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[176572_at]

Description C07H6.1 /REP_DB=WormBase Gene ID /WP=CE00757 /GEN=lig-4 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 50      4grp_high_8_8 > 40      6grp_highest_nonorm > 70      6grp_total > 36      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 06      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 329
1 2 3 4 range
A 420.8
(3)
P 		293.6
(0)
P 		277.8
(-0.4)
P 		166
(-3)
P 		255
B 357.2
(3)
P 		232.9
(-1.1)
P 		174.5
(-3)
P 		192.9
(-2.4)
P 		183
C 489.3
(3)
P 		160.2
(-3)
P 		273.1
(-0.9)
P 		231.6
(-1.7)
P 		329
avr 422.4
(3) 		228.9
(-2.1) 		241.8
(-1.8) 		196.8
(-3) 		226

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 252
1 2 3 4 5 6 range
A 343.4
(3)
P 		309.6
(1.1)
P 		268.7
(-1.2)
P 		310.3
(1.2)
P 		235.9
(-3)
P 		323
(1.9)
P 		108
B 382.1
(3)
P 		304
(-0.2)
P 		316.9
(0.3)
P 		259.3
(-2.1)
P 		236.2
(-3)
P 		303.2
(-0.2)
P 		146
C 459.8
(3)
P 		304.1
(-0.7)
P 		305
(-0.7)
P 		249.8
(-2)
P 		208.3
(-3)
P 		337.4
(0.1)
P 		252
avr 395.1
(3) 		305.9
(-0.2) 		296.9
(-0.5) 		273.1
(-1.3) 		226.8
(-3) 		321.2
(0.4) 		168
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 138
1 2 3 4 range
A 153.2
(3)
P 		63.7
(-1.2)
P 		72.6
(-0.8)
P 		24.3
(-3)
P 		129
B 113.9
(3)
P 		57.5
(-1.6)
P 		40.4
(-3)
P 		41.1
(-2.9)
P 		74
C 162
(3)
P 		46.1
(-2.7)
P 		95.2
(-0.3)
P 		39.1
(-3)
P 		123
avr 143
(3) 		55.8
(-1.8) 		69.4
(-1.1) 		34.8
(-3) 		108

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 120
1 2 3 4 5 6 range
A 63.3
(-2.4)
P 		110.1
(3)
P 		58.5
(-3)
P 		78.7
(-0.7)
P 		71.2
(-1.5)
P 		78.6
(-0.7)
P 		52
B 132.9
(3)
P 		101.2
(0)
P 		76.9
(-2.2)
P 		68.7
(-3)
P 		96
(-0.4)
P 		113.1
(1.1)
P 		64
C 170.4
(3)
P 		92.8
(-0.9)
P 		77.6
(-1.6)
P 		50.2
(-3)
P 		67.4
(-2.1)
P 		113
(0.1)
P 		120
avr 122.2
(3) 		101.4
(0.8) 		71
(-2.5) 		65.9
(-3) 		78.2
(-1.7) 		101.6
(0.8) 		56
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176572_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8083
Sequence Type Exemplar sequence
Representative Public ID C07H6.1 NCBI
Target Description C07H6.1 /REP_DB=WormBase Gene ID /WP=CE00757 /GEN=lig-4 /SUBMIT=ST.LOUIS /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_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:7521386-7524629(+) 100.0 100.0
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:176572_AT
ggtggatacattgatttcgagcgctggcaagtgattaaaatcacatcgaacggtgttcgc
aacggaaaattggttgatcctgttatgagagagtggagacttgataagcctgttgaacag
aaagttcaagaatgtaaattgggtgataacgtggacagtgatgaagaagattctgaagat
aagaaaccagatactttgaaagtggaacgaattacccgcaaagctattcatcaatcagct
cctgttcgtctgaaacgtgccaaattagagtcaagtttgactggaattgaagtcgccgtt
cttcagggaacatctgaaacaattcgacgaaagtgtgaagagatcttgaaacattttgat
gcaactgtagtgaaaggaataactccatccaccaaattatgtattgctactgctccaaaa
tccacacaccctaaaacagctcaagccatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTGGATACATTGATTTCGAGCGCT 202 499 1624 Antisense
GATTTCGAGCGCTGGCAAGTGATTA 697 427 1636 Antisense
CACATCGAACGGTGTTCGCAACGGA 307 191 1665 Antisense
GGAGACTTGATAAGCCTGTTGAACA 445 519 1718 Antisense
AGTGGAACGAATTACCCGCAAAGCT 504 37 1824 Antisense
TACCCGCAAAGCTATTCATCAATCA 676 649 1836 Antisense
TTCATCAATCAGCTCCTGTTCGTCT 435 685 1850 Antisense
CTCCTGTTCGTCTGAAACGTGCCAA 598 233 1862 Antisense
GAAGTCGCCGTTCTTCAGGGAACAT 707 329 1912 Antisense
GTATTGCTACTGCTCCAAAATCCAC 264 453 2024 Antisense
ACACCCTAAAACAGCTCAAGCCATC 85 111 2049 Antisense
Sequence Source Affymetrix Proprietary Database