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[188027_s_at]

Description R07E5.8 /REP_DB=WormBase Gene ID /WP=CE00660 /GEN=cku-80 /TR=Q21829 /GB=CAA83623.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 85      4grp_high_8_8 > 17      6grp_highest_nonorm > 91      6grp_total > 76      4grp_total > 30      6grp_highest_sub > In      6grp_cgc > 67      6grp_cgc_sub > In      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 149
1 2 3 4 range
A 194.1
(3)
P 		111.5
(-0.7)
P 		59.4
(-3)
P 		158.6
(1.4)
P 		135
B 185.6
(3)
P 		114.7
(-1.4)
P 		89.8
(-3)
M 		120.8
(-1.1)
P 		96
C 208.4
(3)
P 		121.9
(-3)
P 		130.7
(-2.4)
P 		178.1
(0.9)
P 		87
avr 196
(3) 		116
(-1.7) 		93.3
(-3) 		152.5
(0.5) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 264
1 2 3 4 5 6 range
A 102.3
(-3)
P 		179.6
(0.1)
P 		163.4
(-0.5)
P 		211.4
(1.4)
P 		228.8
(2.1)
P 		250.4
(3)
P 		148
B 158.6
(-2.5)
P 		148.4
(-3)
P 		239.1
(1.8)
P 		219.3
(0.7)
P 		218.3
(0.7)
P 		262.6
(3)
P 		114
C 158.1
(-3)
P 		179.1
(-2.4)
P 		209
(-1.5)
P 		214.6
(-1.4)
P 		175.5
(-2.5)
P 		366.2
(3)
P 		208
avr 139.7
(-3) 		169
(-1.9) 		203.8
(-0.5) 		215.1
(-0.1) 		207.5
(-0.3) 		293.1
(3) 		153
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 55
1 2 3 4 range
A 70.7
(3)
P 		24.2
(-2.1)
P 		15.5
(-3)
P 		23.2
(-2.2)
P 		55
B 59.2
(3)
P 		28.3
(-1.8)
P 		20.8
(-3)
M 		25.7
(-2.2)
P 		38
C 69
(3)
P 		35
(-2.2)
P 		45.6
(-0.6)
P 		30
(-3)
P 		39
avr 66.3
(3) 		29.2
(-2.6) 		27.3
(-2.9) 		26.3
(-3) 		40

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 104
1 2 3 4 5 6 range
A 18.9
(-3)
P 		63.9
(2.4)
P 		35.6
(-1)
P 		53.6
(1.2)
P 		69
(3)
P 		61
(2)
P 		50
B 55.2
(-2.3)
P 		49.4
(-3)
P 		58.1
(-1.9)
P 		58.1
(-1.9)
P 		88.7
(1.9)
P 		97.9
(3)
P 		49
C 58.6
(-1.8)
P 		54.7
(-2.1)
P 		53.2
(-2.2)
P 		43.2
(-3)
P 		56.8
(-2)
P 		122.6
(3)
P 		79
avr 44.2
(-3) 		56
(-1.6) 		49
(-2.4) 		51.6
(-2.1) 		71.5
(0.3) 		93.8
(3) 		50
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188027_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5989
Sequence Type Exemplar sequence
Representative Public ID R07E5.8 NCBI
Target Description R07E5.8 /REP_DB=WormBase Gene ID /WP=CE00660 /GEN=cku-80 /TR=Q21829 /GB=CAA83623.1 /SUBMIT=HINXTON /CHR=3 /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_065498(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065498 NCBI Caenorhabditis elegans Caenorhabditis KU family member (cku-80) (cku-80) mRNA, complete cds. 11/11 None
GENEFINDER00000012867 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4419825:4423225:1 11/11 None
SNAP00000012855 ENSEMBL cdna:SNAP chromosome:CEL140:III:4419885:4423225:1 11/11 None
R07E5.8.1 ENSEMBL cdna:known chromosome:CEL140:III:4419817:4423294:1 gene:R07E5.8 11/11 None
R07E5.8.2 ENSEMBL cdna:known chromosome:CEL140:III:4419823:4423263:1 gene:R07E5.8 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
chrIII:4419824-4423225(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol cku-80
Ensembl R07E5.8
Entrez Gene 175578 Entrez gene
SwissProt Q21829 EMBL-EBI
WormBase CE00660 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6303 double-strand break repair via nonhomologous end-joining inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
4003 ATP-dependent DNA helicase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA83623 Hypothetical protein R07E5.8 [Caenorhabditis elegans] ref|NP_497899.1| Caenorhabditis KU family member (cku-80) [Caenorhabditis elegans] 0.0
blast CAE71203 Hypothetical protein CBG18065 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006164 EMBL-EBI Ku 1.0E-60
Pfam IPR005161 EMBL-EBI Ku70/Ku80 N-terminal alpha/beta domain 3.4E-60
Pfam IPR006164 EMBL-EBI Ku 1.5E-57
Pfam IPR006164 EMBL-EBI Ku 1.5E-57
Pfam IPR005161 EMBL-EBI Ku70/Ku80 N-terminal alpha/beta domain 1.0E-45
Sequence
Target Sequence 
>C. ELEGANS:188027_S_AT
aatggcaccgaaacgcagagtcgaagcagaacatccggagattttccagaagcttggccg
cgaattcaatctgcaaccaattcagaaaaccaaacgagaacgggttacggtagagcctga
agatctgcagacaatgatatccgaatggacggagaaaaaacagaatatgacacaaccaga
tgaggtagatgatggtgcaagtcaaaagaaaaagaaaaaaccaaatgcaaagaaattgac
gagaaaagaagaagttcaaatggatatcatggaagatggcggagctagtcgtgtttgctc
gaaaattcttgaaatgatttcaaatacttgcaaatttcaaccaaatggagcagttactga
gttctttacgcttctcgtcaatgaattgaatgttattcgctcagttttcgttgaaaactc
aaaatgtgacgagttcaatgaacttctcaagaagttgaaagacgaagaagactttgaacc
atttgctgaagttctttctgaagaaaaatcatgcaatccaattgattcttccgaagtcag
catgtcagaagtctccgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGGCACCGAAACGCAGAGTCGAA 656 161 1608 Antisense
GAGTCGAAGCAGAACATCCGGAGAT 45 401 1625 Antisense
GAGATTTTCCAGAAGCTTGGCCGCG 413 397 1645 Antisense
TTGGCCGCGAATTCAATCTGCAACC 290 709 1661 Antisense
GAGAACGGGTTACGGTAGAGCCTGA 89 383 1703 Antisense
AGATGGCGGAGCTAGTCGTGTTTGC 546 67 1881 Antisense
GTCGTGTTTGCTCGAAAATTCTTGA 684 471 1895 Antisense
AATGTTATTCGCTCAGTTTTCGTTG 548 163 1996 Antisense
AGAAGACTTTGAACCATTTGCTGAA 290 75 2073 Antisense
AATCCAATTGATTCTTCCGAAGTCA 679 147 2122 Antisense
AAGTCAGCATGTCAGAAGTCTCCGT 625 157 2141 Antisense
Sequence Source Affymetrix Proprietary Database