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[189020_at] endonuclease

Description Y47G6A.8 /REP_DB=WormBase Gene ID /WP=CE22109 /TR=Q9N3T2 /GB=AAF60653.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=endonuclease
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 78      4grp_highest_8_8 > 10      4grp_high_8_8 > 62      6grp_highest_nonorm > 94      6grp_total > 69      4grp_total > 57      6grp_highest_sub > Da      6grp_cgc > 39      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 342
1 2 3 4 range
A 301.4
(-2.1)
P 		480.3
(2.4)
P 		505.3
(3)
P 		266.9
(-3)
P 		238
B 306.6
(-1.8)
P 		477.7
(1.5)
P 		556.9
(3)
P 		244
(-3)
P 		313
C 338
(-1.6)
P 		438.2
(0.3)
P 		585.5
(3)
P 		261.3
(-3)
P 		324
avr 315.3
(-1.8) 		465.4
(1.3) 		549.2
(3) 		257.4
(-3) 		292

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 665
1 2 3 4 5 6 range
A 449.3
(-1.5)
P 		326.3
(-3)
P 		384.6
(-2.3)
P 		383.7
(-2.3)
P 		481.5
(-1.1)
P 		827.8
(3)
P 		502
B 481.1
(-1.2)
P 		316.5
(-3)
P 		356
(-2.6)
P 		427.2
(-1.8)
P 		545.9
(-0.5)
P 		875.9
(3)
P 		559
C 482.8
(-1.7)
P 		343.4
(-3)
P 		365.6
(-2.8)
P 		399.4
(-2.5)
P 		496.3
(-1.6)
P 		981.9
(3)
P 		639
avr 471.1
(-1.5) 		328.7
(-3) 		368.7
(-2.6) 		403.4
(-2.2) 		507.9
(-1.1) 		895.2
(3) 		567
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 165
1 2 3 4 range
A 109.7
(1.6)
P 		104.3
(1.2)
P 		132.1
(3)
P 		39.1
(-3)
P 		93
B 97.8
(0.6)
P 		118
(2.1)
P 		129.1
(3)
P 		52
(-3)
P 		77
C 111.9
(-0.5)
P 		126
(0.1)
P 		204.1
(3)
P 		44.1
(-3)
P 		160
avr 106.5
(0.3) 		116.1
(0.9) 		155.1
(3) 		45.1
(-3) 		110

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 248
1 2 3 4 5 6 range
A 82.8
(-3)
P 		116
(-1.3)
P 		83.8
(-2.9)
P 		97.3
(-2.3)
P 		145.3
(0.2)
P 		201.6
(3)
P 		119
B 167.4
(-1)
P 		105.3
(-2.5)
P 		86.4
(-3)
P 		113.2
(-2.3)
P 		221.8
(0.4)
P 		326.6
(3)
P 		240
C 178.9
(-0.6)
P 		104.8
(-2.4)
P 		93
(-2.7)
P 		80.3
(-3)
P 		160.6
(-1.1)
P 		328.7
(3)
P 		248
avr 143
(-1.3) 		108.7
(-2.4) 		87.7
(-3) 		96.9
(-2.7) 		175.9
(-0.3) 		285.6
(3) 		198
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189020_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.81
Sequence Type Exemplar sequence
Representative Public ID Y47G6A.8 NCBI
Target Description Y47G6A.8 /REP_DB=WormBase Gene ID /WP=CE22109 /TR=Q9N3T2 /GB=AAF60653.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058767(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058767 NCBI Caenorhabditis elegans Y47G6A.8 (endonuclease) mRNA, complete cds. 11/11 None
SNAP00000033977 ENSEMBL cdna:SNAP chromosome:CEL140:I:3482031:3484366:1 11/11 None
GENEFINDER00000034077 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3482031:3484366:1 11/11 None
Y47G6A.8 ENSEMBL cdna:known chromosome:CEL140:I:3481988:3484484:1 gene:Y47G6A.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
chrI:3482030-3484366(+) 100.0 100.0
Public Domain and Genome References
Gene Title endonuclease
Gene Symbol crn-1
Ensembl Y47G6A.8
Entrez Gene 171917 Entrez gene
SwissProt Q9N3T2 EMBL-EBI
WormBase CE22109 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18772_AT endonuclease, putative at
ATH1-121501:246838_AT endonuclease, putative at
CANINE:1604729_AT similar to flap structure-specific endonuclease 1 cfa
CANINE:1593944_AT similar to flap structure-specific endonuclease 1 cfa
CANINE_2:CFA.1780.1.S1_AT similar to flap structure-specific endonuclease 1 cfa
CANINE_2:CFAAFFX.24613.1.S1_S_AT similar to flap structure-specific endonuclease 1 cfa
DROSOPHILA_2:1624557_AT Flap endonuclease 1 dm
DROSGENOME1:144102_AT Flap endonuclease 1 dm
HG-U133A:204768_S_AT flap structure-specific endonuclease 1 hs
HG-U133_PLUS_2:204768_S_AT flap structure-specific endonuclease 1 hs
HG-U133A_2:204768_S_AT flap structure-specific endonuclease 1 hs
HU35KSUBA:RC_AA620553_S_AT flap structure-specific endonuclease 1 hs
HG-U133A:204767_S_AT flap structure-specific endonuclease 1 hs
HG-U133_PLUS_2:204767_S_AT flap structure-specific endonuclease 1 hs
HG-FOCUS:204767_S_AT flap structure-specific endonuclease 1 hs
HG-U133A_2:204767_S_AT flap structure-specific endonuclease 1 hs
U133_X3P:G6325465_3P_A_AT flap structure-specific endonuclease 1 hs
U133_X3P:G12653112_3P_A_AT flap structure-specific endonuclease 1 hs
HG-U95AV2:41583_AT flap structure-specific endonuclease 1 hs
HG-U95E:70769_AT Flap structure-specific endonuclease 1 hs
MU11KSUBA:L26320_S_AT flap structure specific endonuclease 1 mm
MG-U74AV2:97327_AT flap structure specific endonuclease 1 mm
MOE430A:1421731_A_AT flap structure specific endonuclease 1 mm
MOUSE430A_2:1421731_A_AT flap structure specific endonuclease 1 mm
MOUSE430_2:1421731_A_AT flap structure specific endonuclease 1 mm
MOE430A:1436454_X_AT flap structure specific endonuclease 1 mm
MOUSE430A_2:1436454_X_AT flap structure specific endonuclease 1 mm
MOUSE430_2:1436454_X_AT flap structure specific endonuclease 1 mm
MU19KSUBB:TC27668_I_AT Flap structure specific endonuclease 1, mRNA (cDNA clone MGC:28169 IMAGE:3985840) mm
RT-U34:RC_AA819793_AT flap structure-specific endonuclease 1 rn
RG-U34A:RC_AA819793_AT flap structure-specific endonuclease 1 rn
RAE230A:1367983_AT flap structure-specific endonuclease 1 rn
RAT230_2:1367983_AT flap structure-specific endonuclease 1 rn
YEAST_2:1777959_AT 5' to 3' exonuclease, 5' flap endonuclease, required for Okazaki fragment processing and maturation as well as for long-patch base-excision repair; member of the S. pombe RAD2/FEN1 family Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4518 nuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_491168 Y47G6A.8 [Caenorhabditis elegans] gb|AAF60653.1| Cell-death-related nuclease protein 1 [Caenorhabditis elegans] gb|AAP57297.1| cell death-related nuclease 1 [Caenorhabditis elegans] 0.0
blast CAE68965 Hypothetical protein CBG14945 [Caenorhabditis briggsae] 1.0E-155
blast AAQ91235 flap structure-specific endonuclease 1 [Danio rerio] gb|AAH71488.1| Fen1 protein [Danio rerio] 1.0E-125
Protein Domains
Database ID Description E-Value
Pfam IPR002421 EMBL-EBI 5-3 exonuclease 2.8E-8
Pfam IPR006086 EMBL-EBI XPG I domain 4.9E-38
Pfam IPR006085 EMBL-EBI XPG N-terminal 2.3E-54
Sequence
Target Sequence 
>C. ELEGANS:189020_AT
tgaggatatggacgcgctgaccttcggctccacggttcttctcagacatttcctggctcc
agtcgccaagaaaatcccgatcaaggagttcaatctttctttggctctcgaagaaatgaa
gctaagcgttgaggaatttattgatttgtgtattcttctcggctgtgactattgtggaac
tattcgaggcgtcgggcctaagaaggctgttgagctgatcagacagcacaagaatattga
gacgattcttgagaatatcgatcaaaataaatacccaccaccagaggattggccatacaa
gcgtgctcgtgagcttttcctcaatccagaagtgacaaaaccggaagaagttgaactgac
atggaaggaagccgatgtcgaaggtgtcattcagttcttgtgcggagagaagaacttcaa
tgaggagcgcatccgaaacgcgttggcaaaactgaagactagccgtaaatctggaacaca
aggacgaattgactcgttcttcggaaactcgacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAGGATATGGACGCGCTGACCTTC 441 567 543 Antisense
CACGGTTCTTCTCAGACATTTCCTG 134 197 573 Antisense
TTTCCTGGCTCCAGTCGCCAAGAAA 687 669 591 Antisense
TTCAATCTTTCTTTGGCTCTCGAAG 550 685 631 Antisense
TATTCTTCTCGGCTGTGACTATTGT 326 663 693 Antisense
GGAACTATTCGAGGCGTCGGGCCTA 325 525 718 Antisense
TGGCCATACAAGCGTGCTCGTGAGC 330 545 832 Antisense
TCGTGAGCTTTTCCTCAATCCAGAA 626 605 849 Antisense
AGGTGTCATTCAGTTCTTGTGCGGA 685 55 924 Antisense
AGCGCATCCGAAACGCGTTGGCAAA 203 83 968 Antisense
GACTCGTTCTTCGGAAACTCGACCA 675 371 1033 Antisense
Sequence Source Affymetrix Proprietary Database