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[172643_s_at]

Description Y55F3AM.3B /REP_DB=WormBase Gene ID /WP=CE25485 /TR=Q9N367 /GB=AAF60796.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 96      4grp_total > 03      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 55
1 2 3 4 range
A 43.3
(-3)
A 		48.1
(-2.1)
A 		54.9
(-0.9)
A 		77.1
(3)
A 		34
B 51.3
(3)
P 		26.2
(-2.2)
A 		23
(-2.9)
A 		22.5
(-3)
A 		29
C 34.8
(-3)
A 		49.7
(1.1)
A 		43.8
(-0.5)
A 		56.8
(3)
A 		22
avr 43.1
(-1.7) 		41.3
(-2.6) 		40.6
(-3) 		52.1
(3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 44
1 2 3 4 5 6 range
A 47
(3)
A 		40.8
(1.6)
A 		25.7
(-1.7)
A 		20
(-3)
A 		38.2
(1)
A 		41.6
(1.8)
A 		27
B 31.2
(-1)
A 		20.8
(-3)
A 		27.6
(-1.7)
A 		41.9
(1.1)
A 		51.8
(3)
A 		50.6
(2.8)
A 		31
C 11.2
(-2.5)
A 		22.7
(-0.7)
A 		8.3
(-3)
A 		44.1
(2.7)
A 		27
(-0)
A 		45.7
(3)
A 		37
avr 29.8
(-0.8) 		28.1
(-1.2) 		20.5
(-3) 		35.3
(0.5) 		39
(1.4) 		46
(3) 		26
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 15.8
(3)
A 		10.4
(-3)
A 		14.3
(1.3)
A 		11.3
(-2)
A 		5
B 16.4
(3)
P 		6.5
(-2.1)
A 		5.3
(-2.7)
A 		4.8
(-3)
A 		12
C 11.5
(-1)
A 		14.3
(1.9)
A 		15.3
(3)
A 		9.6
(-3)
A 		6
avr 14.6
(3) 		10.4
(-1.2) 		11.6
(0) 		8.6
(-3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19
1 2 3 4 5 6 range
A 8.7
(-0.7)
A 		14.5
(3)
A 		5.6
(-2.7)
A 		5.1
(-3)
A 		11.5
(1.1)
A 		10.1
(0.2)
A 		9
B 10.9
(-1.3)
A 		6.9
(-2.9)
A 		6.7
(-3)
A 		11.1
(-1.2)
A 		21.1
(3)
A 		18.9
(2.1)
A 		14
C 4.2
(-2)
A 		6.9
(-0.8)
A 		2.1
(-3)
A 		8.9
(0.1)
A 		8.7
(-0)
A 		15.3
(3)
A 		13
avr 7.9
(-1.1) 		9.4
(-0.2) 		4.8
(-3) 		8.4
(-0.8) 		13.8
(2.4) 		14.8
(3) 		10
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172643_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11003
Sequence Type Exemplar sequence
Representative Public ID Y55F3AM.3B NCBI
Target Description Y55F3AM.3B /REP_DB=WormBase Gene ID /WP=CE25485 /TR=Q9N367 /GB=AAF60796.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=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_067624(11), NM_067625(11), NM_171252(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067624 NCBI Caenorhabditis elegans Y55F3AM.3a (Y55F3AM.3) mRNA, complete cds. 11/11 A 
NM_067625 NCBI Caenorhabditis elegans Y55F3AM.3b (Y55F3AM.3) mRNA, complete cds. 11/11 None
NM_171252 NCBI Caenorhabditis elegans Y55F3AM.3c (Y55F3AM.3) mRNA, complete cds. 11/11 None
SNAP00000030049 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1012788:1013561:1 11/11 None
GENEFINDER00000030074 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1012788:1019268:1 9/11 None
Y55F3AM.3a ENSEMBL cdna:known chromosome:CEL140:IV:1012652:1019547:1 gene:Y55F3AM.3 11/11 A 
Y55F3AM.3b ENSEMBL cdna:known chromosome:CEL140:IV:1012703:1013427:1 gene:Y55F3AM.3 11/11 None
Y55F3AM.3c.1 ENSEMBL cdna:known chromosome:CEL140:IV:1012704:1019268:1 gene:Y55F3AM.3 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
chrIV:1012793-1013117(+) 100.0 100.0
Public Domain and Genome References
Ensembl Y55F3AM.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAF60795 Hypothetical protein Y55F3AM.3a [Caenorhabditis elegans] ref|NP_500025.1| Y55F3AM.3a [Caenorhabditis elegans] 0.0
blast AAM97977 Hypothetical protein Y55F3AM.3c [Caenorhabditis elegans] ref|NP_741301.1| Y55F3AM.3c [Caenorhabditis elegans] 0.0
blast CAE68285 Hypothetical protein CBG13969 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.2E-15
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.7E-18
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.2E-15
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.7E-18
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.2E-15
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.7E-18
Sequence
Target Sequence 
>C. ELEGANS:172643_S_AT
tgaccgacggatcgatggacatcgacgcgatgctcgagggaggccttgagatggcgaaaa
acgacagatcacaaagtcgtcaaagatcgccggcaagatcgaatcgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGACCGACGGATCGATGGACATCGA 665 569 14 Antisense
GATGGACATCGACGCGATGCTCGAG 424 407 27 Antisense
GGACATCGACGCGATGCTCGAGGGA 619 525 30 Antisense
CATCGACGCGATGCTCGAGGGAGGC 567 209 33 Antisense
CGATGCTCGAGGGAGGCCTTGAGAT 299 249 41 Antisense
GCTCGAGGGAGGCCTTGAGATGGCG 638 299 45 Antisense
GAGGGAGGCCTTGAGATGGCGAAAA 154 403 49 Antisense
GAGATGGCGAAAAACGACAGATCAC 653 395 61 Antisense
GACAGATCACAAAGTCGTCAAAGAT 333 367 76 Antisense
CACAAAGTCGTCAAAGATCGCCGGC 145 195 83 Antisense
AAGATCGCCGGCAAGATCGAATCGT 387 155 96 Antisense
Sequence Source Affymetrix Proprietary Database