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[193524_at]

Description Y48E1A.1 /REP_DB=WormBase Gene ID /WP=CE22157 /TR=O17628 /GB=CAB05699.2 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA-directed RNA polymerase I largest subunit
Cluster 6grp_high1_10_10 > 18      6grp_total > 28      4grp_total > 54      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 274
1 2 3 4 range
A 344.9
(3)
P 		212.4
(0.1)
P 		148.7
(-1.3)
A 		70.9
(-3)
A 		274
B 288.5
(3)
P 		168.7
(-1)
A 		144.8
(-1.8)
A 		110.3
(-3)
M 		178
C 324.3
(3)
P 		171.6
(-2)
A 		140
(-3)
A 		154
(-2.5)
A 		184
avr 319.2
(3) 		184.2
(-0.9) 		144.5
(-2.1) 		111.7
(-3) 		208

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 241
1 2 3 4 5 6 range
A 211.8
(3)
P 		143.5
(0.6)
P 		106.3
(-0.8)
P 		44.4
(-3)
A 		113.4
(-0.5)
P 		170.6
(1.5)
P 		167
B 211.3
(3)
P 		167.9
(0.7)
P 		119.2
(-1.9)
P 		140.2
(-0.8)
P 		97.8
(-3)
M 		124.9
(-1.6)
P 		114
C 285.2
(3)
P 		135.2
(-1.1)
P 		189.8
(0.4)
P 		66.5
(-3)
A 		225.3
(1.4)
P 		110.8
(-1.8)
M 		219
avr 236.1
(3) 		148.9
(-0.4) 		138.4
(-0.8) 		83.7
(-3) 		145.5
(-0.6) 		135.4
(-1) 		152
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 125.6
(3)
P 		46.1
(-1.1)
P 		38.9
(-1.5)
A 		10.4
(-3)
A 		115
B 92
(3)
P 		41.7
(-1.4)
A 		33.5
(-2.1)
A 		23.5
(-3)
M 		69
C 107.3
(3)
P 		49.3
(-1.3)
A 		48.8
(-1.3)
A 		26
(-3)
A 		81
avr 108.3
(3) 		45.7
(-1.3) 		40.4
(-1.6) 		20
(-3) 		88

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 94
1 2 3 4 5 6 range
A 39.1
(1.2)
P 		51.1
(3)
P 		23.1
(-1.2)
P 		11.3
(-3)
A 		34.2
(0.5)
P 		41.5
(1.6)
P 		40
B 73.5
(3)
P 		55.9
(0.6)
P 		28.9
(-3)
P 		37.1
(-1.9)
P 		39.7
(-1.5)
M 		46.6
(-0.6)
P 		45
C 105.7
(3)
P 		41.3
(-1.2)
P 		48.3
(-0.7)
P 		13.4
(-3)
A 		72.9
(0.9)
P 		37.1
(-1.5)
M 		92
avr 72.8
(3) 		49.4
(0.3) 		33.4
(-1.5) 		20.6
(-3) 		48.9
(0.3) 		41.7
(-0.6) 		52
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193524_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3678
Sequence Type Exemplar sequence
Representative Public ID Y48E1A.1 NCBI
Target Description Y48E1A.1 /REP_DB=WormBase Gene ID /WP=CE22157 /TR=O17628 /GB=CAB05699.2 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA-directed RNA polymerase I largest subunit
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_001027279(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027279 NCBI Caenorhabditis elegans Y48E1A.1a (Y48E1A.1) mRNA, complete cds. 11/11 None
Y48E1A.1a ENSEMBL cdna:known chromosome:CEL140:II:13670703:13694677:-1 gene:Y48E1A.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001027280 7/11 Cross Hyb Matching Probes None
SNAP00000002049 2/11 Cross Hyb Matching Probes None
GENEFINDER00000002054 2/11 Cross Hyb Matching Probes None
SNAP00000014716 5/11 Cross Hyb Matching Probes None
GENEFINDER00000014718 5/11 Cross Hyb Matching Probes None
GENEFINDER00000014720 3/11 Cross Hyb Matching Probes None
Y48E1A.1b 7/11 Cross Hyb Matching Probes None
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
175015 2 1 NM_001027279 193524_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:13670699-13694674(-) 100.0 100.0
Public Domain and Genome References
Ensembl Y48E1A.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB54460 Hypothetical protein Y48E1A.1a [Caenorhabditis elegans] emb|CAB07687.2| Hypothetical protein Y48E1A.1a [Caenorhabditis elegans] emb|CAB05699.2| Hypothetical protein Y48E1A.1a [Caenorhabditis elegans] ref|NP_001022450.1| Y48E1A.1a [Caenorhabditis elegans] 0.0
blast CAE73307 Hypothetical protein CBG20734 [Caenorhabditis briggsae] 0.0
blast NP_033114 RNA polymerase 1-4 [Mus musculus] gb|AAH53744.1| RNA polymerase 1-4 [Mus musculus] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000722 EMBL-EBI RNA polymerase, alpha subunit 1.7E-100
Pfam IPR007066 EMBL-EBI RNA polymerase Rpb1, domain 3 2.1E-62
Pfam IPR007083 EMBL-EBI RNA polymerase Rpb1, domain 4 1.4E-27
Pfam IPR007081 EMBL-EBI RNA polymerase Rpb1, domain 5 7.3E-48
Pfam IPR007081 EMBL-EBI RNA polymerase Rpb1, domain 5 3.1E-36
Pfam IPR007081 EMBL-EBI RNA polymerase Rpb1, domain 5 1.6E-28
Pfam IPR007080 EMBL-EBI RNA polymerase Rpb1, domain 1 1.7E-13
Sequence
Target Sequence 
>C. ELEGANS:193524_AT
aactattcatcgtccatcaaactccgggaatcgagcgatgcgtcgagacgactgagcaga
aaaacggaaaagaaatgacaattctgcagacgcaaggagtcaatttggctgcattcttca
agcacgcagacgtgctcgacgtcaattcggtctattcgaacgatctgaacttgattctcg
agaattatggagttgaagcttgctctaaggctatcactactgaaatgaacaacgtgttcg
ccgtctacggtatcgaggtctcgaagcgacatctctctctaactgccgactacatgacat
tcaccggacaaatccaaccattcaaccgcggagccatgtcgtcgagctcatcacccctcc
aaaaaatgacgttcgaaacgacgatggccttcttgcgagaggcgctcttgcatggcgaag
aagacaatgtgaactctccgtcggctcgtctcgtaatgggagcccttccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTATTCATCGTCCATCAAACTCC 458 139 4646 Antisense
TTTGGCTGCATTCTTCAAGCACGCA 539 665 4749 Antisense
GTGCTCGACGTCAATTCGGTCTATT 301 479 4777 Antisense
CTTGCTCTAAGGCTATCACTACTGA 118 219 4844 Antisense
TCGCCGTCTACGGTATCGAGGTCTC 334 599 4883 Antisense
TCGAGGTCTCGAAGCGACATCTCTC 83 603 4898 Antisense
AACTGCCGACTACATGACATTCACC 35 143 4926 Antisense
TTCGAAACGACGATGGCCTTCTTGC 598 685 5017 Antisense
TTCTTGCGAGAGGCGCTCTTGCATG 470 689 5035 Antisense
AAGACAATGTGAACTCTCCGTCGGC 133 153 5066 Antisense
TCGTCTCGTAATGGGAGCCCTTCCG 467 603 5091 Antisense
Sequence Source Affymetrix Proprietary Database