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[192261_s_at] RNA Pol I/III 16Kd polypeptide

Description F58A4.9 /REP_DB=WormBase Gene ID /WP=CE00225 /TR=SW:P34476 /GB=CAA80165.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=RNA Pol I-III 16Kd polypeptide
Cluster 6grp_highest_10_10 > 67      6grp_high1_10_10 > 86      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 83      6grp_total > 66      4grp_total > 09      6grp_highest_sub > In      6grp_high1_sub > In      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 966
1 2 3 4 range
A 422.8
(-3)
P 		590.3
(-2)
P 		524.3
(-2.4)
P 		1389.2
(3)
P 		966
B 439.3
(-3)
P 		572.6
(-2.1)
P 		684.5
(-1.4)
P 		1339
(3)
P 		900
C 556
(-3)
P 		596.8
(-2.7)
P 		627.5
(-2.5)
P 		1355.2
(3)
P 		799
avr 472.7
(-3) 		586.6
(-2.2) 		612.1
(-2.1) 		1361.1
(3) 		888

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 510
1 2 3 4 5 6 range
A 349.3
(-3)
P 		351.9
(-2.9)
P 		606.2
(3)
P 		409
(-1.6)
P 		353.1
(-2.9)
P 		500.5
(0.5)
P 		257
B 366.1
(-2.9)
P 		416.4
(-2.2)
P 		571.4
(-0.1)
P 		359.3
(-3)
P 		459.4
(-1.7)
P 		804.6
(3)
P 		445
C 349.5
(-2.3)
P 		342.1
(-2.4)
P 		294.2
(-3)
P 		372.3
(-2)
P 		434.8
(-1.1)
P 		749.9
(3)
P 		456
avr 355
(-3) 		370.1
(-2.7) 		490.6
(-0.5) 		380.2
(-2.5) 		415.8
(-1.9) 		685
(3) 		330
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 157
1 2 3 4 range
A 153.9
(-0.9)
P 		128.1
(-3)
P 		137.1
(-2.3)
P 		203.4
(3)
P 		75
B 140.1
(-3)
P 		141.4
(-2.9)
P 		158.6
(-2.2)
P 		285.3
(3)
P 		145
C 184
(-1.7)
P 		171.6
(-3)
P 		218.7
(2)
P 		228.5
(3)
P 		57
avr 159.3
(-2.2) 		147
(-3) 		171.5
(-1.4) 		239.1
(3) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 236
1 2 3 4 5 6 range
A 64.4
(-3)
P 		125.1
(2.4)
P 		132
(3)
P 		103.7
(0.5)
P 		106.6
(0.7)
P 		121.9
(2.1)
P 		68
B 127.4
(-2.1)
P 		138.6
(-1.7)
P 		138.7
(-1.7)
P 		95.2
(-3)
P 		186.6
(-0.3)
P 		300
(3)
P 		205
C 129.5
(-1.1)
P 		104.4
(-2)
P 		74.9
(-3)
P 		74.9
(-3)
P 		140.7
(-0.8)
P 		251
(3)
P 		176
avr 107.1
(-2.3) 		122.7
(-1.6) 		115.2
(-1.9) 		91.3
(-3) 		144.6
(-0.6) 		224.3
(3) 		133
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192261_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7554
Sequence Type Exemplar sequence
Representative Public ID F58A4.9 NCBI
Target Description F58A4.9 /REP_DB=WormBase Gene ID /WP=CE00225 /TR=SW:P34476 /GB=CAA80165.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=RNA Pol I-III 16Kd polypeptide
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_066731(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066731 NCBI Caenorhabditis elegans F58A4.9 (F58A4.9) mRNA, complete cds. 11/11 None
SNAP00000012199 ENSEMBL cdna:SNAP chromosome:CEL140:III:9629246:9629775:-1 11/11 None
GENEFINDER00000012207 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9629246:9629775:-1 11/11 None
F58A4.9 ENSEMBL cdna:known chromosome:CEL140:III:9629142:9629781:-1 gene:F58A4.9 11/11 None
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:9629241-9629771(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA Pol I/III 16Kd polypeptide
Ensembl F58A4.9
Entrez Gene 176362 Entrez gene
SwissProt P34476 EMBL-EBI
WormBase CE00225 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6350 transcription inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3899 DNA-directed RNA polymerase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA80165 Hypothetical protein F58A4.9 [Caenorhabditis elegans] ref|NP_499132.1| F58A4.9 [Caenorhabditis elegans] sp|P34476|RPC19_CAEEL Probable DNA-directed RNA polymerases I/III 16 kDa polypeptide 4.0E-67
blast CAE65166 Hypothetical protein CBG10036 [Caenorhabditis briggsae] 3.0E-57
blast CAG84870 unnamed protein product [Debaryomyces hansenii CBS767] ref|XP_456893.1| unnamed protein product [Debaryomyces hansenii] 8.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR008193 EMBL-EBI DNA-directed RNA polymerase, 13 to 16 kDa subunit 6.3E-18
Sequence
Target Sequence 
>C. ELEGANS:192261_S_AT
ggaagtcgacgaacaaccacaggaaaccccacaagtggacgacgaagaagatttgaacgt
accttcaaaaaagaaaatggaaattctggacccaaaaagtttcgaacaagatccatctaa
tttgacgcttatcatgtacgaggaagatcacactattggaaattcaatcaagcacatttt
gagcagaatggatgaagttgaattttgtggttacaacgttccacatcctctggaagacaa
gattttgttcagagtgcagacaaaggatggtattaatgctctggaagttctcgcgaaggc
attcgaaagtgttgaacaaattttttccacgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAAGTCGACGAACAACCACAGGAA 646 529 72 Antisense
ACAACCACAGGAAACCCCACAAGTG 31 113 84 Antisense
AAAGTTTCGAACAAGATCCATCTAA 244 123 167 Antisense
GATCCATCTAATTTGACGCTTATCA 110 417 181 Antisense
ATTTGACGCTTATCATGTACGAGGA 29 19 191 Antisense
GTACGAGGAAGATCACACTATTGGA 457 459 207 Antisense
TGAATTTTGTGGTTACAACGTTCCA 424 571 270 Antisense
CAACGTTCCACATCCTCTGGAAGAC 294 187 285 Antisense
GATGGTATTAATGCTCTGGAAGTTC 318 407 337 Antisense
CTGGAAGTTCTCGCGAAGGCATTCG 517 241 352 Antisense
GTGTTGAACAAATTTTTTCCACGAT 231 485 380 Antisense
Sequence Source Affymetrix Proprietary Database