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[194081_at] Ubiquitin carboxyl-terminal hydrolase

Description F38B7.5 /REP_DB=WormBase Gene ID /WP=CE05829 /TR=Q20150 /GB=CAA98471.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ubiquitin carboxyl-terminal hydrolases family 2, Ubiquitin carboxyl-terminal hydrolases family 2
Cluster 6grp_high1_10_10 > 87      4grp_high_8_8 > 0      6grp_total > 87      4grp_total > 18      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 113
1 2 3 4 range
A 102.3
(-2.8)
M 		179.3
(3)
A 		133
(-0.5)
P 		100
(-3)
P 		79
B 140.4
(3)
P 		98.3
(-3)
A 		104.7
(-2.1)
P 		122.9
(0.5)
P 		42
C 89.4
(-3)
M 		93.3
(-2.8)
P 		96.4
(-2.6)
A 		202.8
(3)
P 		113
avr 110.7
(-3) 		123.6
(-0.5) 		111.4
(-2.9) 		141.9
(3) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 315
1 2 3 4 5 6 range
A 74.7
(-3)
A 		101.2
(-2.4)
P 		124
(-2)
P 		121.1
(-2)
P 		232.4
(0.3)
P 		357.7
(3)
P 		283
B 127.5
(-2.4)
P 		98.9
(-3)
P 		145.8
(-2)
P 		183.4
(-1.3)
P 		233.9
(-0.2)
P 		389.8
(3)
P 		291
C 121
(-3)
P 		142.3
(-2.2)
P 		158.9
(-1.6)
P 		140.4
(-2.3)
P 		187
(-0.5)
P 		281.4
(3)
P 		160
avr 107.7
(-3) 		114.1
(-2.8) 		142.9
(-2.1) 		148.3
(-2) 		217.8
(-0.2) 		343
(3) 		235
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 37.3
(2.6)
M 		38.9
(3)
A 		34.8
(2)
P 		14.6
(-3)
P 		24
B 44.8
(3)
P 		24.3
(-3)
A 		24.3
(-3)
P 		26.2
(-2.4)
P 		21
C 29.6
(-0.7)
M 		26.8
(-3)
P 		33.6
(2.5)
A 		34.2
(3)
P 		7
avr 37.2
(3) 		30
(-0.5) 		30.9
(-0.1) 		25
(-3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 132
1 2 3 4 5 6 range
A 13.8
(-3)
A 		36
(-1.2)
P 		27
(-1.9)
P 		30.7
(-1.6)
P 		70.1
(1.6)
P 		87.1
(3)
P 		73
B 44.4
(-2.4)
P 		32.9
(-3)
P 		35.4
(-2.9)
P 		48.6
(-2.2)
P 		95
(0.3)
P 		145.4
(3)
P 		113
C 44.8
(-1.5)
P 		43.4
(-1.6)
P 		40.4
(-1.9)
P 		28.2
(-3)
P 		60.5
(-0.1)
P 		94.2
(3)
P 		66
avr 34.3
(-3) 		37.4
(-2.8) 		34.3
(-3) 		35.8
(-2.9) 		75.2
(0.3) 		108.9
(3) 		75
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194081_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12619
Sequence Type Exemplar sequence
Representative Public ID F38B7.5 NCBI
Target Description F38B7.5 /REP_DB=WormBase Gene ID /WP=CE05829 /TR=Q20150 /GB=CAA98471.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ubiquitin carboxyl-terminal hydrolases family 2, 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_073530(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073530 NCBI Caenorhabditis elegans Deubiquitylating with USP/UBP and OTU domains family member (duo-1) (duo-1) mRNA, complete cds. 11/11 None
SNAP00000015624 ENSEMBL cdna:SNAP chromosome:CEL140:V:11557391:11560527:1 11/11 None
GENEFINDER00000015630 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11555268:11562470:1 11/11 None
F38B7.5 ENSEMBL cdna:known chromosome:CEL140:V:11557391:11560650:1 gene:F38B7.5 11/11 None
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
chrV:11557390-11560527(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ubiquitin carboxyl-terminal hydrolase
Gene Symbol duo-1
Ensembl F38B7.5
Entrez Gene 179586 Entrez gene
SwissProt Q8IU19 EMBL-EBI
WormBase CE33394 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 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] 0.0
blast T21950 hypothetical protein F38B7.5 - Caenorhabditis elegans 0.0
blast CAA98472 Hypothetical protein F38B7.4 [Caenorhabditis elegans] ref|NP_505930.2| Serpentine Receptor, class X family member (srx-85) [Caenorhabditis elegans] 1.0E-119
blast AAC19188 Deubiquitylating with usp/ubp and otu domains protein 2 [Caenorhabditis elegans] ref|NP_499864.1| Deubiquitylating with USP/UBP and OTU domains family member (duo-2) [Caenorhabditis elegans] 1.0E-115
Protein Domains
Database ID Description E-Value
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 9.8E-38
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 1.0E-126
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 9.8E-38
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 2.9E-123
Pfam IPR003323 EMBL-EBI Ovarian tumour, otubain 9.8E-38
Pfam IPR003845 EMBL-EBI Protein of unknown function DUF216 1.2E-32
Pfam IPR003845 EMBL-EBI Protein of unknown function DUF216 5.0E-7
Pfam IPR001394 EMBL-EBI Peptidase C19, ubiquitin carboxyl-terminal hydrolase family 2 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000015630 6 22-44,65-82,97-119,126-148,158-177,189-211
Sequence
Target Sequence 
>C. ELEGANS:194081_AT
ggattaccggagttcaatcgcatcatatgatctttcgcgaagcagtcggcaagcatctca
agaagaacgaattaatgttcaaaaagtactgtcataatgagatatacgagaagtacgttg
agaatgcaatgcgtgatggagtttgggcgacaacttgtgaaattttcgctatggccaata
tgctcaacgttgagattataacgtatcttggagatagtggatgggtacctcattccccac
aaaataattatccaccaagaaaaggagctatatatttgaagaatacaaatatgcattatg
agcctacaacttcattgagaaagaattcaccagaaaggtcgccaatgaaaaaagaaaaca
ctaatgggagttcaatgcatgatgagctggatgaaaatgattatttgaaaagcgatattc
atcctggaacatattcattggttgctgtcgtgtgtcatctcggagattcgccaaataaag
gacattatgtagcttatacaaaagaattgtataagaactcaagttggctccgctgctctg
atgataatatatatgctgtttcaaagaacgatgtctccgaagctatccgatcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATTACCGGAGTTCAATCGCATCA 114 509 1733 Antisense
AATGCGTGATGGAGTTTGGGCGACA 74 165 1860 Antisense
TTCGCTATGGCCAATATGCTCAACG 359 691 1897 Antisense
TAGTGGATGGGTACCTCATTCCCCA 215 653 1947 Antisense
ATATGCATTATGAGCCTACAACTTC 182 21 2021 Antisense
AAAGCGATATTCATCCTGGAACATA 235 125 2141 Antisense
CATATTCATTGGTTGCTGTCGTGTG 222 215 2162 Antisense
TGCTGTCGTGTGTCATCTCGGAGAT 664 581 2175 Antisense
TAAGAACTCAAGTTGGCTCCGCTGC 11 637 2244 Antisense
GCTCCGCTGCTCTGATGATAATATA 459 299 2259 Antisense
CGATGTCTCCGAAGCTATCCGATCG 232 249 2301 Antisense
Sequence Source Affymetrix Proprietary Database