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[187389_s_at]

Description Y55F3AM.3A /REP_DB=WormBase Gene ID /WP=CE25484 /TR=Q9N368 /GB=AAF60795.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 29      4grp_highest_8_8 > 12      4grp_high_8_8 > 39      6grp_highest_nonorm > 50      6grp_total > 26      4grp_total > 40      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 144
1 2 3 4 range
A 375.2
(-3)
P 		448.6
(0.8)
P 		491.5
(3)
P 		466.9
(1.7)
P 		116
B 394.5
(-3)
P 		479.6
(1.2)
P 		516.2
(3)
P 		493.6
(1.9)
P 		122
C 372
(-3)
P 		406.6
(-0.3)
P 		450
(3)
P 		405.5
(-0.4)
P 		78
avr 380.6
(-3) 		444.9
(0.7) 		485.9
(3) 		455.3
(1.3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 428
1 2 3 4 5 6 range
A 559.8
(2.6)
P 		569.2
(3)
P 		430.3
(-3)
P 		435.4
(-2.8)
P 		483.9
(-0.7)
P 		476
(-1)
P 		139
B 588.7
(2.3)
P 		608.4
(3)
P 		460.5
(-2.1)
P 		487.6
(-1.1)
P 		432.7
(-3)
P 		492.3
(-1)
P 		176
C 551.3
(3)
P 		553.1
(3)
P 		481.7
(1.9)
P 		180.4
(-3)
P 		511.5
(2.3)
P 		440.1
(1.2)
P 		373
avr 566.6
(2.7) 		576.9
(3) 		457.5
(-0.4) 		367.8
(-3) 		476
(0.1) 		469.5
(-0.1) 		209
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 136.6
(3)
P 		97.4
(-0.4)
P 		128.5
(2.3)
P 		68.3
(-3)
P 		68
B 125.8
(3)
P 		118.4
(0.8)
P 		119.6
(1.2)
P 		105.2
(-3)
P 		21
C 123.1
(0.7)
P 		116.9
(0.3)
P 		156.8
(3)
P 		68.4
(-3)
P 		88
avr 128.5
(2.3) 		110.9
(0.3) 		135
(3) 		80.6
(-3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 169
1 2 3 4 5 6 range
A 103.2
(-2.5)
P 		202.4
(3)
P 		93.7
(-3)
P 		110.4
(-2.1)
P 		146
(-0.1)
P 		115.9
(-1.8)
P 		109
B 204.8
(3)
P 		202.5
(2.9)
P 		111.8
(-3)
P 		129.2
(-1.9)
P 		175.8
(1.1)
P 		183.6
(1.6)
P 		93
C 204.3
(3)
P 		168.8
(1.7)
P 		122.6
(0.1)
P 		36.3
(-3)
P 		165.5
(1.6)
P 		147.3
(1)
P 		168
avr 170.8
(1.8) 		191.2
(3) 		109.4
(-1.9) 		92
(-3) 		162.4
(1.3) 		148.9
(0.4) 		99
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187389_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10971
Sequence Type Exemplar sequence
Representative Public ID Y55F3AM.3A NCBI
Target Description Y55F3AM.3A /REP_DB=WormBase Gene ID /WP=CE25484 /TR=Q9N368 /GB=AAF60795.1 /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_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_171252 NCBI Caenorhabditis elegans Y55F3AM.3c (Y55F3AM.3) mRNA, complete cds. 11/11 None
SNAP00000030050 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1013878:1019268:1 11/11 None
GENEFINDER00000030074 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1012788:1019268:1 11/11 None
Y55F3AM.3a ENSEMBL cdna:known chromosome:CEL140:IV:1012652:1019547:1 gene:Y55F3AM.3 11/11 A 
Y55F3AM.3c.1 ENSEMBL cdna:known chromosome:CEL140:IV:1012704:1019268:1 gene:Y55F3AM.3 11/11 A 
Y55F3AM.3c.2 ENSEMBL cdna:known chromosome:CEL140:IV:1014235:1019268:1 gene:Y55F3AM.3 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176922 3 2 NM_067624 187389_s_at (11)
NM_171252 187389_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:1012793-1019274(+) 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
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:187389_S_AT
cagtgtctggctcacggtggagcacttcatgtatttgtggataaaggctcagagcaagga
aatgtctatgtaaagtgtccatcgattgtgattgcacatcaggcagttagtgcgctccac
ggaagatggttcagtggaaaagttatcactgctaactatgtacctgttaattcatatcat
gacttgttcccggatgcagtacatgctagaattgtgctcacgacgcgtggagctgctccg
gtggttcctattgtacctatggttccagttgtgccacctcaaggaatcgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTGTCTGGCTCACGGTGGAGCAC 536 207 1363 Antisense
ACGGTGGAGCACTTCATGTATTTGT 55 97 1376 Antisense
GTGTCCATCGATTGTGATTGCACAT 596 487 1437 Antisense
ACATCAGGCAGTTAGTGCGCTCCAC 578 105 1458 Antisense
GTGCGCTCCACGGAAGATGGTTCAG 459 479 1472 Antisense
TTATCACTGCTAACTATGTACCTGT 74 681 1505 Antisense
CTTGTTCCCGGATGCAGTACATGCT 41 215 1545 Antisense
TTGTGCTCACGACGCGTGGAGCTGC 91 707 1574 Antisense
TCCGGTGGTTCCTATTGTACCTATG 271 595 1599 Antisense
GTACCTATGGTTCCAGTTGTGCCAC 404 457 1615 Antisense
AGTTGTGCCACCTCAAGGAATCGCA 73 65 1629 Antisense
Sequence Source Affymetrix Proprietary Database