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[190785_s_at] DNA topoisomerase II

Description K12D12.1 /REP_DB=WormBase Gene ID /WP=CE06184 /TR=SW:Q23670 /GB=CAA94177.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA topoisomerase II
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 67      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 95      6grp_total > 68      4grp_total > 52      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 572
1 2 3 4 range
A 655
(1.3)
P 		818.1
(3)
P 		604.2
(0.8)
P 		245.7
(-3)
P 		572
B 686
(3)
P 		667.1
(2.6)
P 		622.3
(1.7)
P 		402.6
(-3)
P 		283
C 620.8
(1.5)
P 		674.2
(2.5)
P 		702.1
(3)
P 		384.5
(-3)
P 		318
avr 653.9
(1.9) 		719.8
(3) 		642.9
(1.8) 		344.3
(-3) 		376

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 926
1 2 3 4 5 6 range
A 553
(-1.7)
P 		641.1
(-1.1)
P 		355.1
(-3)
P 		529.5
(-1.8)
P 		523.5
(-1.9)
P 		1264.8
(3)
P 		910
B 588.5
(-1.9)
P 		527.7
(-2.7)
P 		499.2
(-3)
P 		552.8
(-2.4)
P 		521
(-2.7)
P 		995.2
(3)
P 		496
C 610.9
(-0.4)
P 		558.9
(-0.9)
P 		521.6
(-1.3)
P 		339.2
(-3)
P 		619.3
(-0.3)
P 		967.1
(3)
P 		628
avr 584.1
(-1.8) 		575.9
(-1.9) 		458.6
(-3) 		473.8
(-2.9) 		554.6
(-2.1) 		1075.7
(3) 		617
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 209
1 2 3 4 range
A 238.5
(3)
P 		177.6
(1.2)
P 		157.9
(0.6)
P 		36
(-3)
P 		203
B 218.8
(3)
P 		164.7
(0.6)
P 		144.2
(-0.4)
P 		85.8
(-3)
P 		133
C 205.5
(1.7)
P 		193.8
(1.3)
P 		244.7
(3)
P 		64.8
(-3)
P 		180
avr 220.9
(3) 		178.7
(1.4) 		182.3
(1.5) 		62.2
(-3) 		159

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 303
1 2 3 4 5 6 range
A 101.9
(-2.4)
P 		228
(0.9)
P 		77.3
(-3)
P 		134.3
(-1.5)
P 		158
(-0.9)
P 		307.9
(3)
P 		231
B 204.8
(-1)
P 		175.6
(-1.7)
P 		121.2
(-3)
P 		146.4
(-2.4)
P 		211.7
(-0.8)
P 		371.1
(3)
P 		250
C 226.5
(0.7)
P 		170.5
(-0.6)
P 		132.7
(-1.5)
P 		68.2
(-3)
P 		200.4
(0.1)
P 		323.7
(3)
P 		256
avr 177.7
(-1.2) 		191.4
(-0.8) 		110.4
(-3) 		116.3
(-2.8) 		190
(-0.9) 		334.2
(3) 		224
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190785_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3300
Sequence Type Exemplar sequence
Representative Public ID K12D12.1 NCBI
Target Description K12D12.1 /REP_DB=WormBase Gene ID /WP=CE06184 /TR=SW:Q23670 /GB=CAA94177.1 /SUBMIT=HINXTON /CHR=2 /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_064135(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064135 NCBI Caenorhabditis elegans K12D12.1 (K12D12.1) mRNA, complete cds. 11/11 None
SNAP00000000319 ENSEMBL cdna:SNAP chromosome:CEL140:II:11877312:11880207:1 11/11 None
GENEFINDER00000000332 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11877458:11880207:1 11/11 None
K12D12.1 ENSEMBL cdna:known chromosome:CEL140:II:11875061:11880492:1 gene:K12D12.1 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
chrII:11875057-11880204(+) 98.38 100.0
Public Domain and Genome References
Gene Title DNA topoisomerase II
Ensembl K12D12.1
Entrez Gene 174825 Entrez gene
SwissProt Q23670 EMBL-EBI
WormBase CE06184 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18777_S_AT DNA topoisomerase, ATP-hydrolyzing / DNA topoisomerase II / DNA gyrase (TOP2) at
ATH1-121501:256864_AT DNA topoisomerase, ATP-hydrolyzing / DNA topoisomerase II / DNA gyrase (TOP2) at
CANINE_2:CFA.18946.1.S1_S_AT similar to DNA topoisomerase II, alpha isozyme cfa
CANINE_2:CFAAFFX.24692.1.S1_AT similar to DNA topoisomerase II, alpha isozyme cfa
DROSOPHILA_2:1631837_AT Topoisomerase 2 dm
DROSGENOME1:143380_AT Topoisomerase 2 dm
CHICKEN:GGA.2010.1.S1_AT topoisomerase (DNA) II alpha 170kDa gga
CHICKEN:GGA.2010.2.S1_A_AT topoisomerase (DNA) II alpha 170kDa gga
HG-U133_PLUS_2:201292_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133A_2:201292_AT topoisomerase (DNA) II alpha 170kDa hs
HG-FOCUS:201292_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133A:201292_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133_PLUS_2:201291_S_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133A_2:201291_S_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133A:201291_S_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U95AV2:904_S_AT topoisomerase (DNA) II alpha 170kDa hs
HC-G110:904_S_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U95AV2:1592_AT topoisomerase (DNA) II alpha 170kDa hs
HC-G110:1592_AT topoisomerase (DNA) II alpha 170kDa hs
HU35KSUBC:RC_AA026682_S_AT topoisomerase (DNA) II alpha 170kDa hs
HUGENEFL:L47276_S_AT topoisomerase (DNA) II alpha 170kDa hs
HUGENEFL:J04088_AT topoisomerase (DNA) II alpha 170kDa hs
U133_X3P:HS.156346.0.S3_3P_AT topoisomerase (DNA) II alpha 170kDa hs
U133_X3P:HS.156346.0.S1_3P_A_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U95AV2:40145_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U95D:74096_AT topoisomerase (DNA) II alpha 170kDa hs
HG-U133_PLUS_2:237469_AT Topoisomerase (DNA) II alpha 170kDa hs
HG-U133B:237469_AT Topoisomerase (DNA) II alpha 170kDa hs
HG-U95B:59369_AT Topoisomerase (DNA) II alpha 170kDa hs
HU35KSUBB:RC_T96523_AT Topoisomerase (DNA) II alpha 170kDa hs
U133_X3P:HS.242998.0.A1_3P_AT Topoisomerase (DNA) II alpha 170kDa hs
MOUSE430A_2:1427724_AT topoisomerase (DNA) II alpha mm
MOUSE430_2:1427724_AT topoisomerase (DNA) II alpha mm
MOE430A:1427724_AT topoisomerase (DNA) II alpha mm
MU11KSUBA:D12513_F_AT topoisomerase (DNA) II alpha mm
MU11KSUBB:MSA.47.0_F_AT topoisomerase (DNA) II alpha mm
MG-U74AV2:99578_AT topoisomerase (DNA) II alpha mm
MOE430A:1454694_A_AT topoisomerase (DNA) II alpha mm
MOUSE430A_2:1454694_A_AT topoisomerase (DNA) II alpha mm
MOUSE430_2:1454694_A_AT topoisomerase (DNA) II alpha mm
MOE430B:1442454_AT topoisomerase (DNA) II alpha mm
MOUSE430_2:1442454_AT topoisomerase (DNA) II alpha mm
MU19KSUBA:TC15204_S_AT Topoisomerase (DNA) II alpha (Top2a), mRNA mm
MU19KSUBA:TC16708_S_AT Topoisomerase (DNA) II alpha (Top2a), mRNA mm
YEAST_2:1779900_AT Essential type II topoisomerase, relieves torsional strain in DNA by cleaving and re-sealing the phosphodiester backbone of both positively and negatively supercoiled DNA; cleaves complementary strands; localizes to axial cores in meiosis Sc
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 Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus 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 CAA94177 Hypothetical protein K12D12.1 [Caenorhabditis elegans] emb|CAA88867.1| Hypothetical protein K12D12.1 [Caenorhabditis elegans] ref|NP_496536.1| K12D12.1 [Caenorhabditis elegans] sp|Q23670|TOP2_CAEEL Probable DNA topoisomerase 2 (DNA topoisomerase II) 0.0
blast CAE59389 Hypothetical protein CBG02746 [Caenorhabditis briggsae] 0.0
blast AAH72193 LOC398512 protein [Xenopus laevis] 0.0
blast AAB93429 Hypothetical protein ZK1127.7 [Caenorhabditis elegans] ref|NP_495440.2| ZK1127.7 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Tetracyclin repressor-like, N-terminal domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Tetracyclin repressor-like, N-terminal domain 9.10000038146973
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 1.0E-126
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 1.0E-126
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 1.2E-58
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 6.5E-13
Pfam IPR002205 EMBL-EBI DNA gyrase/topoisomerase IV, subunit A 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:190785_S_AT
taaaaagttcatgtctccagctgctccgaagactgcgaagaaggagaaaagcgacggctt
caactctgacatgtcagaggaaagtgacgtggagttcgatgaaggaatcgatttcgattc
ggacgatgacggtgtggagcgtgaggatgtcgtctcaaagccaaaacctcgtactggaaa
aggagctgcgaaagcggaagttatcgatttgtcagatgatgatgaagttcctgcaaagaa
gcctgctccagcgaagaaagctgctccgaagaagaaaaagagcgagttcagcgatctgtc
tggcggcgacagtgatgaagaagctgagaagaagccgtccaccagcaaaaagccgtctcc
aaagaaggctgctccgaagacggccgagcccaagtcgaaggcggtgaccgatttctttgg
tgcttcaaagaagaacggaaagaaggccgctggttccgatgatgaagacgacgaaagctt
cgttgtggctccaagagagaagagcggaagagctcgcaaggcgccaccaacttacgacgt
ggatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAAAAAGTTCATGTCTCCAGCTGCT 226 641 3966 Antisense
GACGGCTTCAACTCTGACATGTCAG 252 375 4018 Antisense
GATGTCGTCTCAAAGCCAAAACCTC 511 397 4111 Antisense
GAAGCCTGCTCCAGCGAAGAAAGCT 338 345 4203 Antisense
AGAGCGAGTTCAGCGATCTGTCTGG 503 69 4244 Antisense
CACCAGCAAAAAGCCGTCTCCAAAG 510 201 4305 Antisense
GCCGAGCCCAAGTCGAAGGCGGTGA 418 231 4348 Antisense
GCGGTGACCGATTTCTTTGGTGCTT 71 293 4366 Antisense
GGCCGCTGGTTCCGATGATGAAGAC 247 543 4410 Antisense
AAAGCTTCGTTGTGGCTCCAAGAGA 364 123 4439 Antisense
GCGCCACCAACTTACGACGTGGATT 146 285 4486 Antisense
Sequence Source Affymetrix Proprietary Database