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[175259_at]

Description AV185445_rc /REP_DB=TREMBL Accession /GB=AV185445 /CHR=5 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk678d4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 88      4grp_highest_8_8 > 31      4grp_high_8_8 > 05      6grp_highest_nonorm > 94      6grp_total > 88      4grp_total > 03      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1138
1 2 3 4 range
A 518.9
(-1.7)
P 		404.4
(-2.4)
P 		296.4
(-3)
P 		1295.6
(3)
P 		999
B 456.5
(-2)
P 		287
(-3)
P 		328.1
(-2.8)
P 		1353.6
(3)
P 		1067
C 494
(-2.1)
P 		343.8
(-3)
P 		337.4
(-3)
P 		1424.5
(3)
P 		1087
avr 489.8
(-2) 		345.1
(-2.9) 		320.6
(-3) 		1357.9
(3) 		1037

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 549
1 2 3 4 5 6 range
A 375.2
(-2.2)
P 		314.7
(-3)
P 		468
(-0.9)
P 		383.5
(-2)
P 		579.5
(0.7)
P 		746.7
(3)
P 		432
B 407.2
(-2.2)
P 		336.2
(-3)
P 		422.5
(-2)
P 		404.5
(-2.2)
P 		700.9
(1.3)
P 		840.7
(3)
P 		505
C 322.9
(-3)
P 		394.7
(-2.2)
P 		331.2
(-2.9)
P 		347.9
(-2.7)
P 		588.5
(-0.1)
P 		863.4
(3)
P 		541
avr 368.4
(-2.7) 		348.5
(-3) 		407.2
(-2.2) 		378.6
(-2.6) 		623
(0.5) 		816.9
(3) 		468
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 218
1 2 3 4 range
A 188.9
(3)
P 		87.8
(-2.4)
P 		77.5
(-3)
P 		189.6
(3)
P 		112
B 145.6
(-0.9)
P 		70.9
(-3)
P 		76
(-2.9)
P 		288.4
(3)
P 		218
C 163.5
(-0.3)
P 		98.8
(-3)
P 		117.6
(-2.2)
P 		240.2
(3)
P 		141
avr 166
(0.1) 		85.8
(-3) 		90.4
(-2.8) 		239.4
(3) 		154

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 244
1 2 3 4 5 6 range
A 69.2
(-3)
P 		111.9
(-0.7)
P 		101.9
(-1.3)
P 		97.3
(-1.5)
P 		174.9
(2.6)
P 		181.8
(3)
P 		113
B 141.7
(-1.9)
P 		111.9
(-2.7)
P 		102.6
(-3)
P 		107.2
(-2.9)
P 		284.8
(2.2)
P 		313.5
(3)
P 		211
C 119.7
(-1.6)
P 		120.4
(-1.6)
P 		84.3
(-2.6)
P 		70
(-3)
P 		190.4
(0.3)
P 		289
(3)
P 		219
avr 110.2
(-2.3) 		114.7
(-2.2) 		96.3
(-2.8) 		91.5
(-3) 		216.7
(1.4) 		261.4
(3) 		170
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175259_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21911
Sequence Type Exemplar sequence
Representative Public ID AV185445 NCBI
Target Description AV185445_rc /REP_DB=TREMBL Accession /GB=AV185445 /CHR=5 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk678d4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic 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_171570(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171570 NCBI Caenorhabditis elegans Y39B6A.37 (Y39B6A.37) mRNA, complete cds. 11/11 None
SNAP00000030529 ENSEMBL cdna:SNAP chromosome:CEL140:V:18984527:19000682:1 10/11 None
Y39B6A.37 ENSEMBL cdna:known chromosome:CEL140:V:18993431:18996372:1 gene:Y39B6A.37 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000030713 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:18995720-18996012(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y39B6A.37
Entrez Gene 180242 Entrez gene
SwissProt Q8MYM7 EMBL-EBI
WormBase CE29874 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB61063 Hypothetical protein Y39B6A.39 [Caenorhabditis elegans] ref|NP_741658.1| Y39B6A.39 [Caenorhabditis elegans] 1.0E-169
blast CAD31829 Hypothetical protein Y39B6A.37 [Caenorhabditis elegans] ref|NP_741660.1| Y39B6A.37 [Caenorhabditis elegans] 1.0E-151
blast CAD31828 Hypothetical protein Y39B6A.36 [Caenorhabditis elegans] ref|NP_741661.1| Y39B6A.36 [Caenorhabditis elegans] 1.0E-142
blast CAD31829 Hypothetical protein Y39B6A.37 [Caenorhabditis elegans] ref|NP_741660.1| Y39B6A.37 [Caenorhabditis elegans] 1.0E-137
blast CAE56104 Hypothetical protein CBG23702 [Caenorhabditis briggsae] 4.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 1.9E-7
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 7.9E-41
Sequence
Target Sequence 
>C. ELEGANS:175259_AT
agctctggattatggtgcaatttcgtgatatctccggatgattttgtgagaaaaaatgat
gtggaaaaactggaaatttccgaggaaaaatcgatgacaataccgcttgatggtgacaaa
ttggcacagatatccgctgcaatggcgaattttcagttgcctacaccgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCTCTGGATTATGGTGCAATTTCG 650 79 105 Antisense
GGTGCAATTTCGTGATATCTCCGGA 532 501 118 Antisense
TTTCGTGATATCTCCGGATGATTTT 335 671 125 Antisense
GTGATATCTCCGGATGATTTTGTGA 42 485 129 Antisense
GAAAAATCGATGACAATACCGCTTG 608 353 189 Antisense
GATGACAATACCGCTTGATGGTGAC 228 407 197 Antisense
ACCGCTTGATGGTGACAAATTGGCA 452 87 206 Antisense
ATTGGCACAGATATCCGCTGCAATG 110 3 224 Antisense
GGCACAGATATCCGCTGCAATGGCG 528 533 227 Antisense
ATATCCGCTGCAATGGCGAATTTTC 444 21 234 Antisense
GCGAATTTTCAGTTGCCTACACCGC 166 289 249 Antisense
Sequence Source Affymetrix Proprietary Database