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[185129_at]

Description Y48C3A.15 /REP_DB=WormBase Gene ID /WP=CE24381 /TR=Q9U288 /GB=CAB60422.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 38      6grp_total > 38      4grp_total > 53      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 181
1 2 3 4 range
A 209.8
(3)
P 		186.4
(2)
P 		171.2
(1.4)
P 		62.6
(-3)
A 		147
B 153.4
(1.2)
P 		177.6
(3)
P 		162.1
(1.8)
P 		98.8
(-3)
A 		79
C 243.9
(3)
P 		202.7
(1)
P 		138.9
(-2.1)
P 		119.5
(-3)
A 		124
avr 202.4
(3) 		188.9
(2.3) 		157.4
(0.5) 		93.6
(-3) 		109

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 138
1 2 3 4 5 6 range
A 172.8
(3)
P 		120.3
(-0.7)
P 		87.6
(-3)
P 		107.9
(-1.6)
P 		106.7
(-1.7)
P 		156.5
(1.9)
A 		85
B 159.7
(2.7)
P 		150.8
(1.9)
P 		106.1
(-1.9)
P 		163.1
(3)
P 		92.9
(-3)
P 		153
(2.1)
P 		70
C 225.4
(3)
P 		101.6
(-3)
P 		132.7
(-1.5)
P 		121.2
(-2.1)
A 		150.4
(-0.6)
P 		144.5
(-0.9)
P 		124
avr 186
(3) 		124.2
(-1.8) 		108.8
(-3) 		130.7
(-1.3) 		116.7
(-2.4) 		151.3
(0.3) 		77
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 76.4
(3)
P 		40.5
(-0.2)
P 		44.7
(0.2)
P 		9.2
(-3)
A 		67
B 48.9
(3)
P 		43.9
(1.9)
P 		37.6
(0.6)
P 		21.1
(-3)
A 		28
C 80.8
(3)
P 		58.3
(0.8)
P 		48.4
(-0.2)
P 		20.2
(-3)
A 		61
avr 68.7
(3) 		47.6
(0.6) 		43.6
(0.1) 		16.8
(-3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 64
1 2 3 4 5 6 range
A 31.9
(0.2)
P 		42.8
(3)
P 		19.1
(-3)
P 		27.4
(-0.9)
P 		32.2
(0.3)
P 		38.1
(1.8)
A 		24
B 55.6
(2.7)
P 		50.2
(1.7)
P 		25.8
(-3)
P 		43.2
(0.3)
P 		37.8
(-0.7)
P 		57.1
(3)
P 		31
C 83.5
(3)
P 		31
(-2.3)
P 		33.8
(-2)
P 		24.4
(-3)
A 		48.7
(-0.5)
P 		48.4
(-0.6)
P 		59
avr 57
(3) 		41.3
(-0.1) 		26.2
(-3) 		31.7
(-1.9) 		39.6
(-0.4) 		47.9
(1.2) 		31
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 185129_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3651
Sequence Type Exemplar sequence
Representative Public ID Y48C3A.15 NCBI
Target Description Y48C3A.15 /REP_DB=WormBase Gene ID /WP=CE24381 /TR=Q9U288 /GB=CAB60422.1 /SUBMIT=HINXTON /CHR=2 /FEA=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_064421(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064421 NCBI Caenorhabditis elegans Y48C3A.14 (Y48C3A.14) mRNA, complete cds. 10/11 A 
GENEFINDER00000006662 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13389657:13401941:1 9/11 None
Y48C3A.14 ENSEMBL cdna:known chromosome:CEL140:II:13389657:13401888:1 gene:Y48C3A.14 10/11 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
chrII:13397020-13401541(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y48C3A.14
Entrez Gene 174978 Entrez gene
SwissProt Q9U286 EMBL-EBI
WormBase CE32972 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:20100_AT DNA topoisomerase family protein at
ATH1-121501:265727_AT DNA topoisomerase family protein at
CANINE:1596202_AT similar to topoisomerase (DNA) III beta cfa
CANINE:1585434_AT similar to topoisomerase (DNA) III beta cfa
CANINE_2:CFA.11606.1.A1_S_AT similar to topoisomerase (DNA) III beta cfa
DROSOPHILA_2:1634282_S_AT Topoisomerase 3 dm
DROSOPHILA_2:1629218_AT Topoisomerase 3 dm
DROSGENOME1:144107_AT Topoisomerase 3 dm
CHICKEN:GGA.16362.1.S1_S_AT topoisomerase (DNA) III beta gga
CHICKEN:GGA.3414.1.S1_AT topoisomerase (DNA) III beta gga
CHICKEN:GGAAFFX.12316.1.S1_AT topoisomerase (DNA) III beta gga
HG-U133_PLUS_2:215781_S_AT topoisomerase (DNA) III beta hs
HG-U133A_2:215781_S_AT topoisomerase (DNA) III beta hs
HG-U133A:215781_S_AT topoisomerase (DNA) III beta hs
HG-U133A_2:213660_S_AT topoisomerase (DNA) III beta hs
HG-U133_PLUS_2:213660_S_AT topoisomerase (DNA) III beta hs
HG-U133A:213660_S_AT topoisomerase (DNA) III beta hs
HU35KSUBC:RC_Z41412_AT topoisomerase (DNA) III beta hs
HUGENEFL:D87012_AT topoisomerase (DNA) III beta hs
U133_X3P:HS.66191.0.A1_3P_S_AT topoisomerase (DNA) III beta hs
U133_X3P:HS.66191.0.A1_3P_AT topoisomerase (DNA) III beta hs
U133_X3P:213660_3P_S_AT topoisomerase (DNA) III beta hs
HG-U95AV2:32360_S_AT topoisomerase (DNA) III beta hs
HG-U95AV2:32361_S_AT topoisomerase (DNA) III beta hs
HG-U95AV2:32362_R_AT topoisomerase (DNA) III beta hs
HG-U95AV2:40324_R_AT topoisomerase (DNA) III beta hs
HG-U95D:68746_AT Topoisomerase (DNA) III beta hs
MOUSE430_2:1438387_X_AT topoisomerase (DNA) III beta mm
MOE430A:1438387_X_AT topoisomerase (DNA) III beta mm
MOUSE430A_2:1438387_X_AT topoisomerase (DNA) III beta mm
MU11KSUBB:MSA.24673.0_S_AT topoisomerase (DNA) III beta mm
MG-U74AV2:103823_AT topoisomerase (DNA) III beta mm
MOE430A:1456009_X_AT topoisomerase (DNA) III beta mm
MOUSE430A_2:1456009_X_AT topoisomerase (DNA) III beta mm
MOUSE430_2:1456009_X_AT topoisomerase (DNA) III beta mm
MOE430A:1448173_A_AT topoisomerase (DNA) III beta mm
MOUSE430A_2:1448173_A_AT topoisomerase (DNA) III beta mm
MOUSE430_2:1448173_A_AT topoisomerase (DNA) III beta mm
RG-U34C:RC_AI233765_AT topoisomerase (DNA) III beta (predicted) rn
RAE230A:1373553_AT topoisomerase (DNA) III beta (predicted) rn
RAT230_2:1373553_AT topoisomerase (DNA) III beta (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6265 DNA topological change inferred from electronic annotation QuickGO AmiGO
6268 DNA unwinding during replication inferred from electronic annotation QuickGO AmiGO
6304 DNA modification inferred from electronic annotation QuickGO AmiGO
6306 DNA methylation inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3916 DNA topoisomerase activity inferred from electronic annotation QuickGO AmiGO
3917 DNA topoisomerase type I activity inferred from electronic annotation QuickGO AmiGO
8170 N-methyltransferase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB60424 Hypothetical protein Y48C3A.14 [Caenorhabditis elegans] ref|NP_496822.2| Y48C3A.14 [Caenorhabditis elegans] 0.0
blast T31599 hypothetical protein Y48C3A.q - Caenorhabditis elegans 0.0
blast CAE73354 Hypothetical protein CBG20786 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 2.3E-36
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 3.1E-30
Pfam IPR006171 EMBL-EBI TOPRIM 1.3E-16
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 1.2E-73
Sequence
Target Sequence 
>C. ELEGANS:185129_AT
actctactgtccgacgtgtcaggagacgtatgcggtgccgaatttcaaggatggggtgct
taaagttattggagatcacaagtgtcctctcgatgattttgatgtcattttgtatcaggg
tcccggcggaaaacttgcccgaacattcaccctctgcccattctgcttcaacaatccacc
attcgaaaaaatgccacaaggagccggttgtgatacttgtgttcatccgtcttgtcagta
ttccattagctcaaacggagtgtgcggttgtcttcaagactgcgggggtgtaatgcttct
cgacactcaatctcatccgaaatggagaatgacatgtaataaatgtccgtcggttgttgg
attatttgaaggagcgattaaagtgaaagtggacagtacgagaagctacaccaccgcttc
agaggtattt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACTCTACTGTCCGACGTGTCAGGAG 710 99 171 Antisense
GTCAGGAGACGTATGCGGTGCCGAA 298 463 188 Antisense
GTGTCCTCTCGATGATTTTGATGTC 225 487 252 Antisense
ATGTCATTTTGTATCAGGGTCCCGG 103 49 272 Antisense
GCGGAAAACTTGCCCGAACATTCAC 82 293 296 Antisense
GGAGCCGGTTGTGATACTTGTGTTC 140 523 370 Antisense
TCATCCGTCTTGTCAGTATTCCATT 116 623 393 Antisense
GGAGTGTGCGGTTGTCTTCAAGACT 369 517 427 Antisense
ACTGCGGGGGTGTAATGCTTCTCGA 331 99 449 Antisense
TTCTCGACACTCAATCTCATCCGAA 145 693 467 Antisense
CTACACCACCGCTTCAGAGGTATTT 667 225 576 Antisense
Sequence Source Affymetrix Proprietary Database