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[192346_s_at] DNA topoisomerase III

Description Y56A3A.27 /REP_DB=WormBase Gene ID /WP=CE28138 /GEN=top-3 /TR=Q9U223 /GB=CAB60518.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA topoisomerase III
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 83      6grp_highest_nonorm > 90      6grp_total > 75      4grp_total > 60      6grp_cgc > 66      6grp_high1_sub > 04      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 135
1 2 3 4 range
A 121.5
(-0.2)
P 		125.5
(0.1)
A 		180.2
(3)
P 		68.8
(-3)
A 		111
B 164
(3)
P 		156.6
(2.6)
P 		114.5
(0.5)
P 		45.5
(-3)
A 		119
C 149.7
(2.4)
P 		159.3
(3)
P 		147.4
(2.3)
P 		59.6
(-3)
A 		100
avr 145.1
(2.8) 		147.1
(3) 		147.4
(3) 		58
(-3) 		89

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 127
1 2 3 4 5 6 range
A 162.7
(-2.1)
P 		190.2
(-0.3)
P 		176.4
(-1.2)
P 		241.1
(3)
P 		149
(-3)
P 		229.3
(2.2)
P 		92
B 113.8
(-3)
P 		126.6
(-2.4)
P 		212.9
(2)
P 		232
(3)
P 		154.5
(-0.9)
P 		210.3
(1.9)
P 		118
C 187.7
(3)
P 		159.6
(-0.9)
P 		150.3
(-2.1)
P 		150.2
(-2.1)
P 		184.7
(2.6)
P 		144
(-3)
P 		44
avr 154.7
(-3) 		158.8
(-2.5) 		179.9
(-0.2) 		207.8
(3) 		162.7
(-2.1) 		194.5
(1.5) 		53
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 44.2
(2.5)
P 		27.2
(-0.2)
A 		47.1
(3)
P 		10.1
(-3)
A 		37
B 52.3
(3)
P 		38.7
(1.1)
P 		26.5
(-0.6)
P 		9.7
(-3)
A 		43
C 49.6
(2.7)
P 		45.8
(2.2)
P 		51.4
(3)
P 		10.1
(-3)
A 		41
avr 48.7
(3) 		37.2
(1.2) 		41.7
(1.9) 		10
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 48
1 2 3 4 5 6 range
A 30
(-3)
P 		67.6
(3)
P 		38.4
(-1.7)
P 		61.1
(2)
P 		45
(-0.6)
P 		55.8
(1.1)
P 		38
B 39.6
(-3)
P 		42.1
(-2.6)
P 		51.7
(-1.1)
P 		61.4
(0.4)
P 		62.8
(0.6)
P 		78.4
(3)
P 		39
C 69.6
(3)
P 		48.7
(-0.2)
P 		38.3
(-1.8)
P 		30.2
(-3)
P 		59.8
(1.5)
P 		48.2
(-0.3)
P 		39
avr 46.4
(-1.8) 		52.8
(0.3) 		42.8
(-3) 		50.9
(-0.3) 		55.9
(1.4) 		60.8
(3) 		18
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192346_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6624
Sequence Type Exemplar sequence
Representative Public ID Y56A3A.27 NCBI
Target Description Y56A3A.27 /REP_DB=WormBase Gene ID /WP=CE28138 /GEN=top-3 /TR=Q9U223 /GB=CAB60518.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA topoisomerase III
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_067157(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067157 NCBI Caenorhabditis elegans TOPoisomerase family member (top-3) (top-3) mRNA, complete cds. 11/11 None
SNAP00000035205 ENSEMBL cdna:SNAP chromosome:CEL140:III:11949894:11964939:-1 11/11 None
GENEFINDER00000035239 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11949894:11960044:-1 11/11 None
Y56A3A.27.1 ENSEMBL cdna:known chromosome:CEL140:III:11949785:11960056:-1 gene:Y56A3A.27 11/11 None
Y56A3A.27.2 ENSEMBL cdna:known chromosome:CEL140:III:11949894:11960060:-1 gene:Y56A3A.27 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:11949889-11960040(-) 99.96 100.0
Public Domain and Genome References
Gene Title DNA topoisomerase III
Gene Symbol top-3
Ensembl Y56A3A.27
Entrez Gene 176631 Entrez gene
SwissProt O61660 EMBL-EBI
WormBase CE28138 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247301_AT DNA topoisomerase III alpha, putative at
CANINE_2:CFA.18365.1.S1_S_AT similar to topoisomerase (DNA) III alpha cfa
CANINE_2:CFAAFFX.27965.1.S1_S_AT similar to topoisomerase (DNA) III alpha cfa
CANINE_2:CFAAFFX.27969.1.S1_AT similar to topoisomerase (DNA) III alpha cfa
CANINE_2:CFAAFFX.27970.1.S1_S_AT similar to topoisomerase (DNA) III alpha cfa
DROSOPHILA_2:1627866_AT Topoisomerase 3 dm
DROSGENOME1:146499_AT Topoisomerase 3 dm
CHICKEN:GGAAFFX.26384.1.S1_AT topoisomerase (DNA) III alpha gga
CHICKEN:GGAAFFX.3133.1.S1_S_AT topoisomerase (DNA) III alpha gga
HG-U95AV2:1028_AT topoisomerase (DNA) III alpha hs
HC-G110:1028_AT topoisomerase (DNA) III alpha hs
HG-U133_PLUS_2:204946_S_AT topoisomerase (DNA) III alpha hs
HG-U133A:204946_S_AT topoisomerase (DNA) III alpha hs
HG-U133A_2:204946_S_AT topoisomerase (DNA) III alpha hs
HU35KSUBA:U43431_AT topoisomerase (DNA) III alpha hs
HUGENEFL:U43431_AT topoisomerase (DNA) III alpha hs
U133_X3P:G10835217_3P_S_AT topoisomerase (DNA) III alpha hs
HG-U133A_2:214300_S_AT topoisomerase (DNA) III alpha hs
HG-U133_PLUS_2:214300_S_AT topoisomerase (DNA) III alpha hs
HG-U133A:214300_S_AT topoisomerase (DNA) III alpha hs
HG-U95AV2:41004_AT topoisomerase (DNA) III alpha hs
HG-U133_PLUS_2:214299_AT Topoisomerase (DNA) III alpha hs
HG-U133A_2:214299_AT Topoisomerase (DNA) III alpha hs
HG-FOCUS:214299_AT Topoisomerase (DNA) III alpha hs
HG-U133A:214299_AT Topoisomerase (DNA) III alpha hs
U133_X3P:HS.91175.1.S1_3P_AT Topoisomerase (DNA) III alpha hs
HG-U95E:77063_AT Topoisomerase (DNA) III alpha hs
MG-U74AV2:94124_AT topoisomerase (DNA) III alpha mm
MOE430A:1418597_AT topoisomerase (DNA) III alpha mm
MOUSE430A_2:1418597_AT topoisomerase (DNA) III alpha mm
MOUSE430_2:1418597_AT topoisomerase (DNA) III alpha mm
RAE230B:1384972_AT topoisomerase (DNA) III alpha (predicted) rn
RAT230_2:1384972_AT topoisomerase (DNA) III alpha (predicted) rn
RG-U34B:RC_AA996824_AT Topoisomerase (DNA) III alpha (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
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
Protein Similarities
Method ID Description E-Value
blast CAB60518 Hypothetical protein Y56A3A.27 [Caenorhabditis elegans] ref|NP_499558.1| TOPoisomerase family member (top-3) [Caenorhabditis elegans] gb|AAC13567.1| DNA topoisomerase III [Caenorhabditis elegans] sp|O61660|TOP3_CAEEL DNA topoisomerase III 0.0
blast CAE67751 Hypothetical protein CBG13326 [Caenorhabditis briggsae] 0.0
blast XP_782119 PREDICTED: similar to topoisomerase (DNA) III alpha, partial [Strongylocentrotus purpuratus] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 1.8E-105
Pfam IPR006171 EMBL-EBI TOPRIM 1.9E-25
Pfam IPR010666 EMBL-EBI GRF zinc finger 6.2E-21
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 1.8E-105
Pfam IPR006171 EMBL-EBI TOPRIM 1.9E-25
Pfam IPR010666 EMBL-EBI GRF zinc finger 6.2E-21
Pfam IPR007087 EMBL-EBI Zn-finger, C2H2 type 3.6E-6
Pfam IPR000380 EMBL-EBI DNA topoisomerase I 1.8E-105
Pfam IPR006171 EMBL-EBI TOPRIM 8.3E-12
Pfam IPR010666 EMBL-EBI GRF zinc finger 6.2E-21
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000035239 1 62-79
Sequence
Target Sequence 
>C. ELEGANS:192346_S_AT
taagcccgatttacgagccaatttggaaatcggcctgaaagaaatttgcgacggtcgacg
acagaaacaagaagttttggatgagcaaatcggcaaatatcgagccatttttgtagagtc
tgaacgcaaaattggcgtgctctcgcaaagtttgcaacgatatttggacaagaataatca
ggctggcggagggcctggagggcctggaggcggtggaggcccaccaagaggacctggagg
tggtggtgggggaggccctacaggcccgccggctcctccaaagccgcctgcaaaaccacg
tggcaggccacccagaaaatcgataagcccagcagtgaagaatgggcatgatgatccgga
aaatgatacgatagtaacactgagcgaggtgttcggcagtatgtccaacccgaaaccagc
cagaaaaccacgtgctccacgaaaaagtgctgctccaaaagaacaggaagaggaagagga
agtgttctgccagtgcccggagccgatgagagccgtcacgaaagtggtgcagaaggaggg
tccgaataagggaaaaaagttctatacatgctcgttaccgtatacatcgtct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAAGCCCGATTTACGAGCCAATTTG 382 637 1623 Antisense
ATTGGCGTGCTCTCGCAAAGTTTGC 197 3 1753 Antisense
AGGCCCACCAAGAGGACCTGGAGGT 18 13 1839 Antisense
GGCAGGCCACCCAGAAAATCGATAA 334 515 1924 Antisense
GGTGTTCGGCAGTATGTCCAACCCG 686 499 2010 Antisense
AAACCAGCCAGAAAACCACGTGCTC 670 125 2035 Antisense
GTGCTCCACGAAAAAGTGCTGCTCC 428 479 2054 Antisense
GAAGAGGAAGTGTTCTGCCAGTGCC 295 339 2095 Antisense
CGGAGCCGATGAGAGCCGTCACGAA 552 243 2120 Antisense
AAGTTCTATACATGCTCGTTACCGT 213 155 2179 Antisense
ATGCTCGTTACCGTATACATCGTCT 334 39 2190 Antisense
Sequence Source Affymetrix Proprietary Database