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[191905_at] DNA directed RNA polymerase II

Description C36B1.3 /REP_DB=WormBase Gene ID /WP=CE05370 /TR=Q93338 /GB=CAB02268.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=DNA directed RNA polymerase II
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 77      4grp_highest_8_8 > 30      4grp_high_8_8 > 07      6grp_highest_nonorm > 97      6grp_total > 77      4grp_total > 01      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.
4 494
1 2 3 4 range
A 829.5
(0)
P 		677.4
(-3)
P 		740.8
(-1.7)
P 		979.3
(3)
P 		302
B 747
(-3)
P 		751.5
(-2.9)
P 		762.8
(-2.8)
P 		1171.8
(3)
P 		425
C 811.7
(-2.3)
P 		788
(-3)
P 		853.2
(-1.2)
P 		1003.6
(3)
P 		216
avr 796.1
(-1.9) 		739
(-3) 		785.6
(-2.1) 		1051.6
(3) 		313

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1154
1 2 3 4 5 6 range
A 861.9
(-2.1)
P 		752.2
(-3)
P 		1023.8
(-0.7)
P 		886.4
(-1.9)
P 		1047.6
(-0.5)
P 		1458.2
(3)
P 		706
B 1020.6
(-1.9)
P 		850.6
(-3)
P 		1062.8
(-1.6)
P 		852.6
(-3)
P 		1136.5
(-1.1)
P 		1758
(3)
P 		907
C 839
(-2.5)
P 		839.1
(-2.5)
P 		733.8
(-3)
P 		1081.8
(-1.2)
P 		1018
(-1.5)
P 		1888.2
(3)
P 		1154
avr 907.2
(-2.4) 		814
(-3) 		940.1
(-2.1) 		940.3
(-2.1) 		1067.4
(-1.3) 		1701.5
(3) 		888
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 159
1 2 3 4 range
A 302
(3)
P 		147
(-2.9)
P 		193.7
(-1.1)
P 		143.3
(-3)
P 		159
B 238.2
(2.1)
P 		185.6
(-2.3)
P 		176.8
(-3)
P 		249.7
(3)
P 		73
C 268.7
(1.7)
P 		226.6
(-0.3)
P 		297.4
(3)
P 		169.2
(-3)
P 		128
avr 269.6
(3) 		186.4
(-3) 		222.6
(-0.4) 		187.4
(-2.9) 		83

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 497
1 2 3 4 5 6 range
A 158.9
(-3)
P 		267.5
(0.3)
P 		223
(-1)
P 		224.8
(-1)
P 		316.1
(1.8)
P 		355
(3)
P 		196
B 355.1
(-1.2)
P 		283.1
(-2.2)
P 		258.1
(-2.5)
P 		225.8
(-3)
P 		461.7
(0.3)
P 		655.5
(3)
P 		430
C 311
(-1.3)
P 		256
(-2.1)
P 		186.8
(-3)
P 		217.6
(-2.6)
P 		329.4
(-1.1)
P 		632.1
(3)
P 		445
avr 275
(-2) 		268.9
(-2.1) 		222.6
(-3) 		222.7
(-3) 		369.1
(-0.3) 		547.5
(3) 		325
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191905_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1719
Sequence Type Exemplar sequence
Representative Public ID C36B1.3 NCBI
Target Description C36B1.3 /REP_DB=WormBase Gene ID /WP=CE05370 /TR=Q93338 /GB=CAB02268.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=DNA directed RNA polymerase II
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_059960(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059960 NCBI Caenorhabditis elegans C36B1.3 (C36B1.3) mRNA, complete cds. 11/11 None
C36B1.3 ENSEMBL cdna:known chromosome:CEL140:I:8736894:8739046:1 gene:C36B1.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000022502 7/11 Cross Hyb Matching Probes None
GENEFINDER00000022514 7/11 Cross Hyb Matching Probes None
GENEFINDER00000022512 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:8736824-8738819(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA directed RNA polymerase II
Ensembl C36B1.3
Entrez Gene 172680 Entrez gene
WormBase CE39091 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12460_S_AT DNA-directed RNA polymerase II 36 kDa polypeptide B / RNA polymerase II subunit 3 (RPB36B) at
ATGENOME1:20353_AT DNA-directed RNA polymerase II 36 kDa polypeptide A / RNA polymerase II subunit 3 (RPB36A) at
ATH1-121501:263564_S_AT DNA-directed RNA polymerase II 36 kDa polypeptide B / RNA polymerase II subunit 3 (RPB36B) at
CANINE:1591575_AT similar to DNA directed RNA polymerase II polypeptide C cfa
CANINE:1585139_AT similar to DNA directed RNA polymerase II polypeptide C cfa
CANINE_2:CFA.10012.1.A1_AT similar to DNA directed RNA polymerase II polypeptide C cfa
CANINE_2:CFA.20672.1.S1_S_AT similar to DNA directed RNA polymerase II polypeptide C cfa
CANINE_2:CFAAFFX.13804.1.S1_AT similar to DNA directed RNA polymerase II polypeptide C cfa
DROSOPHILA_2:1627827_A_AT RNA polymerase II 33kD subunit dm
DROSGENOME1:152117_AT RNA polymerase II 33kD subunit dm
CHICKEN:GGA.11991.1.S1_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa gga
HG-U133_PLUS_2:216282_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A_2:216282_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A:216282_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U95AV2:1594_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HC-G110:1594_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A:208996_S_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A_2:208996_S_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133_PLUS_2:208996_S_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-FOCUS:208996_S_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HUGENEFL:J05448_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
U133_X3P:G12653280_3P_A_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
U133_X3P:HS.79402.1.A1_3P_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
U133_X3P:HS.79402.1.A1_3P_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
U133_X3P:HS.79402.1.A1_3P_A_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
U133_X3P:214263_3P_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A_2:214263_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133_PLUS_2:214263_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U133A:214263_X_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
HG-U95AV2:32601_S_AT polymerase (RNA) II (DNA directed) polypeptide C, 33kDa hs
MU11KSUBA:D83999_S_AT polymerase (RNA) II (DNA directed) polypeptide C mm
MU11KSUBB:MSA.8383.0_S_AT polymerase (RNA) II (DNA directed) polypeptide C mm
MG-U74AV2:160146_R_AT polymerase (RNA) II (DNA directed) polypeptide C mm
MOE430A:1416341_AT polymerase (RNA) II (DNA directed) polypeptide C mm
MOUSE430A_2:1416341_AT polymerase (RNA) II (DNA directed) polypeptide C mm
MOUSE430_2:1416341_AT polymerase (RNA) II (DNA directed) polypeptide C mm
RG-U34C:RC_AI170414_AT polymerase (RNA) II (DNA directed) polypeptide C (predicted) rn
RAE230A:1398899_AT polymerase (RNA) II (DNA directed) polypeptide C (predicted) rn
RAT230_2:1398899_AT polymerase (RNA) II (DNA directed) polypeptide C (predicted) rn
YEAST_2:1778627_AT RNA polymerase II third largest subunit B44, part of central core; similar to prokaryotic alpha subunit Sc
Protein Similarities
Method ID Description E-Value
blast NP_492361 C36B1.3 [Caenorhabditis elegans] 0.0
blast CAE66958 Hypothetical protein CBG12350 [Caenorhabditis briggsae] 0.0
blast CAB02268 Hypothetical protein C36B1.3 [Caenorhabditis elegans] 1.0E-165
Protein Domains
Database ID Description E-Value
Pfam IPR001700 EMBL-EBI RNA polymerase, alpha chain, bacterial and organelle 3.1E-47
Pfam IPR008193 EMBL-EBI DNA-directed RNA polymerase, 13 to 16 kDa subunit 3.5E-20
Sequence
Target Sequence 
>C. ELEGANS:191905_AT
gacaatgctctccgacatacaatttatccgaatgttgaggaatggccaagaagcgatcat
tcatctttaccagaagacagcactgaaaaggaggcaccattcgagccggacaacaagcct
aacaagttctggttctctatcgaaggaactggtgctcttccagcacagcgaatcgtgaca
atgggaatcggaatcttgaagagaaaactggaggaactaaatatggctctttcaaatgaa
cttcaagctcatgcccagcagcacatcttaatatttcattttgtaaaaaaacatacatct
tacaatacggcttttttttcgcagaatatggtgtgtggagactgtgagaagaaacttaca
aaaatcgtcggagttgatccttaccgaaataaaaaagttaatcgaaacgctgatggaagt
ggcccaaaaacagtaactacaaaaaatcgtctgattggagttcagaaaaaagcgactatt
gtgggagccaaatgcaaattgtgtaaaatgctgattcatcagcctggcagtcactattgt
tcgacgtgtgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAATGCTCTCCGACATACAATTT 229 365 595 Antisense
GAAGCGATCATTCATCTTTACCAGA 529 341 644 Antisense
ACCATTCGAGCCGGACAACAAGCCT 162 85 690 Antisense
AAGCCTAACAAGTTCTGGTTCTCTA 652 147 709 Antisense
CGAAGGAACTGGTGCTCTTCCAGCA 527 253 735 Antisense
CTCTTCCAGCACAGCGAATCGTGAC 454 229 749 Antisense
AAATGAACTTCAAGCTCATGCCCAG 465 119 828 Antisense
TCATGCCCAGCAGCACATCTTAATA 163 623 843 Antisense
TACAATACGGCTTTTTTTTCGCAGA 699 641 895 Antisense
GATTCATCAGCCTGGCAGTCACTAT 394 431 1107 Antisense
GCAGTCACTATTGTTCGACGTGTGC 268 311 1121 Antisense
Sequence Source Affymetrix Proprietary Database