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[193194_at] AP endonuclease (family 2)

Description T05H10.2 /REP_DB=WormBase Gene ID /WP=CE01639 /GEN=apn-1 /TR=SW:Q10002 /GB=CAA87789.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=AP endonuclease (family 2)
Cluster 6grp_highest_10_10 > 67      6grp_high1_10_10 > 76      4grp_highest_8_8 > 45      4grp_high_8_8 > 01      6grp_highest_nonorm > 82      6grp_total > 66      4grp_total > 15      6grp_highest_sub > In      6grp_cgc > 47      6grp_high1_sub > Da      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 337
1 2 3 4 range
A 260.8
(0.4)
P 		167.2
(-3)
P 		204.6
(-1.7)
P 		334.7
(3)
P 		168
B 504.6
(3)
P 		261.2
(-3)
P 		298.4
(-2.1)
P 		318.8
(-1.6)
P 		243
C 372.5
(2.1)
P 		196.3
(-3)
P 		218.3
(-2.4)
P 		403.2
(3)
P 		207
avr 379.3
(3) 		208.2
(-3) 		240.4
(-1.9) 		352.2
(2) 		171

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 464
1 2 3 4 5 6 range
A 350.9
(-1.5)
P 		337
(-2)
P 		476.6
(3)
P 		388.9
(-0.1)
P 		308.2
(-3)
P 		402.3
(0.4)
P 		168
B 272
(-3)
P 		385
(-1.1)
P 		352
(-1.6)
P 		361
(-1.5)
P 		364.4
(-1.4)
P 		623.7
(3)
P 		352
C 280.2
(-3)
P 		445.8
(-0.8)
P 		401.9
(-1.4)
P 		308.2
(-2.6)
P 		329.9
(-2.3)
P 		736.3
(3)
P 		456
avr 301
(-3) 		389.3
(-1.2) 		410.2
(-0.7) 		352.7
(-1.9) 		334.2
(-2.3) 		587.4
(3) 		286
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 125
1 2 3 4 range
A 95
(3)
P 		36.3
(-3)
P 		53.5
(-1.2)
P 		49
(-1.7)
P 		59
B 160.9
(3)
P 		64.5
(-3)
P 		69.1
(-2.7)
P 		67.9
(-2.8)
P 		96
C 123.3
(3)
P 		56.4
(-3)
P 		76.1
(-1.2)
P 		68
(-2)
P 		67
avr 126.4
(3) 		52.4
(-3) 		66.2
(-1.9) 		61.6
(-2.3) 		74

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 185
1 2 3 4 5 6 range
A 64.7
(-3)
P 		119.9
(3)
P 		103.8
(1.3)
P 		98.6
(0.7)
P 		93
(0.1)
P 		97.9
(0.6)
P 		55
B 94.6
(-2.6)
P 		128.1
(-1.3)
P 		85.5
(-3)
P 		95.6
(-2.6)
P 		148.1
(-0.4)
P 		232.6
(3)
P 		147
C 103.9
(-1.6)
P 		136
(-0.6)
P 		102.3
(-1.7)
P 		62
(-3)
P 		106.8
(-1.5)
P 		246.5
(3)
P 		185
avr 87.7
(-2.9) 		128
(-0.6) 		97.2
(-2.3) 		85.4
(-3) 		116
(-1.3) 		192.3
(3) 		107
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193194_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2691
Sequence Type Exemplar sequence
Representative Public ID T05H10.2 NCBI
Target Description T05H10.2 /REP_DB=WormBase Gene ID /WP=CE01639 /GEN=apn-1 /TR=SW:Q10002 /GB=CAA87789.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=AP endonuclease (family 2)
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_063286(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063286 NCBI Caenorhabditis elegans APurinic/apyrimidinic endoNuclease family member (apn-1) (apn-1) mRNA, complete cds. 11/11 None
SNAP00000019962 ENSEMBL cdna:SNAP chromosome:CEL140:II:8047485:8048938:1 11/11 None
GENEFINDER00000019970 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8047485:8048938:1 11/11 None
T05H10.2 ENSEMBL cdna:known chromosome:CEL140:II:8047485:8049026:1 gene:T05H10.2 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
chrII:8048047-8048935(+) 100.0 100.0
Public Domain and Genome References
Gene Title AP endonuclease (family 2)
Gene Symbol apn-1
Ensembl T05H10.2
Entrez Gene 174291 Entrez gene
SwissProt Q10002 EMBL-EBI
WormBase CE28953 Wormbase
Functional Annotations
Ortholog
ID Title Organism
YEAST_2:1773644_AT Major apurinic/apyrimidinic endonuclease, 3'-repair diesterase involved in repair of DNA damage by oxidation and alkylating agents; controls spontaneous mutations Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular 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 CAA87789 Hypothetical protein T05H10.2 [Caenorhabditis elegans] ref|NP_495687.1| APurinic/apyrimidinic endoNuclease family member (apn-1) [Caenorhabditis elegans] sp|Q10002|APN1_CAEEL DNA-(Apurinic or apyrimidinic site) lyase (AP endonuclease) (Apurinic-apyrimidinic endonuclease) 0.0
blast CAE67836 Hypothetical protein CBG13421 [Caenorhabditis briggsae] 1.0E-169
blast JC5235 DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) - Caenorhabditis elegans gb|AAB39924.1| apurinic/apyrimidinic endonuclease 1.0E-161
Protein Domains
Database ID Description E-Value
Pfam IPR001719 EMBL-EBI AP endonuclease, family 2 1.7E-97
Sequence
Target Sequence 
>C. ELEGANS:193194_AT
gaatgctggatcgcctgaagctgagaaattagaaaaatcaagacttgctatgctcgacga
atgtcaacgggctgagaaattaggaatcacgatgtacaatttccatccaggatcaactgt
cggaaagtgtgaaaaagaagaatgcatgacaacaattgcagagacaatcgattttgttgt
tgagaaaactgagaatattattttagttctcgagacaatggctggacaagggaactcgat
tggcggaacttttgaagaactcaagttcatcattgataaagtgaaagttaagtcaagagt
cggagtttgtatcgacacgtgtcacatttttgctggaggatatgatattagaactcaaaa
ggcttatgaagaagtgatgaaaaatttcggtgaagtggttggctggaactatctgaaagc
aatacacatcaatgattcgaagggcgatgtcggttcgaagctcgatcgtcatgagcatat
tggtcaaggcaagataggaaaagcggcttttgagcttttgatgaacgacaaccgtctcga
tggaattccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATGCTGGATCGCCTGAAGCTGAG 321 331 228 Antisense
ATCAAGACTTGCTATGCTCGACGAA 316 27 264 Antisense
GCTCGACGAATGTCAACGGGCTGAG 654 297 279 Antisense
TTTCCATCCAGGATCAACTGTCGGA 374 669 327 Antisense
GGGAACTCGATTGGCGGAACTTTTG 25 489 457 Antisense
ACACGTGTCACATTTTTGCTGGAGG 35 111 542 Antisense
GAAGTGGTTGGCTGGAACTATCTGA 123 335 619 Antisense
GAAGGGCGATGTCGGTTCGAAGCTC 410 333 666 Antisense
GGTTCGAAGCTCGATCGTCATGAGC 398 507 679 Antisense
GGCTTTTGAGCTTTTGATGAACGAC 681 535 732 Antisense
GACAACCGTCTCGATGGAATTCCAA 613 365 754 Antisense
Sequence Source Affymetrix Proprietary Database