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[173977_at] Ubiquitin carboxyl-terminal hydrolases family 2

Description C63695 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y106G6H.12 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C63695 /WB_GENE_ID=Y106G6H.12 /WP=CE20421 /CHR=1 /FEA=Genomic Cluster /DEF=Ubiquitin carboxyl-terminal hydrolases family 2; C.elegans cDNA clone yk354a9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 93      6grp_high1_10_10 > 48      4grp_highest_8_8 > 61      4grp_high_8_8 > 17      6grp_highest_nonorm > 83      6grp_total > 38      4grp_total > 30      6grp_highest_sub > Cu      6grp_cgc > 18      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 287
1 2 3 4 range
A 294.5
(-2.8)
P 		291.6
(-3)
P 		291.4
(-3)
P 		400.8
(3)
P 		109
B 343.8
(3)
P 		308.4
(1)
P 		237.7
(-3)
P 		257
(-1.9)
P 		106
C 525.1
(3)
P 		376
(-2.4)
P 		360.2
(-3)
P 		391.1
(-1.9)
P 		165
avr 387.8
(3) 		325.3
(-1.1) 		296.4
(-3) 		349.6
(0.5) 		91

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 566
1 2 3 4 5 6 range
A 861.6
(3)
P 		587.9
(-0.1)
P 		508.4
(-1)
P 		328.8
(-3)
P 		670.6
(0.8)
P 		667.6
(0.8)
P 		533
B 631.3
(0.7)
P 		564
(-0)
P 		296.1
(-3)
P 		519
(-0.5)
P 		379.4
(-2.1)
P 		835
(3)
P 		539
C 452.3
(1.9)
P 		488.3
(3)
P 		295.2
(-3)
P 		351.4
(-1.3)
P 		426.2
(1.1)
P 		384
(-0.2)
P 		193
avr 648.4
(3) 		546.7
(0.8) 		366.6
(-3) 		399.7
(-2.3) 		492.1
(-0.3) 		628.9
(2.6) 		282
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 107.2
(3)
P 		63.3
(-2.4)
P 		76.2
(-0.8)
P 		58.7
(-3)
P 		49
B 109.7
(3)
P 		76.2
(-0.7)
P 		55.1
(-3)
P 		54.8
(-3)
P 		55
C 173.8
(3)
P 		108.1
(-0.7)
P 		125.5
(0.3)
P 		65.9
(-3)
P 		108
avr 130.2
(3) 		82.5
(-1.1) 		85.6
(-0.8) 		59.8
(-3) 		70

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 241
1 2 3 4 5 6 range
A 158.8
(0.6)
P 		209.1
(3)
P 		110.7
(-1.7)
P 		83.4
(-3)
P 		202.4
(2.7)
P 		162.5
(0.8)
P 		126
B 219.6
(0.7)
P 		187.7
(-0.1)
P 		71.9
(-3)
P 		137.5
(-1.4)
P 		154.1
(-0.9)
P 		311.4
(3)
P 		240
C 167.7
(3)
P 		149
(1.8)
P 		75.1
(-2.7)
P 		70.7
(-3)
P 		137.9
(1.2)
P 		128.6
(0.6)
P 		97
avr 182
(2) 		181.9
(2) 		85.9
(-3) 		97.2
(-2.4) 		164.8
(1.1) 		200.8
(3) 		115
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173977_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22605
Sequence Type Exemplar sequence
Representative Public ID C63695 NCBI
Target Description C63695 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y106G6H.12 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C63695 /WB_GENE_ID=Y106G6H.12 /WP=CE20421 /CHR=1 /FEA=Genomic Cluster /DEF=Ubiquitin carboxyl-terminal hydrolases family 2; C.elegans cDNA clone yk354a9 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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
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:10472408-10479051(-) 99.97 100.0
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 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
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-15
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.0E-20
Sequence
Target Sequence 
>C. ELEGANS:173977_AT
atgttacattatattcccactcaaagatttctattcgatatccttttttacttcattaat
cctttgaatatacccattttttgtctttcaacagtttccctacagtatttcccttgtttt
tctcttttttttctaactactgtaacaaatggtatttctttcccgtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTTACATTATATTCCCACTCAAA 52 47 2987 Antisense
TATTCCCACTCAAAGATTTCTATTC 196 665 2998 Antisense
AAAGATTTCTATTCGATATCCTTTT 681 121 3009 Antisense
TTCGATATCCTTTTTTACTTCATTA 668 695 3020 Antisense
TATCCTTTTTTACTTCATTAATCCT 406 657 3025 Antisense
TAATCCTTTGAATATACCCATTTTT 362 633 3043 Antisense
TTTGTCTTTCAACAGTTTCCCTACA 701 665 3066 Antisense
TCAACAGTTTCCCTACAGTATTTCC 570 627 3074 Antisense
TACAGTATTTCCCTTGTTTTTCTCT 693 641 3087 Antisense
TTTTTTCTAACTACTGTAACAAATG 517 673 3113 Antisense
TAACAAATGGTATTTCTTTCCCGTG 50 639 3129 Antisense
Sequence Source Affymetrix Proprietary Database