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[188636_at] DNA topoisomerase II

Description R05D3.1 /REP_DB=WormBase Gene ID /WP=CE25068 /GB=AAK21438.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=DNA topoisomerase II
Cluster 6grp_highest_10_10 > 66      6grp_high1_10_10 > 75      4grp_high_8_8 > 03      6grp_highest_nonorm > 91      6grp_total > 66      4grp_total > 13      6grp_highest_sub > Da      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 193
1 2 3 4 range
A 129.1
(-0.7)
P 		76
(-3)
P 		76.6
(-3)
P 		214.3
(3)
P 		138
B 161.1
(-0.2)
P 		84.1
(-2.6)
P 		70
(-3)
P 		263.2
(3)
P 		193
C 186.7
(2.3)
P 		76.8
(-3)
A 		86.2
(-2.5)
P 		200.2
(3)
P 		123
avr 159
(0.3) 		79
(-2.9) 		77.6
(-3) 		225.9
(3) 		148

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 168
1 2 3 4 5 6 range
A 163.4
(-0.7)
P 		226.7
(3)
P 		189.3
(0.8)
P 		199.4
(1.4)
P 		123.8
(-3)
P 		220.8
(2.7)
P 		103
B 189.2
(-1.8)
P 		164.4
(-3)
P 		226.2
(-0.1)
P 		221.4
(-0.3)
P 		187.5
(-1.9)
P 		291.9
(3)
P 		128
C 172
(-0.6)
P 		170.2
(-0.7)
P 		124.1
(-3)
P 		232.9
(2.5)
P 		137.5
(-2.3)
P 		243.4
(3)
P 		119
avr 174.9
(-1.5) 		187.1
(-0.8) 		179.9
(-1.2) 		217.9
(1) 		149.6
(-3) 		252
(3) 		102
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 47
(3)
P 		16.5
(-3)
P 		20
(-2.3)
P 		31.4
(-0.1)
P 		31
B 51.4
(2.3)
P 		20.8
(-2.3)
P 		16.2
(-3)
P 		56.1
(3)
P 		40
C 61.8
(3)
P 		22.1
(-3)
A 		30
(-1.8)
P 		33.8
(-1.2)
P 		40
avr 53.4
(3) 		19.8
(-3) 		22.1
(-2.6) 		40.4
(0.7) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 79
1 2 3 4 5 6 range
A 30.1
(-3)
P 		80.6
(3)
P 		41.2
(-1.7)
P 		50.6
(-0.6)
P 		37.4
(-2.1)
P 		53.8
(-0.2)
P 		51
B 65.8
(-1.8)
P 		54.7
(-3)
P 		54.9
(-3)
P 		58.6
(-2.6)
P 		76.2
(-0.6)
P 		108.8
(3)
P 		54
C 63.7
(0.9)
P 		51.9
(-0.6)
P 		31.6
(-3)
P 		46.8
(-1.2)
P 		44.5
(-1.4)
P 		81.5
(3)
P 		50
avr 53.2
(-1.4) 		62.4
(0.1) 		42.6
(-3) 		52
(-1.5) 		52.7
(-1.4) 		81.4
(3) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188636_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7674
Sequence Type Exemplar sequence
Representative Public ID R05D3.1 NCBI
Target Description R05D3.1 /REP_DB=WormBase Gene ID /WP=CE25068 /GB=AAK21438.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=DNA topoisomerase II
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_066448(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066448 NCBI Caenorhabditis elegans R05D3.1 (R05D3.1) mRNA, complete cds. 10/11 None
SNAP00000035981 ENSEMBL cdna:SNAP chromosome:CEL140:III:8375215:8387369:1 10/11 None
GENEFINDER00000035994 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8385285:8387369:1 10/11 None
R05D3.1 ENSEMBL cdna:known chromosome:CEL140:III:8381631:8387414:1 gene:R05D3.1 10/11 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
chrIII:8381118-8387365(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA topoisomerase II
Ensembl R05D3.1
Entrez Gene 176184 Entrez gene
SwissProt P34534 EMBL-EBI
WormBase CE31047 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6259 DNA metabolism inferred from electronic annotation QuickGO AmiGO
6265 DNA topological change inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3918 DNA topoisomerase (ATP-hydrolyzing) activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAM54162 Hypothetical protein R05D3.1 [Caenorhabditis elegans] ref|NP_498849.2| R05D3.1 [Caenorhabditis elegans] sp|P34534|TOP2M_CAEEL Putative DNA topoisomerase II, mitochondrial precursor 0.0
blast S44861 DNA topoisomerase II - Caenorhabditis elegans 0.0
blast CAE71273 Hypothetical protein CBG18156 [Caenorhabditis briggsae] 0.0
blast AAK21437 Hypothetical protein R05D3.11 [Caenorhabditis elegans] ref|NP_498848.1| R05D3.11 [Caenorhabditis elegans] sp|P34544|YNCA_CAEEL Hypothetical protein R05D3.11 in chromosome III 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 3.4E-45
Pfam IPR007728 EMBL-EBI Pre-SET 1.5E-49
Pfam IPR001739 EMBL-EBI Methyl-CpG binding 1.1E-27
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.8E-12
Pfam IPR001214 EMBL-EBI Nuclear protein SET 3.1E-37
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 6.1E-31
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 9.9E-10
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 9.0E-41
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 3.4E-45
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.4E-6
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 2.2E-47
Sequence
Target Sequence 
>C. ELEGANS:188636_AT
aatcgtcacgatttctacaaaagagcaactcggatcttctgaattatttcaaacttcgga
caagcttaacagaaaatcgagtgttgtttgatagaaatggagaattgaaagaattcggaa
atatttcggaaatcgctgccgaattttttgaagttcgcagagatctttatgaaaaacggc
tgaaaattcaaaaagaggaatgtgaagcaaaactgatatatgttgaaaatcagctcaatt
tcatcgaaatggtgaccaatggaactattgagatacgatcaatgggacgtaatcaattgg
aagaaaaacttcaggaaatgggtttcagagttgatcctatggcaactattgctaagaact
ccaaaaaagtaaatttaatcaattatgaagactttcaatatctgaattttcaggcaaact
acggataccttcttgaaatgccggtctcacgactaacttctgatgaaatgaaaagattgg
aagaacgaaaatcacgacggagaactgagcttgaagcagctgaatctgcagattggaaat
ctgtgtggcgttccgaattggac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATCGTCACGATTTCTACAAAAGAG 179 169 2756 Antisense
GAGCAACTCGGATCTTCTGAATTAT 94 391 2778 Antisense
TTCAAACTTCGGACAAGCTTAACAG 113 685 2803 Antisense
GAAATATTTCGGAAATCGCTGCCGA 548 363 2873 Antisense
GAAATGGGTTTCAGAGTTGATCCTA 243 361 3070 Antisense
GGCAACTATTGCTAAGAACTCCAAA 365 533 3096 Antisense
CAGGCAAACTACGGATACCTTCTTG 395 209 3166 Antisense
TACCTTCTTGAAATGCCGGTCTCAC 205 649 3181 Antisense
CGGTCTCACGACTAACTTCTGATGA 102 245 3197 Antisense
CACGACGGAGAACTGAGCTTGAAGC 512 199 3248 Antisense
ATCTGTGTGGCGTTCCGAATTGGAC 581 29 3294 Antisense
Sequence Source Affymetrix Proprietary Database