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[193190_at] DNA topoisomerase II (N-terminal region)

Description F32A11.4 /REP_DB=WormBase Gene ID /WP=CE17740 /TR=O62199 /GB=CAB04227.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA topoisomerase II (N-terminal region)
Cluster 6grp_total > 11      4grp_total > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 124
1 2 3 4 range
A 5.2
(-3)
A 		19.7
(-1.3)
A 		7.3
(-2.8)
A 		57.9
(3)
A 		53
B 29.8
(3)
A 		9.3
(-3)
A 		11.5
(-2.4)
A 		12.8
(-2)
A 		21
C 25.5
(-2.1)
A 		6.1
(-3)
A 		6.9
(-3)
A 		129.3
(3)
A 		123
avr 20.2
(-1.8) 		11.7
(-2.7) 		8.6
(-3) 		66.7
(3) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 8.8
(3)
A 		5.7
(-0.9)
A 		7.7
(1.6)
A 		8
(2)
A 		5.6
(-1)
A 		4
(-3)
A 		5
B 6.8
(-2.2)
A 		33.1
(3)
A 		6.9
(-2.2)
A 		8.1
(-1.9)
A 		4.3
(-2.7)
A 		2.7
(-3)
A 		30
C 7.5
(-1.5)
A 		12
(1.2)
A 		8.5
(-0.9)
A 		7.6
(-1.4)
A 		5
(-3)
A 		15
(3)
A 		10
avr 7.7
(-1.6) 		16.9
(3) 		7.7
(-1.6) 		7.9
(-1.5) 		5
(-3) 		7.2
(-1.9) 		12
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 1.9
(-3)
A 		4.3
(-0.8)
A 		1.9
(-3)
A 		8.5
(3)
A 		7
B 9.5
(3)
A 		2.3
(-3)
A 		2.7
(-2.7)
A 		2.7
(-2.7)
A 		7
C 8.5
(-1)
A 		1.8
(-3)
A 		2.4
(-2.8)
A 		21.8
(3)
A 		20
avr 6.6
(-0) 		2.8
(-2.7) 		2.3
(-3) 		11
(3) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10
1 2 3 4 5 6 range
A 1.6
(0.6)
A 		2
(3)
A 		1.7
(1.2)
A 		2
(3)
A 		1.7
(1.2)
A 		1
(-3)
A 		1
B 2.4
(-2.2)
A 		11
(3)
A 		1.7
(-2.6)
A 		2.2
(-2.3)
A 		1.7
(-2.6)
A 		1
(-3)
A 		10
C 2.8
(-0.8)
A 		3.7
(0.8)
A 		2.2
(-1.8)
A 		1.5
(-3)
A 		1.6
(-2.8)
A 		5
(3)
A 		4
avr 2.3
(-2.1) 		5.6
(3) 		1.9
(-2.7) 		1.9
(-2.7) 		1.7
(-3) 		2.3
(-2.1) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193190_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3542
Sequence Type Exemplar sequence
Representative Public ID F32A11.4 NCBI
Target Description F32A11.4 /REP_DB=WormBase Gene ID /WP=CE17740 /TR=O62199 /GB=CAB04227.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA topoisomerase II (N-terminal region)
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_064390(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064390 NCBI Caenorhabditis elegans F32A11.4 (F32A11.4) mRNA, complete cds. 11/11 None
SNAP00000006595 ENSEMBL cdna:SNAP chromosome:CEL140:II:13134930:13153212:-1 11/11 None
GENEFINDER00000006600 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13134930:13144897:-1 11/11 None
F32A11.4 ENSEMBL cdna:known chromosome:CEL140:II:13134930:13137290:-1 gene:F32A11.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000037013 7/11 Cross Hyb Matching Probes None
SNAP00000037007 7/11 Cross Hyb Matching Probes None
K08E5.1 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:13134926-13137287(-) 100.0 100.0
chrIII:10144370-10146537(-) 91.2 91.2
Public Domain and Genome References
Gene Title DNA topoisomerase II (N-terminal region)
Ensembl F32A11.4
Entrez Gene 185188 Entrez gene
SwissProt O62199 EMBL-EBI
WormBase CE17740 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 CAB04227 Hypothetical protein F32A11.4 [Caenorhabditis elegans] ref|NP_496791.1| F32A11.4 [Caenorhabditis elegans] 0.0
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 CAE17802 Hypothetical protein F32A11.7 [Caenorhabditis elegans] ref|NP_001022132.1| F32A11.7 [Caenorhabditis elegans] 0.0
blast CAE59412 Hypothetical protein CBG02776 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 6.0E-42
Pfam IPR006954 EMBL-EBI Protein of unknown function DUF644 1.0E-126
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.9E-6
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 6.0E-42
Pfam IPR006954 EMBL-EBI Protein of unknown function DUF644 1.6E-40
Pfam IPR006954 EMBL-EBI Protein of unknown function DUF644 7.1E-92
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.9E-6
Pfam IPR001241 EMBL-EBI DNA topoisomerase II 6.0E-42
Pfam IPR003594 EMBL-EBI ATP-binding region, ATPase-like 1.9E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000006595 4 721-743,750-772,787-809,816-838
GENEFINDER00000006600 4 537-559,566-588,603-625,632-654
Sequence
Target Sequence 
>C. ELEGANS:193190_AT
agaaagcctcggaaagctcgccaataaagtgcattccaaagcttgaagatgccaaagaag
ctggaaccaaaacttccgaacggtgcacattgattgtgacggaaggagactcggccaaaa
cgcttgctatttcgggactttccgttgttggacgggacaagttcggagtcttcccgctcc
gaggaaagttgctgaatgtccgcgacgcaagtgtgaagcagatcgccgagaatgctgaag
tcaacgcgatgatcaagatcctcggacttcagagagatttaaagtacgagtttgatgatg
agttcaggacacttcgatacgggaagctgatgatcatggctgatcaggatcaggatggct
ctcacatcaaaggtctcattatcagttttctacatcatttctggccatcactgattcaac
ggaacttcgtcgaggagttcatcactccaattgtcaaagccaccaaaggaaaagaagaag
tctccttctactcgctcccagaatactctgagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAAAGCCTCGGAAAGCTCGCCAAT 441 71 1376 Antisense
ACTTCCGAACGGTGCACATTGATTG 506 101 1447 Antisense
GCTTGCTATTTCGGGACTTTCCGTT 609 303 1497 Antisense
TCTTCCCGCTCCGAGGAAAGTTGCT 87 617 1544 Antisense
GAAAGTTGCTGAATGTCCGCGACGC 136 361 1559 Antisense
GATGATCAAGATCCTCGGACTTCAG 348 411 1623 Antisense
GATCAGGATCAGGATGGCTCTCACA 392 421 1717 Antisense
TGGCTCTCACATCAAAGGTCTCATT 275 543 1731 Antisense
AGGTCTCATTATCAGTTTTCTACAT 540 57 1746 Antisense
TTTTCTACATCATTTCTGGCCATCA 511 675 1761 Antisense
TACTCGCTCCCAGAATACTCTGAGT 104 647 1864 Antisense
Sequence Source Affymetrix Proprietary Database