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[191936_at] DNA directed RNA polymerase

Description C06A1.5 /REP_DB=WormBase Gene ID /WP=CE02117 /TR=SW:Q17684 /GB=CAA90053.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA directed RNA polymerase
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 78      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 77      6grp_total > 68      4grp_total > 57      6grp_highest_sub > Da      6grp_high1_sub > Cu      6grp_total_sub > Increase      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 789
1 2 3 4 range
A 1551.6
(-3)
P 		2055.1
(3)
P 		2029.7
(2.7)
P 		1577.1
(-2.7)
P 		504
B 1619.6
(-0.5)
P 		1854.7
(1.2)
P 		2085.3
(3)
P 		1295.9
(-3)
P 		789
C 1527.5
(-1.8)
P 		2000.3
(2.5)
P 		2057.5
(3)
P 		1390
(-3)
P 		668
avr 1566.2
(-1.6) 		1970
(2.2) 		2057.5
(3) 		1421
(-3) 		637

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 474
1 2 3 4 5 6 range
A 1168.5
(-3)
P 		1384.5
(0.1)
P 		1299.1
(-1.1)
P 		1287.2
(-1.3)
P 		1198.4
(-2.6)
P 		1585.5
(3)
P 		417
B 1413.8
(3)
P 		1211.2
(-3)
P 		1228.9
(-2.5)
P 		1227.7
(-2.5)
P 		1330.9
(0.5)
P 		1393.3
(2.4)
P 		203
C 1334.7
(0.1)
P 		1141.6
(-2.6)
P 		1281.2
(-0.7)
P 		1111.3
(-3)
P 		1425.3
(1.3)
P 		1545.1
(3)
P 		434
avr 1305.7
(-1.1) 		1245.8
(-2.3) 		1269.7
(-1.8) 		1208.7
(-3) 		1318.2
(-0.8) 		1508
(3) 		299
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 486
1 2 3 4 range
A 564.9
(3)
P 		446.1
(0.9)
P 		530.6
(2.4)
P 		230.9
(-3)
P 		334
B 516.5
(3)
P 		458.1
(1.5)
P 		483.2
(2.2)
P 		276.2
(-3)
P 		240
C 505.6
(0.4)
P 		575.1
(1.2)
P 		717.1
(3)
P 		234.4
(-3)
P 		483
avr 529
(2.1) 		493.1
(1.5) 		577
(3) 		247.2
(-3) 		330

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 325
1 2 3 4 5 6 range
A 215.4
(-3)
P 		492.4
(3)
P 		282.9
(-1.5)
P 		326.5
(-0.6)
P 		361.6
(0.2)
P 		386
(0.7)
P 		277
B 491.9
(1.8)
P 		403.1
(-0.4)
P 		298.4
(-3)
P 		325.2
(-2.3)
P 		540.7
(3)
P 		519.6
(2.5)
P 		242
C 494.7
(2.5)
P 		348.3
(-0.5)
P 		326.1
(-0.9)
P 		223.5
(-3)
P 		461.2
(1.9)
P 		517.2
(3)
P 		294
avr 400.7
(0.6) 		414.6
(1) 		302.5
(-2.6) 		291.7
(-3) 		454.5
(2.3) 		474.3
(3) 		183
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191936_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3612
Sequence Type Exemplar sequence
Representative Public ID C06A1.5 NCBI
Target Description C06A1.5 /REP_DB=WormBase Gene ID /WP=CE02117 /TR=SW:Q17684 /GB=CAA90053.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DNA directed RNA polymerase
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_063877(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063877 NCBI Caenorhabditis elegans C06A1.5 (C06A1.5) mRNA, complete cds. 11/11 None
SNAP00000011346 ENSEMBL cdna:SNAP chromosome:CEL140:II:10579291:10579704:1 11/11 None
GENEFINDER00000011349 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10579291:10579704:1 11/11 None
C06A1.5 ENSEMBL cdna:known chromosome:CEL140:II:10579291:10579704:1 gene:C06A1.5 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
chrII:10579287-10579701(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA directed RNA polymerase
Ensembl C06A1.5
Entrez Gene 174630 Entrez gene
SwissProt Q17684 EMBL-EBI
WormBase CE02117 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:248386_AT DNA-directed RNA polymerase II, putative at
CANINE:1586379_AT similar to DNA directed RNA polymerase II polypeptide F cfa
CANINE_2:CFA.5996.1.S1_S_AT similar to DNA directed RNA polymerase II polypeptide F cfa
DROSOPHILA_2:1636644_AT RNA polymerase II 18kD subunit dm
DROSGENOME1:143745_AT RNA polymerase II 18kD subunit dm
CHICKEN:GGA.3737.1.S1_AT polymerase (RNA) II (DNA directed) polypeptide F gga
HG-U133_PLUS_2:209511_AT polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U133A:209511_AT polymerase (RNA) II (DNA directed) polypeptide F hs
HG-FOCUS:209511_AT polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U133A_2:209511_AT polymerase (RNA) II (DNA directed) polypeptide F hs
HUGENEFL:Z27113_AT polymerase (RNA) II (DNA directed) polypeptide F hs
U133_X3P:G13097770_3P_X_AT polymerase (RNA) II (DNA directed) polypeptide F hs
U133_X3P:G13097770_3P_AT polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U95AV2:36027_AT polymerase (RNA) II (DNA directed) polypeptide F hs
U133_X3P:HS.287709.0.S1_3P_AT Polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U133_PLUS_2:232643_AT Polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U133B:232643_AT Polymerase (RNA) II (DNA directed) polypeptide F hs
HG-U95D:73630_AT Polymerase (RNA) II (DNA directed) polypeptide F hs
MOE430A:1415754_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOE430B:1415754_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOUSE430A_2:1415754_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOUSE430_2:1415754_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MG-U74AV2:104279_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MG-U74CV2:169808_I_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOE430A:1427402_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOUSE430A_2:1427402_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MOUSE430_2:1427402_AT polymerase (RNA) II (DNA directed) polypeptide F mm
MG-U74CV2:167270_R_AT Polymerase (RNA) II (DNA directed) polypeptide F, mRNA (cDNA clone MGC:36565 IMAGE:4983359) mm
MU11KSUBB:MSA.6500.0_S_AT Polymerase (RNA) II (DNA directed) polypeptide F, mRNA (cDNA clone MGC:36565 IMAGE:4983359) mm
MU19KSUBA:TC15097_AT Polymerase (RNA) II (DNA directed) polypeptide F, mRNA (cDNA clone MGC:36565 IMAGE:4983359) mm
MU19KSUBA:TC15097_G_AT Polymerase (RNA) II (DNA directed) polypeptide F, mRNA (cDNA clone MGC:36565 IMAGE:4983359) mm
RG-U34A:RC_AI639282_S_AT polymerase (RNA) II (DNA directed) polypeptide F rn
RG-U34A:AB017711_AT polymerase (RNA) II (DNA directed) polypeptide F rn
RAE230A:1369996_AT polymerase (RNA) II (DNA directed) polypeptide F rn
RAT230_2:1369996_AT polymerase (RNA) II (DNA directed) polypeptide F rn
RAE230B:1391699_AT polymerase (RNA) II (DNA directed) polypeptide F rn
RAT230_2:1391699_AT polymerase (RNA) II (DNA directed) polypeptide F rn
YEAST_2:1770777_AT RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III; part of central core; similar to bacterial omega subunit Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6351 transcription, DNA-dependent 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
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90053 Hypothetical protein C06A1.5 [Caenorhabditis elegans] ref|NP_496278.1| C06A1.5 [Caenorhabditis elegans] sp|Q17684|RPB6_CAEEL Probable DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (RPB6) 2.0E-44
blast CAE59649 Hypothetical protein CBG03063 [Caenorhabditis briggsae] 1.0E-43
blast XP_787961 PREDICTED: similar to polymerase II [Strongylocentrotus purpuratus] 4.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR006110 EMBL-EBI RNA polymerase Rpb6 7.3E-20
Sequence
Target Sequence 
>C. ELEGANS:191936_AT
tccacaacgccctgacaatgaggacgaggacgatgacaacgtggacgagaatttcgagct
tttcgatcaaggaaaggctgttccgactagtgagcatgtgacaactccattcatgacaaa
atacgaacgagctcgagttcttggcactcgcgctctccaaatcgccatgggagctccggt
tatggttgaacttgaaggagagaccgatccattggagattgctcgcaaggagcttaaaca
acgccgtatcccgatcattgtccgccgctaccttccagatggatcata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCACAACGCCCTGACAATGAGGAC 102 589 96 Antisense
GAGAATTTCGAGCTTTTCGATCAAG 374 391 142 Antisense
AAGGCTGTTCCGACTAGTGAGCATG 493 161 169 Antisense
GTGAGCATGTGACAACTCCATTCAT 400 483 185 Antisense
GAACGAGCTCGAGTTCTTGGCACTC 289 347 220 Antisense
GCGCTCTCCAAATCGCCATGGGAGC 578 287 245 Antisense
GGGAGCTCCGGTTATGGTTGAACTT 591 493 264 Antisense
GACCGATCCATTGGAGATTGCTCGC 30 383 297 Antisense
GCTCGCAAGGAGCTTAAACAACGCC 92 299 316 Antisense
TAAACAACGCCGTATCCCGATCATT 553 639 330 Antisense
GCCGCTACCTTCCAGATGGATCATA 339 285 359 Antisense
Sequence Source Affymetrix Proprietary Database