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[172064_x_at]

Description g6272677 /REP_DB=GenBank Identifier /GB=AF180730.1 /PROTEIN_GB=AAF06159.1 /CHR=5 /FEA=Mapped Transcript /DEF=RNA interference promoting factor RDE-1
Cluster 6grp_highest_10_10 > 47      6grp_high1_10_10 > 74      4grp_highest_8_8 > 51      4grp_high_8_8 > 24      6grp_highest_nonorm > 64      6grp_total > 65      4grp_total > 47      6grp_cgc > 66      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 896
1 2 3 4 range
A 1060.5
(3)
P 		432.9
(-2.1)
P 		329.1
(-3)
P 		681.6
(-0.1)
P 		731
B 1115.1
(3)
P 		625.8
(-1.7)
P 		601.8
(-1.9)
P 		491.1
(-3)
P 		624
C 1224.7
(3)
P 		501.3
(-2.8)
P 		476.3
(-3)
P 		571.6
(-2.2)
P 		748
avr 1133.4
(3) 		520
(-2.5) 		469.1
(-3) 		581.4
(-2) 		664

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 463
1 2 3 4 5 6 range
A 773.2
(-3)
P 		921.6
(2)
P 		819.4
(-1.4)
P 		873.2
(0.4)
P 		828.2
(-1.1)
P 		950.3
(3)
P 		177
B 777.4
(-0.2)
P 		645.2
(-3)
P 		807.9
(0.5)
P 		924.9
(3)
P 		734
(-1.1)
P 		902.8
(2.5)
P 		280
C 662.8
(-2.2)
P 		716.5
(-1.5)
P 		1064.9
(3)
P 		1037.3
(2.6)
P 		601.6
(-3)
P 		1016.6
(2.4)
P 		463
avr 737.8
(-2.6) 		761.1
(-2) 		897.4
(1.5) 		945.1
(2.7) 		721.3
(-3) 		956.6
(3) 		235
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 319
1 2 3 4 range
A 386.1
(3)
P 		94
(-2.8)
P 		86
(-3)
P 		99.8
(-2.7)
P 		300
B 355.6
(3)
P 		154.6
(-1.8)
P 		139.4
(-2.2)
P 		104.7
(-3)
P 		251
C 405.4
(3)
P 		144.1
(-2.1)
P 		166
(-1.6)
P 		96.4
(-3)
P 		309
avr 382.4
(3) 		130.9
(-2.3) 		130.5
(-2.4) 		100.3
(-3) 		282

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 198
1 2 3 4 5 6 range
A 142.5
(-3)
P 		327.8
(3)
P 		178.4
(-1.8)
P 		221.5
(-0.4)
P 		249.9
(0.5)
P 		231.4
(-0.1)
P 		185
B 270.5
(0.2)
P 		214.8
(-2.2)
P 		196.2
(-3)
P 		245
(-0.9)
P 		298.2
(1.4)
P 		336.7
(3)
P 		141
C 245.7
(-0.9)
P 		218.6
(-2)
P 		271
(0.1)
P 		208.6
(-2.4)
P 		194.7
(-3)
P 		340.3
(3)
P 		146
avr 219.6
(-2.7) 		253.7
(-0.4) 		215.2
(-3) 		225
(-2.3) 		247.6
(-0.8) 		302.8
(3) 		88
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172064_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19907
Sequence Type Exemplar sequence
Representative Public ID 6272677 NCBI
Target Description g6272677 /REP_DB=GenBank Identifier /GB=AF180730.1 /PROTEIN_GB=AAF06159.1 /CHR=5 /FEA=Mapped Transcript /DEF=RNA interference promoting factor RDE-1
Cluster Evidence This cluster is supported by a Mapped Transcript.
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_171525(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171525 NCBI Caenorhabditis elegans RNAi DEfective family member (rde-1) (rde-1) mRNA, complete cds. 11/11 A 
SNAP00000005147 ENSEMBL cdna:SNAP chromosome:CEL140:V:9990625:9994196:-1 10/11 None
GENEFINDER00000005161 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9989653:9994196:-1 9/11 None
K08H10.7 ENSEMBL cdna:known chromosome:CEL140:V:9990498:9994224:-1 gene:K08H10.7 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
chrV:9990496-9994216(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rde-1
Ensembl K08H10.7
Entrez Gene 179393 Entrez gene
SwissProt Q9XU82 EMBL-EBI
WormBase CE28243 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB05546 Hypothetical protein K08H10.7 [Caenorhabditis elegans] ref|NP_741611.1| RNAi DEfective family member (rde-1) [Caenorhabditis elegans] gb|AAF06159.1| RNA interference promoting factor RDE-1 [Caenorhabditis elegans] 0.0
blast CAE72296 Hypothetical protein CBG19426 [Caenorhabditis briggsae] 0.0
blast CAB02797 Hypothetical protein C27H6.8 [Caenorhabditis elegans] emb|CAB05549.1| Hypothetical protein C27H6.8 [Caenorhabditis elegans] ref|NP_741610.1| C27H6.8 [Caenorhabditis elegans] sp|O17606|YK4P_CAEEL Hypothetical UPF0160 protein C27H6.8 in chromosome V 1.0E-101
blast CAE63062 Hypothetical protein CBG07340 [Caenorhabditis briggsae] 3.0E-44
Protein Domains
Database ID Description E-Value
Pfam IPR003100 EMBL-EBI Argonaute and Dicer protein, PAZ 3.2E-25
Pfam IPR003165 EMBL-EBI Stem cell self-renewal protein Piwi 4.7E-60
Pfam IPR003226 EMBL-EBI Metal-dependent protein hydrolase 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:172064_X_AT
aaagatcttactcctgctgaaacagatgtcgctgttgctgctgttaaacaatgggaggag
gatatgaaagaaagcaaagaaactggaattgtgaacccatcatccggaacaactgtggat
aaacttatcgtttcgaaatacaaattcgattttttcttggcatctcatcatggtgtcctt
ggtacatctcgtccaggacattacactgttatgtatgacgataaaggaatgagccaagat
gaagtctataaaatgacctacggacttgcttttctctctgctagatgtcgaaaacccatc
tcgttgcctgttccggttcattatgctcatttatcatgtgaaaaagcgaaagagctttat
cgaacttacaaggaacattacatcggtgactatgcacagccacggactcgacacgaaatg
gaacattttctccaaactaacgtgaagtaccctggaatgtcgttcgcataacattttgca
aaagtgtcgcccgtttcaatcaaattttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAGATCTTACTCCTGCTGAAACAG 430 121 2625 Antisense
AGATGTCGCTGTTGCTGCTGTTAAA 621 67 2648 Antisense
AATTGTGAACCCATCATCCGGAACA 99 177 2711 Antisense
TCTTGGCATCTCATCATGGTGTCCT 128 619 2779 Antisense
TCATGGTGTCCTTGGTACATCTCGT 320 623 2792 Antisense
GCTTTTCTCTCTGCTAGATGTCGAA 221 305 2892 Antisense
GATGTCGAAAACCCATCTCGTTGCC 261 407 2908 Antisense
CTGTTCCGGTTCATTATGCTCATTT 390 239 2932 Antisense
ACATCGGTGACTATGCACAGCCACG 576 105 3004 Antisense
GAAGTACCCTGGAATGTCGTTCGCA 288 335 3068 Antisense
TGTCGCCCGTTTCAATCAAATTTTT 275 555 3109 Antisense
Sequence Source GenBank