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[171949_x_at]

Description AV200064_rc /REP_DB=TREMBL Accession /GB=AV200064 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk556b4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 68      4grp_high_8_8 > 28      6grp_highest_nonorm > 82      6grp_total > 58      4grp_total > 20      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 294
1 2 3 4 range
A 287.4
(-0.1)
P 		354.3
(3)
P 		225.9
(-3)
P 		336
(2.1)
P 		128
B 360.2
(1.9)
P 		226.6
(-3)
A 		243.8
(-2.4)
A 		390.6
(3)
P 		164
C 246.1
(-0.5)
P 		254.6
(-0.3)
M 		122.9
(-3)
P 		417
(3)
P 		294
avr 297.9
(0.3) 		278.5
(-0.4) 		197.5
(-3) 		381.2
(3) 		184

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 246
1 2 3 4 5 6 range
A 323.2
(1.8)
P 		236.5
(-3)
P 		247.1
(-2.4)
P 		289.5
(-0)
P 		252
(-2.1)
P 		344.1
(3)
P 		108
B 368.6
(-0.2)
P 		295.6
(-2.3)
P 		269
(-3)
P 		270.2
(-3)
P 		292.2
(-2.3)
P 		482.5
(3)
P 		214
C 294.1
(-1.6)
P 		368.5
(0.5)
P 		257.9
(-2.6)
P 		243.4
(-3)
P 		332.3
(-0.5)
P 		457.9
(3)
P 		215
avr 328.6
(-0.5) 		300.2
(-1.5) 		258
(-3) 		267.7
(-2.7) 		292.2
(-1.8) 		428.2
(3) 		170
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 104.6
(3)
P 		76.9
(0)
P 		59.1
(-1.9)
P 		49.2
(-3)
P 		55
B 114.9
(3)
P 		56
(-3)
A 		56.5
(-2.9)
A 		83.2
(-0.2)
P 		59
C 81.5
(3)
P 		73.2
(1.7)
M 		42.9
(-3)
P 		70.3
(1.3)
P 		39
avr 100.3
(3) 		68.7
(-1) 		52.8
(-3) 		67.6
(-1.1) 		48

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 131
1 2 3 4 5 6 range
A 59.6
(-1.9)
P 		84.1
(3)
P 		53.8
(-3)
P 		73.4
(0.9)
P 		76
(1.4)
P 		83.8
(2.9)
P 		30
B 128.2
(0.3)
P 		98.4
(-1.3)
P 		65.3
(-3)
P 		71.6
(-2.7)
P 		118.7
(-0.2)
P 		179.9
(3)
P 		115
C 109
(0.5)
P 		112.5
(0.7)
P 		65.6
(-2)
P 		48.9
(-3)
P 		107.5
(0.4)
P 		153.3
(3)
P 		104
avr 98.9
(-0.1) 		98.3
(-0.2) 		61.6
(-3) 		64.6
(-2.8) 		100.7
(0) 		139
(3) 		77
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171949_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27703
Sequence Type Exemplar sequence
Representative Public ID AV200064 NCBI
Target Description AV200064_rc /REP_DB=TREMBL Accession /GB=AV200064 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk556b4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
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_066938(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066938 NCBI Caenorhabditis elegans Y39A1A.24 (Y39A1A.24) mRNA, complete cds. 10/11 A 
SNAP00000012906 ENSEMBL cdna:SNAP chromosome:CEL140:III:10613792:10614762:1 10/11 None
GENEFINDER00000012942 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10613792:10614762:1 10/11 None
Y39A1A.24 ENSEMBL cdna:known chromosome:CEL140:III:10613444:10614807:1 gene:Y39A1A.24 10/11 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
chrIII:10614450-10614722(+) 86.9 86.9
Public Domain and Genome References
Gene Title
Ensembl Y39A1A.24
Entrez Gene 3564902 Entrez gene
SwissProt Q9XX20 EMBL-EBI
WormBase CE19124 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA21020 Hypothetical protein Y39A1A.24 [Caenorhabditis elegans] ref|NP_499339.1| Y39A1A.24 [Caenorhabditis elegans] 4.0E-55
blast T26732 hypothetical protein Y39A1A.5a - Caenorhabditis elegans 2.0E-49
blast CAE71439 Hypothetical protein CBG18350 [Caenorhabditis briggsae] 4.0E-33
Sequence
Target Sequence 
>C. ELEGANS:171949_X_AT
agaagggtggcgaaggactcggcgcggctggtccaattctcgaagaaatggaggcacttg
tgctcaaaattgcgagcatcttcaagaaacaggcggccggaaataccgtatccgcatcga
aaagaggatcgacacagagtccagtcatccgaacagctgaagcatcgactcagagagcat
cgccggcgattgcancaagttgaaaagtttgaaagtgttcgtcaaccgagagaaccgaga
agcacgatcgaaac

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAAGGGTGGCGAAGGACTCGGCGC 121 75 38 Antisense
CGGCTGGTCCAATTCTCGAAGAAAT 44 243 62 Antisense
GAGGCACTTGTGCTCAAAATTGCGA 507 405 88 Antisense
GCATCTTCAAGAAACAGGCGGCCGG 105 309 113 Antisense
GGCGGCCGGAAATACCGTATCCGCA 19 535 129 Antisense
AATACCGTATCCGCATCGAAAAGAG 208 167 139 Antisense
GATCGACACAGAGTCCAGTCATCCG 515 417 164 Antisense
GTCCAGTCATCCGAACAGCTGAAGC 24 477 176 Antisense
AGCATCGACTCAGAGAGCATCGCCG 663 77 198 Antisense
GTGTTCGTCAACCGAGAGAACCGAG 462 485 252 Antisense
GAGAACCGAGAAGCACGATCGAAAC 271 391 267 Antisense
Sequence Source Affymetrix Proprietary Database