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[189170_at] endonuclease

Description R10E4.5 /REP_DB=WormBase Gene ID /WP=CE03559 /TR=SW:P54137 /GB=CAA90766.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=endonuclease
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 97      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 91      6grp_total > 97      4grp_total > 18      6grp_highest_sub > Da      6grp_high1_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 95.2
(-2.8)
P 		105.4
(-1.8)
P 		93.2
(-3)
P 		154.2
(3)
P 		61
B 79.9
(-3)
P 		125.7
(0.3)
P 		88.2
(-2.4)
P 		162.9
(3)
P 		83
C 97.9
(-2.5)
P 		107.2
(-0.1)
P 		96
(-3)
P 		118.9
(3)
P 		23
avr 91
(-3) 		112.8
(-0.6) 		92.5
(-2.8) 		145.3
(3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 389
1 2 3 4 5 6 range
A 116.6
(-2.7)
P 		105.1
(-3)
P 		130.1
(-2.4)
P 		219.3
(-0.3)
P 		252.1
(0.5)
P 		360.1
(3)
P 		255
B 93.2
(-2.8)
P 		85.9
(-3)
P 		123.6
(-2.2)
P 		127.4
(-2.1)
P 		300.8
(1.6)
P 		363.2
(3)
P 		277
C 91.8
(-2.8)
P 		82
(-3)
P 		117.3
(-2.5)
P 		161.6
(-1.8)
P 		248
(-0.4)
P 		471.1
(3)
P 		389
avr 100.5
(-2.8) 		91
(-3) 		123.7
(-2.4) 		169.4
(-1.5) 		267
(0.4) 		398.1
(3) 		307
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 34.7
(3)
P 		22.9
(-2.9)
P 		24.4
(-2.1)
P 		22.6
(-3)
P 		12
B 25.5
(-0.9)
P 		31
(1.4)
P 		20.4
(-3)
P 		34.7
(3)
P 		14
C 32.4
(2.5)
P 		30.8
(1.8)
P 		33.4
(3)
P 		20.1
(-3)
P 		13
avr 30.9
(3) 		28.2
(-0.2) 		26.1
(-2.6) 		25.8
(-3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 136
1 2 3 4 5 6 range
A 21.5
(-3)
P 		37.4
(-1.6)
P 		28.3
(-2.4)
P 		55.6
(0.1)
P 		76.1
(1.9)
P 		87.7
(3)
P 		66
B 32.4
(-2.8)
P 		28.6
(-3)
P 		30
(-2.9)
P 		33.7
(-2.7)
P 		122.2
(2.3)
P 		135.4
(3)
P 		107
C 34
(-2.6)
P 		25
(-3)
P 		29.9
(-2.8)
P 		32.5
(-2.7)
P 		80.3
(-0.5)
P 		157.7
(3)
P 		133
avr 29.3
(-3) 		30.3
(-2.9) 		29.4
(-3) 		40.6
(-2.3) 		92.9
(0.9) 		126.9
(3) 		98
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189170_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7063
Sequence Type Exemplar sequence
Representative Public ID R10E4.5 NCBI
Target Description R10E4.5 /REP_DB=WormBase Gene ID /WP=CE03559 /TR=SW:P54137 /GB=CAA90766.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=endonuclease
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_065458(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065458 NCBI Caenorhabditis elegans R10E4.5 (endonuclease) mRNA, complete cds. 11/11 None
SNAP00000016398 ENSEMBL cdna:SNAP chromosome:CEL140:III:4291654:4293368:-1 11/11 None
GENEFINDER00000016403 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4291654:4293368:-1 11/11 None
R10E4.5 ENSEMBL cdna:known chromosome:CEL140:III:4291654:4293266:-1 gene:R10E4.5 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:4291653-4293266(-) 100.0 100.0
Public Domain and Genome References
Gene Title endonuclease
Ensembl R10E4.5
Entrez Gene 187770 Entrez gene
SwissProt P54137 EMBL-EBI
WormBase CE03559 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:263248_AT endonuclease-related at
CANINE_2:CFAAFFX.29724.1.S1_AT similar to Endonuclease III-like protein 1 cfa
DROSOPHILA_2:1624901_AT dm
DROSGENOME1:146565_AT dm
CHICKEN:GGA.11851.1.S1_AT nth endonuclease III-like 1 (E. coli) gga
CHICKEN:GGA.11851.3.S1_A_AT nth endonuclease III-like 1 (E. coli) gga
HUGENEFL:U79718_AT nth endonuclease III-like 1 (E. coli) hs
HG-U133A:209731_AT nth endonuclease III-like 1 (E. coli) hs
HG-U133_PLUS_2:209731_AT nth endonuclease III-like 1 (E. coli) hs
HG-FOCUS:209731_AT nth endonuclease III-like 1 (E. coli) hs
HG-U133A_2:209731_AT nth endonuclease III-like 1 (E. coli) hs
U133_X3P:G1800270_3P_AT nth endonuclease III-like 1 (E. coli) hs
HG-U95AV2:40325_AT nth endonuclease III-like 1 (E. coli) hs
MG-U74AV2:93385_AT nth (endonuclease III)-like 1 (E.coli) mm
MOE430A:1419433_AT nth (endonuclease III)-like 1 (E.coli) mm
MOUSE430_2:1419433_AT nth (endonuclease III)-like 1 (E.coli) mm
MOUSE430A_2:1419433_AT nth (endonuclease III)-like 1 (E.coli) mm
MU11KSUBA:AB006812_AT nth (endonuclease III)-like 1 (E.coli) mm
RG-U34A:RC_H33255_AT thymine glycol DNA glycosylase/AP lyase (predicted) rn
RAE230A:1393963_AT thymine glycol DNA glycosylase/AP lyase (predicted) rn
RAT230_2:1393963_AT thymine glycol DNA glycosylase/AP lyase (predicted) rn
RAE230A:1376553_AT thymine glycol DNA glycosylase/AP lyase (predicted) rn
RAT230_2:1376553_AT thymine glycol DNA glycosylase/AP lyase (predicted) rn
YEAST_2:1771826_AT DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase involved in base excision repair, localizes to the nucleus Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
6284 base-excision repair inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
4519 endonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90766 Hypothetical protein R10E4.5 [Caenorhabditis elegans] ref|NP_497859.1| R10E4.5 [Caenorhabditis elegans] sp|P54137|NTH1_CAEEL Probable endonuclease III homolog (DNA-(Apurinic or apyrimidinic site) lyase) 1.0E-131
blast CAE66916 Hypothetical protein CBG12304 [Caenorhabditis briggsae] 4.0E-98
blast CAE66916 Hypothetical protein CBG12304 [Caenorhabditis briggsae] 4.0E-93
blast XP_642760 hypothetical protein DDB0169140 [Dictyostelium discoideum] gb|AAO51250.1| similar to endonuclease [Caenorhabditis elegans] [Dictyostelium discoideum] gb|EAL68809.1| hypothetical protein DDB0169140 [Dictyostelium discoideum] 8.0E-64
Protein Domains
Database ID Description E-Value
Pfam IPR003265 EMBL-EBI HhH-GPD 5.3E-23
Pfam IPR000445 EMBL-EBI Helix-hairpin-helix motif 6.6E-8
Pfam IPR003265 EMBL-EBI HhH-GPD 5.3E-23
Pfam IPR000445 EMBL-EBI Helix-hairpin-helix motif 6.6E-8
Sequence
Target Sequence 
>C. ELEGANS:189170_AT
ggccgtgtaccttcaaaagactgcaaaaattctgaaagatgatttttctggcgatatccc
tgattccctggacggactgtgcgcactgccaggagttggcccaaaaatggcgaatctcgt
catgcaaattgcttggggagaatgtgtgggaattgcagtcgacacacatgttcacagaat
ttctaatcgactcggctggatcaagaccagcaccccagaaaagacacaaaaagcgcttga
aattctacttccaaagtcggaatggcaaccaattaatcatcttctcgttggattcggtca
gatgcaatgccaaccagttcgtccgaaatgtggaacttgtctctgtagatttacgtgccc
cag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCCGTGTACCTTCAAAAGACTGCA 507 541 264 Antisense
TTTTTCTGGCGATATCCCTGATTCC 462 675 306 Antisense
TGTGCGCACTGCCAGGAGTTGGCCC 675 555 341 Antisense
GGCGAATCTCGTCATGCAAATTGCT 373 539 372 Antisense
TGCAGTCGACACACATGTTCACAGA 356 579 417 Antisense
TAATCGACTCGGCTGGATCAAGACC 578 627 447 Antisense
AAAGCGCTTGAAATTCTACTTCCAA 319 125 493 Antisense
GGCAACCAATTAATCATCTTCTCGT 223 535 527 Antisense
GGATTCGGTCAGATGCAATGCCAAC 229 509 553 Antisense
ATGCCAACCAGTTCGTCCGAAATGT 256 41 570 Antisense
GTCTCTGTAGATTTACGTGCCCCAG 662 469 602 Antisense
Sequence Source Affymetrix Proprietary Database