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[173363_s_at]

Description AV180978_rc /REP_DB=TREMBL Accession /GB=AV180978 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk614e1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 68      4grp_high_8_8 > 40      6grp_highest_nonorm > 82      6grp_total > 56      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 455
1 2 3 4 range
A 614.4
(3)
P 		269.3
(-1.6)
P 		270.6
(-1.5)
P 		159.9
(-3)
A 		455
B 451.5
(3)
P 		305.4
(-1.7)
P 		278.3
(-2.6)
P 		265.2
(-3)
P 		186
C 496.3
(3)
P 		303.8
(-1.2)
P 		320.9
(-0.8)
P 		219.3
(-3)
P 		277
avr 520.7
(3) 		292.8
(-1.5) 		289.9
(-1.5) 		214.8
(-3) 		306

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 286
1 2 3 4 5 6 range
A 262.7
(-1.5)
P 		355.1
(3)
P 		234.1
(-2.9)
P 		233
(-3)
P 		281.6
(-0.6)
P 		304.9
(0.5)
P 		122
B 313.7
(-1.3)
P 		346.5
(-0.5)
P 		386.8
(0.5)
P 		245
(-3)
P 		300
(-1.6)
P 		487
(3)
P 		242
C 342.7
(0.2)
P 		411
(1.7)
P 		201.5
(-3)
P 		270.1
(-1.5)
P 		208.7
(-2.8)
P 		469.8
(3)
P 		268
avr 306.4
(-1) 		370.9
(1.3) 		274.1
(-2.1) 		249.4
(-3) 		263.4
(-2.5) 		420.6
(3) 		171
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 200
1 2 3 4 range
A 223.7
(3)
P 		58.5
(-1.9)
P 		70.7
(-1.6)
P 		23.4
(-3)
A 		200
B 144
(3)
P 		75.4
(-1.7)
P 		64.5
(-2.5)
P 		56.5
(-3)
P 		88
C 164.3
(3)
P 		87.3
(-0.6)
P 		111.9
(0.5)
P 		37
(-3)
P 		127
avr 177.3
(3) 		73.7
(-1.5) 		82.4
(-1.1) 		39
(-3) 		138

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 133
1 2 3 4 5 6 range
A 48.4
(-3)
P 		126.3
(3)
P 		51
(-2.8)
P 		59.1
(-2.2)
P 		85
(-0.2)
P 		74.2
(-1)
P 		78
B 109.1
(-0.7)
P 		115.3
(-0.4)
P 		93.9
(-1.5)
P 		64.9
(-3)
P 		121.9
(-0.1)
P 		181.6
(3)
P 		117
C 127
(1.3)
P 		125.4
(1.2)
P 		51.3
(-3)
P 		54.3
(-2.8)
P 		67.5
(-2.1)
P 		157.3
(3)
P 		106
avr 94.8
(-0.3) 		122.3
(1.8) 		65.4
(-2.5) 		59.4
(-3) 		91.5
(-0.5) 		137.7
(3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173363_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27717
Sequence Type Exemplar sequence
Representative Public ID AV180978 NCBI
Target Description AV180978_rc /REP_DB=TREMBL Accession /GB=AV180978 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk614e1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
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_066252(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066252 NCBI Caenorhabditis elegans LIGase family member (lig-4) (lig-4) mRNA, complete cds. 11/11 A 
SNAP00000039495 ENSEMBL cdna:SNAP chromosome:CEL140:III:7521389:7524631:1 11/11 None
GENEFINDER00000039504 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7521389:7524631:1 11/11 None
C07H6.1 ENSEMBL cdna:known chromosome:CEL140:III:7521382:7524732:1 gene:C07H6.1 11/11 A 
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:7524020-7524688(+) 96.42 96.42
Public Domain and Genome References
Gene Title
Gene Symbol lig-4
Ensembl C07H6.1
Entrez Gene 176067 Entrez gene
SwissProt Q95YE6 EMBL-EBI
WormBase CE34522 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6260 DNA replication inferred from electronic annotation QuickGO AmiGO
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
6310 DNA recombination inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3910 DNA ligase (ATP) activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK85439 Ligase protein 4 [Caenorhabditis elegans] ref|NP_498653.2| LIGase family member (lig-4) [Caenorhabditis elegans] 0.0
blast CAE64455 Hypothetical protein CBG09168 [Caenorhabditis briggsae] 0.0
blast XP_698012 PREDICTED: similar to DNA ligase IV [Danio rerio] 3.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR000977 EMBL-EBI ATP-dependent DNA ligase 5.9E-32
Sequence
Target Sequence 
>C. ELEGANS:173363_S_AT
gaaacattttgatgcaactgtagtgaaaggaataactccatccaccaaattatgtattgc
tactgcnnnnnnnnnnnnnnnnnnnnnnnnnnctcaagccatcgcttcgaactcttgtac
tgttctgaaacccgcctggctcgaacgttgcaataaagatgatctgattcaggcttggtt
gccttctgatgtgtttcatgccatcgaaggtggattc

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAACATTTTGATGCAACTGTAGTG 170 357 24 Antisense
AAGGAATAACTCCATCCACCAAATT 416 159 50 Antisense
CCACCAAATTATGTATTGCTACTGC 87 273 65 Antisense
TCAAGCCATCGCTTCGAACTCTTGT 477 631 117 Antisense
ATCGCTTCGAACTCTTGTACTGTTC 376 37 124 Antisense
CTCTTGTACTGTTCTGAAACCCGCC 295 229 135 Antisense
CGCCTGGCTCGAACGTTGCAATAAA 545 257 156 Antisense
GATGATCTGATTCAGGCTTGGTTGC 234 65 181 Antisense
GATTCAGGCTTGGTTGCCTTCTGAT 410 431 189 Antisense
GTTGCCTTCTGATGTGTTTCATGCC 164 441 201 Antisense
GTTTCATGCCATCGAAGGTGGATTC 618 449 216 Antisense
Sequence Source Affymetrix Proprietary Database