctgaaagaagaagacagcctccacgggatgccgaagacaatggaaat
cattacaagaaaatgaacgcgaacactgatcaaatcgccaaatatcgcctcttcgccgcc
atctgccacattggagaattcccggatagaggtcactacttggcactcactcgtgatctt
tacaatccatcaaaatggcttgattgttcggatgcagtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACACATTTCTATCGGATGGCTGGA 154 643 2404 Antisense
ATGGCTGGATATGCACATCACCTCA 277 53 2420 Antisense
AAATAGTTCAACATCTCGCAGTGGA 237 117 2445 Antisense
GGATTGCCACTATGAACCAGTTCTC 302 509 2490 Antisense
AGCCCGATGATGATGCTTCACGTAA 168 83 2612 Antisense
AGCCTCCACGGGATGCCGAAGACAA 24 83 2672 Antisense
CAAATCGCCAAATATCGCCTCTTCG 490 193 2734 Antisense
CCGCCATCTGCCACATTGGAGAATT 142 263 2759 Antisense
TAGAGGTCACTACTTGGCACTCACT 382 653 2790 Antisense
CACTCACTCGTGATCTTTACAATCC 460 197 2807 Antisense
ATGGCTTGATTGTTCGGATGCAGTT 43 53 2838 Antisense
Sequence Source Affymetrix Proprietary Database