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[180392_at]

Description W09C3.4 /REP_DB=WormBase Gene ID /WP=CE14750 /TR=P91529 /GB=AAC24412.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 69      6grp_high1_10_10 > 95      4grp_highest_8_8 > 11      4grp_high_8_8 > 55      6grp_highest_nonorm > 84      6grp_total > 86      4grp_total > 48      6grp_highest_sub > In      6grp_high1_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 256
1 2 3 4 range
A 525.7
(-3)
P 		642.9
(1.1)
P 		697.2
(3)
P 		552.5
(-2.1)
P 		172
B 547.8
(-3)
P 		658
(-0.2)
P 		782
(3)
P 		573.4
(-2.3)
P 		234
C 587.4
(-3)
P 		597.6
(-2.3)
P 		677.5
(3)
P 		607
(-1.7)
P 		90
avr 553.6
(-3) 		632.8
(-0.1) 		718.9
(3) 		577.6
(-2.1) 		165

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 393
1 2 3 4 5 6 range
A 465.5
(-2.8)
P 		452.7
(-3)
P 		522.4
(-1.7)
P 		634
(0.3)
P 		655.3
(0.7)
P 		783.6
(3)
P 		331
B 405.2
(-3)
P 		506
(-1.3)
P 		592.3
(0.1)
P 		592.5
(0.1)
P 		703
(1.9)
P 		766.3
(3)
P 		361
C 390.8
(-3)
P 		497.1
(-1.4)
P 		555
(-0.5)
P 		594.1
(0.1)
P 		589.1
(0.1)
P 		780.5
(3)
P 		390
avr 420.5
(-3) 		485.3
(-1.9) 		556.6
(-0.7) 		606.9
(0.1) 		649.1
(0.8) 		776.8
(3) 		356
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 155
1 2 3 4 range
A 191.4
(3)
P 		139.6
(0.2)
P 		182.3
(2.5)
P 		80.9
(-3)
P 		111
B 174.7
(2.3)
P 		162.5
(1.1)
P 		181.2
(3)
P 		122.2
(-3)
P 		59
C 194.5
(1.1)
P 		171.8
(0.1)
P 		236.1
(3)
P 		102.3
(-3)
P 		134
avr 186.9
(2.2) 		158
(0.4) 		199.9
(3) 		101.8
(-3) 		98

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 85.8
(-3)
P 		161
(1)
P 		113.8
(-1.5)
P 		160.8
(1)
P 		197.7
(3)
P 		190.8
(2.6)
P 		112
B 141
(-3)
P 		168.4
(-1.9)
P 		143.8
(-2.9)
P 		156.9
(-2.3)
P 		285.6
(3)
P 		285.8
(3)
P 		145
C 144.8
(-1.9)
P 		151.7
(-1.6)
P 		141.3
(-2.1)
P 		119.5
(-3)
P 		190.6
(0)
P 		261.3
(3)
P 		142
avr 123.9
(-3) 		160.4
(-1.2) 		133
(-2.6) 		145.7
(-1.9) 		224.6
(1.9) 		246
(3) 		122
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 180392_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.675
Sequence Type Exemplar sequence
Representative Public ID W09C3.4 NCBI
Target Description W09C3.4 /REP_DB=WormBase Gene ID /WP=CE14750 /TR=P91529 /GB=AAC24412.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059026(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059026 NCBI Caenorhabditis elegans W09C3.4 (W09C3.4) mRNA, complete cds. 11/11 None
GENEFINDER00000028198 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4704623:4705714:1 11/11 None
SNAP00000028184 ENSEMBL cdna:SNAP chromosome:CEL140:I:4704677:4705714:1 11/11 None
W09C3.4 ENSEMBL cdna:known chromosome:CEL140:I:4704623:4705803:1 gene:W09C3.4 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
chrI:4704622-4705714(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl W09C3.4
Entrez Gene 172081 Entrez gene
SwissProt P91529 EMBL-EBI
WormBase CE14750 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1591497_S_AT similar to DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) cfa
CANINE_2:CFA.15684.1.A1_AT similar to DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) cfa
CANINE_2:CFA.15684.1.A1_S_AT similar to DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) cfa
CANINE_2:CFAAFFX.9063.1.S1_AT similar to DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) cfa
DROSOPHILA_2:1633650_AT dm
DROSGENOME1:150356_AT dm
CHICKEN:GGA.5581.1.S1_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa gga
HG-FOCUS:205218_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HG-U133A:205218_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HG-U133_PLUS_2:205218_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HG-U133A_2:205218_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HU35KSUBA:U93869_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
U133_X3P:G5454019_3P_S_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
U133_X3P:205218_3P_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HG-U95AV2:41702_R_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
HG-U95D:69687_AT polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa hs
MOUSE430A_2:1451773_S_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430_2:1451773_S_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOE430A:1451773_S_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MG-U74BV2:111220_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MG-U74BV2:114765_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MG-U74BV2:110049_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MG-U74BV2:110494_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOE430A:1439075_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430A_2:1439075_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430_2:1439075_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOE430B:1429686_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430_2:1429686_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOE430B:1430328_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430_2:1430328_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOE430B:1431999_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MOUSE430_2:1431999_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MU19KSUBA:TC22130_AT polymerase (RNA) III (DNA directed) polypeptide F mm
MU19KSUBC:TC38952_AT Polymerase (RNA) III (DNA directed) polypeptide F (Polr3f), mRNA mm
YEAST_2:1770276_AT RNA polymerase III subunit C34; interacts with TFIIIB70 and is a key determinant in pol III recruitment by the preinitiation complex Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6350 transcription inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus 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 AAC24412 Hypothetical protein W09C3.4 [Caenorhabditis elegans] ref|NP_491427.1| W09C3.4 [Caenorhabditis elegans] sp|P91529|RPC6_CAEEL Probable DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) 1.0E-162
blast AAC24412 Hypothetical protein W09C3.4 [Caenorhabditis elegans] ref|NP_491427.1| W09C3.4 [Caenorhabditis elegans] sp|P91529|RPC6_CAEEL Probable DNA-directed RNA polymerase III 39 kDa polypeptide (RNA polymerase III C39 subunit) 1.0E-153
blast CAE74539 Hypothetical protein CBG22296 [Caenorhabditis briggsae] 1.0E-138
blast CAE74539 Hypothetical protein CBG22296 [Caenorhabditis briggsae] 1.0E-132
blast AAH64209 Polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa [Xenopus tropicalis] ref|NP_989319.1| polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa [Xenopus tropicalis] 9.0E-45
Protein Domains
Database ID Description E-Value
Pfam IPR007832 EMBL-EBI RNA polymerase Rpc34 subunit 1.0E-126
Pfam IPR007832 EMBL-EBI RNA polymerase Rpc34 subunit 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:180392_AT
ggttcaggactcaaccagcttcaacttcgaaaaacattgaaaagtctggaaacgaaaaag
ttgatcaagactatcaaagctgttggaactacgaggaagtgctatattttgtttagtatt
gaaccagatatgtcattgactggtggaacattctattctgatcaacaactcgattcggaa
ctcatcaatacattgatcagtgtttgtggttcatatgctgccagcagacgaaagcatgcg
attgatgaaaatccgaataatattcaaatgcaaagagaagccagctatattcgtcctcaa
gagatagcccaattcatcaccgaaaaacgagtattgaatgttccactatcattggaagat
ttagaaagaattctcgaagtcgctgtgttggatggaacaattgaacgaagagctgatgga
aagatccgtgcatgtccaccacgttccagtatttctccattagtgtcggttccgtgtgct
atttgtccagttgtcgaggattgtcgaccaggatatgtgatctctcctcaatcatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTTCAGGACTCAACCAGCTTCAAC 410 507 334 Antisense
CATTCTATTCTGATCAACAACTCGA 692 215 482 Antisense
GTTTGTGGTTCATATGCTGCCAGCA 14 453 535 Antisense
GAGAAGCCAGCTATATTCGTCCTCA 646 391 608 Antisense
AAGAGATAGCCCAATTCATCACCGA 59 155 632 Antisense
TTCTCGAAGTCGCTGTGTTGGATGG 312 691 704 Antisense
TGGAAAGATCCGTGCATGTCCACCA 586 547 750 Antisense
CACGTTCCAGTATTTCTCCATTAGT 333 199 773 Antisense
ATTTCTCCATTAGTGTCGGTTCCGT 311 17 784 Antisense
TCCGTGTGCTATTTGTCCAGTTGTC 32 593 804 Antisense
GATATGTGATCTCTCCTCAATCATG 481 425 845 Antisense
Sequence Source Affymetrix Proprietary Database