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[176392_at]

Description Y105E8B.NN /REP_DB=WormBase Gene ID /WP=CE24097 /CHR=1 /FEA=Sanger Annotation /DEF=(HINXTON)
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 68      4grp_highest_8_8 > 23      4grp_high_8_8 > 05      6grp_highest_nonorm > 83      6grp_total > 58      4grp_total > 03      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1373
1 2 3 4 range
A 648.5
(-2.2)
P 		487.4
(-3)
P 		598.6
(-2.5)
P 		1729.3
(3)
P 		1242
B 700.8
(-2.5)
P 		606.8
(-3)
P 		597.8
(-3)
P 		1840.9
(3)
P 		1243
C 692.5
(-1.7)
P 		545.5
(-2.6)
P 		468.3
(-3)
P 		1543.6
(3)
P 		1075
avr 680.6
(-2.3) 		546.6
(-3) 		554.9
(-3) 		1704.6
(3) 		1158

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 487
1 2 3 4 5 6 range
A 329.1
(-2.8)
P 		513.6
(-0.4)
P 		310.2
(-3)
P 		352.3
(-2.5)
P 		361.3
(-2.3)
P 		772.8
(3)
P 		463
B 440.7
(-0.5)
P 		392.9
(-2.2)
P 		368.7
(-3)
P 		424.6
(-1.1)
P 		399.9
(-1.9)
P 		543.7
(3)
P 		175
C 634.1
(3)
P 		369.2
(-1.6)
P 		445.6
(-0.2)
P 		285.6
(-3)
P 		497.3
(0.6)
P 		575
(2)
P 		349
avr 468
(-0.5) 		425.2
(-1.5) 		374.8
(-2.6) 		354.2
(-3) 		419.5
(-1.6) 		630.5
(3) 		276
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 287
1 2 3 4 range
A 236.1
(2.3)
P 		105.8
(-3)
P 		156.5
(-0.9)
P 		253.1
(3)
P 		147
B 223.5
(-1)
P 		149.9
(-2.7)
P 		138.5
(-3)
P 		392.3
(3)
P 		254
C 229.2
(1.2)
P 		156.8
(-3)
P 		163.2
(-2.6)
P 		260.3
(3)
P 		104
avr 229.6
(0.4) 		137.5
(-3) 		152.7
(-2.4) 		301.9
(3) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 178
1 2 3 4 5 6 range
A 60.7
(-3)
P 		182.7
(2.7)
P 		67.6
(-2.7)
P 		89.3
(-1.7)
P 		109
(-0.7)
P 		188.2
(3)
P 		128
B 153.3
(0.4)
P 		130.8
(-0.8)
P 		89.5
(-3)
P 		112.5
(-1.8)
P 		162.5
(0.9)
P 		202.7
(3)
P 		113
C 235
(3)
P 		112.7
(-1.1)
P 		113.4
(-1.1)
P 		57.4
(-3)
P 		160.9
(0.5)
P 		192.5
(1.6)
P 		178
avr 149.7
(0.5) 		142.1
(0.1) 		90.2
(-2.8) 		86.4
(-3) 		144.1
(0.2) 		194.5
(3) 		108
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176392_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18767
Sequence Type Exemplar sequence
Representative Public ID Y105E8B.NN NCBI
Target Description Y105E8B.NN /REP_DB=WormBase Gene ID /WP=CE24097 /CHR=1 /FEA=Sanger Annotation /DEF=(HINXTON)
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_061143(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061143 NCBI Caenorhabditis elegans Y105E8B.3 (Y105E8B.3) mRNA, complete cds. 11/11 A 
SNAP00000011735 ENSEMBL cdna:SNAP chromosome:CEL140:I:14660234:14665188:1 11/11 None
GENEFINDER00000011748 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:14660234:14665188:1 11/11 None
Y105E8B.3.2 ENSEMBL cdna:known chromosome:CEL140:I:14660233:14665296:1 gene:Y105E8B.3 11/11 None
Y105E8B.3.1 ENSEMBL cdna:known chromosome:CEL140:I:14660234:14665393:1 gene:Y105E8B.3 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:14660164-14663727(+) 96.55 100.0
Public Domain and Genome References
Gene Title
Ensembl Y105E8B.3
Entrez Gene 173322 Entrez gene
SwissProt Q95Q34 EMBL-EBI
WormBase CE33542 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252147_AT RIO1 family protein at
CANINE:1601250_AT similar to RIO kinase 2 cfa
CANINE_2:CFA.17049.1.S1_AT similar to RIO kinase 2 cfa
CANINE_2:CFA.17049.1.S1_S_AT similar to RIO kinase 2 cfa
CANINE_2:CFA.18727.1.S1_AT similar to RIO kinase 2 cfa
DROSOPHILA_2:1630557_AT dm
DROSGENOME1:150571_AT dm
CHICKEN:GGAAFFX.12693.1.S1_AT RIO kinase 2 (yeast) gga
CHICKEN:GGAAFFX.9739.1.S1_S_AT RIO kinase 2 (yeast) gga
HG-U133_PLUS_2:218535_S_AT RIO kinase 2 (yeast) hs
HG-U133A:218535_S_AT RIO kinase 2 (yeast) hs
HG-U133A_2:218535_S_AT RIO kinase 2 (yeast) hs
HU35KSUBA:RC_AA405449_AT RIO kinase 2 (yeast) hs
HU35KSUBC:RC_N49229_AT RIO kinase 2 (yeast) hs
U133_X3P:G8922904_3P_A_AT RIO kinase 2 (yeast) hs
U133_X3P:HS.27021.0.S2_3P_AT RIO kinase 2 (yeast) hs
HG-U133_PLUS_2:222663_AT RIO kinase 2 (yeast) hs
HG-U133B:222663_AT RIO kinase 2 (yeast) hs
HG-U95B:43998_AT RIO kinase 2 (yeast) hs
HG-U95C:56793_AT RIO kinase 2 (yeast) hs
MOUSE430A_2:1423481_AT RIO kinase 2 (yeast) mm
MOE430A:1423481_AT RIO kinase 2 (yeast) mm
MOUSE430_2:1423481_AT RIO kinase 2 (yeast) mm
MOE430A:1436684_A_AT RIO kinase 2 (yeast) mm
MOUSE430A_2:1436684_A_AT RIO kinase 2 (yeast) mm
MOUSE430_2:1436684_A_AT RIO kinase 2 (yeast) mm
MG-U74BV2:111355_AT RIO kinase 2 (yeast) mm
MOE430B:1442911_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
MOUSE430_2:1442911_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
MOUSE430_2:1445384_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
MOE430B:1445384_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
MU19KSUBA:TC14374_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
MU19KSUBA:TC14374_G_AT RIO kinase 2 (yeast), mRNA (cDNA clone MGC:18713 IMAGE:4216633) mm
RAE230A:1377503_AT RIO kinase 2 (yeast) (predicted) rn
RAT230_2:1377503_AT RIO kinase 2 (yeast) (predicted) rn
RAE230B:1394878_AT RIO kinase 2 (yeast) (predicted) rn
RAT230_2:1394878_AT RIO kinase 2 (yeast) (predicted) rn
YEAST_2:1775669_AT Essential serine kinase involved in the processing of the 20S pre-rRNA into mature 18S rRNA; has similarity to Rio1p Sc
Protein Similarities
Method ID Description E-Value
blast CAC70109 Hypothetical protein Y105E8B.3 [Caenorhabditis elegans] ref|NP_493544.2| Y105E8B.3 [Caenorhabditis elegans] 0.0
blast CAE72608 Hypothetical protein CBG19799 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000687 EMBL-EBI Protein of unknown function RIO1 8.7E-70
Pfam IPR000687 EMBL-EBI Protein of unknown function RIO1 8.7E-70
Sequence
Target Sequence 
>C. ELEGANS:176392_AT
caggaagagcctgaggatctcgaaaaagaccacgaagagctccaggctcaggagaacacc
gtcaaacagcagaaaatcgtgctctcccagacgacacgcttcacagattggctctcagac
gccacaaatcaactggaagccgtggatcttgatgctctgaaatcggaggaaggttataag
gatattgagttgccgccggaggattttaagcgtccagccgattctgaaaatgacgatgaa
aatgatgaagatgaggaggagggggaggaagaggacgcggatggccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGAAGAGCCTGAGGATCTCGAAA 655 207 1174 Antisense
AAAGACCACGAAGAGCTCCAGGCTC 555 121 1198 Antisense
CAGGCTCAGGAGAACACCGTCAAAC 710 207 1216 Antisense
GACGACACGCTTCACAGATTGGCTC 242 379 1263 Antisense
GATTGGCTCTCAGACGCCACAAATC 280 435 1279 Antisense
GACGCCACAAATCAACTGGAAGCCG 132 381 1291 Antisense
GGAAGCCGTGGATCTTGATGCTCTG 384 531 1308 Antisense
TAAGGATATTGAGTTGCCGCCGGAG 407 635 1350 Antisense
GCCGCCGGAGGATTTTAAGCGTCCA 658 281 1365 Antisense
TTAAGCGTCCAGCCGATTCTGAAAA 319 685 1379 Antisense
GGAGGAAGAGGACGCGGATGGCCAC 79 515 1437 Antisense
Sequence Source Affymetrix Proprietary Database