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[192489_s_at] DNA-directed RNA polymerase II

Description C26E6.4 /REP_DB=WormBase Gene ID /WP=CE01162 /TR=SW:Q10578 /GB=AAA21158.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=DNA-directed RNA polymerase II
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 36      4grp_highest_8_8 > 40      4grp_high_8_8 > 42      6grp_highest_nonorm > 75      6grp_total > 36      4grp_total > 53      6grp_highest_sub > Cu      6grp_cgc > 25      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 663
1 2 3 4 range
A 1012.1
(3)
P 		801.3
(0.4)
P 		684
(-1.1)
P 		533.1
(-3)
P 		479
B 806.6
(-0.2)
P 		950.5
(3)
P 		679.3
(-3)
P 		797.3
(-0.4)
P 		271
C 1193
(3)
P 		959.2
(0.9)
P 		1015.1
(1.4)
P 		530.4
(-3)
P 		663
avr 1003.9
(3) 		903.7
(1.4) 		792.8
(-0.3) 		620.3
(-3) 		384

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 757
1 2 3 4 5 6 range
A 698.6
(-1.5)
P 		1032
(3)
P 		632.6
(-2.3)
P 		977.5
(2.3)
P 		583.1
(-3)
P 		969.6
(2.2)
P 		449
B 1021
(3)
P 		792.8
(0.3)
P 		588.9
(-2.1)
P 		586.7
(-2.1)
P 		511.8
(-3)
P 		690.9
(-0.9)
P 		509
C 1269
(3)
P 		915.6
(-0.9)
P 		997.7
(0)
P 		819.8
(-1.9)
P 		721.4
(-3)
P 		742.6
(-2.8)
P 		548
avr 996.2
(3) 		913.5
(1.7) 		739.7
(-0.9) 		794.7
(-0.1) 		605.4
(-3) 		801
(0) 		391
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 317
1 2 3 4 range
A 368.5
(3)
P 		173.9
(-1)
P 		178.8
(-0.9)
P 		78
(-3)
P 		291
B 257.2
(3)
P 		234.8
(1.7)
P 		157.4
(-3)
P 		169.9
(-2.2)
P 		100
C 394.9
(3)
P 		275.8
(0.7)
P 		353.8
(2.2)
P 		89.4
(-3)
P 		306
avr 340.2
(3) 		228.2
(0.1) 		230
(0.1) 		112.4
(-3) 		228

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 342
1 2 3 4 5 6 range
A 128.8
(-3)
P 		367
(3)
P 		137.8
(-2.8)
P 		247.9
(0)
P 		175.9
(-1.8)
P 		236.1
(-0.3)
P 		238
B 355.2
(3)
P 		263.9
(0.4)
P 		143
(-3)
P 		155.4
(-2.6)
P 		207.9
(-1.2)
P 		257.6
(0.2)
P 		212
C 470.4
(3)
P 		279.4
(-0.8)
P 		253.9
(-1.3)
P 		164.9
(-3)
P 		233.4
(-1.7)
P 		248.6
(-1.4)
P 		306
avr 318.1
(3) 		303.4
(2.4) 		178.2
(-3) 		189.4
(-2.5) 		205.7
(-1.8) 		247.4
(-0) 		140
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192489_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6092
Sequence Type Exemplar sequence
Representative Public ID C26E6.4 NCBI
Target Description C26E6.4 /REP_DB=WormBase Gene ID /WP=CE01162 /TR=SW:Q10578 /GB=AAA21158.1 /SUBMIT=ST.LOUIS /CHR=3 /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_065646(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065646 NCBI Caenorhabditis elegans RNA Polymerase II (B) subunit family member (rpb-2) (rpb-2) mRNA, complete cds. 11/11 None
GENEFINDER00000014708 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4937322:4944024:1 11/11 None
SNAP00000014703 ENSEMBL cdna:SNAP chromosome:CEL140:III:4939562:4944024:1 11/11 None
C26E6.4 ENSEMBL cdna:known chromosome:CEL140:III:4939527:4944364:1 gene:C26E6.4 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
chrIII:4939564-4944024(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA-directed RNA polymerase II
Gene Symbol rpb-2
Ensembl C26E6.4
Entrez Gene 175668 Entrez gene
SwissProt Q10578 EMBL-EBI
WormBase CE01162 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12248_S_AT DNA-directed RNA polymerase II 135 kDa polypeptide / RNA polymerase II subunit 2 (RPB135) (RPB2) (RP140) at
ATH1-121501:254368_AT DNA-directed RNA polymerase II 135 kDa polypeptide / RNA polymerase II subunit 2 (RPB135) (RPB2) (RP140) at
CANINE_2:CFA.19898.1.S1_S_AT similar to DNA-directed RNA polymerase II 140 kDa polypeptide (RNA polymerase II subunit 2) (RPB2) cfa
CANINE_2:CFAAFFX.4357.1.S1_AT similar to DNA-directed RNA polymerase II 140 kDa polypeptide (RNA polymerase II subunit 2) (RPB2) cfa
CANINE_2:CFAAFFX.4357.1.S1_S_AT similar to DNA-directed RNA polymerase II 140 kDa polypeptide (RNA polymerase II subunit 2) (RPB2) cfa
DROSOPHILA_2:1625962_AT RNA polymerase II 140kD subunit dm
DROSGENOME1:154098_AT RNA polymerase II 140kD subunit dm
CHICKEN:GGA.9356.1.S1_S_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa gga
CHICKEN:GGA.9356.3.S1_AT Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa gga
HG-FOCUS:201803_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U133A:201803_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U133_PLUS_2:201803_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U133A_2:201803_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HU35KSUBD:RC_T89038_S_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HUGENEFL:X63563_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
U133_X3P:G4505940_3P_S_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U133_PLUS_2:1555837_S_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U95AV2:39746_AT polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
U133_X3P:HS2.432712.1.A1_3P_AT Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U133_PLUS_2:1555836_AT Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U95D:67766_AT Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
HG-U95D:86861_AT Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa hs
MU11KSUBB:MSA.33546.0_S_AT polymerase (RNA) II (DNA directed) polypeptide B mm
MOE430A:1433552_A_AT polymerase (RNA) II (DNA directed) polypeptide B mm
MOUSE430A_2:1433552_A_AT polymerase (RNA) II (DNA directed) polypeptide B mm
MOUSE430_2:1433552_A_AT polymerase (RNA) II (DNA directed) polypeptide B mm
MG-U74BV2:113800_AT Polymerase (RNA) II (DNA directed) polypeptide B (Polr2b), mRNA mm
MU19KSUBC:TC40406_AT Polymerase (RNA) II (DNA directed) polypeptide B (Polr2b), mRNA mm
RAE230A:1372083_AT polymerase (RNA) II (DNA directed) polypeptide B (predicted) rn
RAT230_2:1372083_AT polymerase (RNA) II (DNA directed) polypeptide B (predicted) rn
RG-U34C:RC_AI233350_AT polymerase (RNA) II (DNA directed) polypeptide B (predicted) rn
YEAST_2:1772025_AT RNA polymerase II second largest subunit B150, part of central core; similar to bacterial beta subunit Sc
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 AAA21158 Hypothetical protein C26E6.4 [Caenorhabditis elegans] ref|NP_498047.1| RNA Polymerase II (B) subunit family member (rpb-2) [Caenorhabditis elegans] sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II second largest subunit (RNA polymerase I subunit 2) 0.0
blast CAE71308 Hypothetical protein CBG18197 [Caenorhabditis briggsae] 0.0
blast NP_000929 DNA directed RNA polymerase II polypeptide B [Homo sapiens] gb|AAH23503.2| DNA directed RNA polymerase II polypeptide B [Homo sapiens] emb|CAA45124.1| RNA polymerase II 140 kDa subunit [Homo sapiens] gb|AAB23139.1| RNA polymerase II second largest subunit, RNA polymerase B second largest subunit [human, HeLa cells, Peptide, 1174 aa] ref|XP_214021.3| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa polypeptide (RNA polymerase II subunit 2) (RPB2) [Rattus norvegicus] sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II 140 kDa polypeptide (RNA polymerase II subunit 2) (RPB2) 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 1.6E-51
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 1.5E-112
Pfam IPR001810 EMBL-EBI Cyclin-like F-box 1.3E-10
Pfam IPR003877 EMBL-EBI SPla/RYanodine receptor SPRY 2.5E-15
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 3.8E-102
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 3.8E-31
Pfam IPR007646 EMBL-EBI RNA polymerase Rpb2, domain 4 6.4E-39
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 2.2E-28
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-126
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 1.6E-51
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 1.5E-112
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 3.8E-102
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 3.8E-31
Pfam IPR007646 EMBL-EBI RNA polymerase Rpb2, domain 4 6.4E-39
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 2.2E-28
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-126
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 1.6E-51
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 1.5E-112
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 3.8E-102
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 3.8E-31
Pfam IPR007646 EMBL-EBI RNA polymerase Rpb2, domain 4 6.4E-39
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 2.2E-28
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:192489_S_AT
gtcacttgatcgaatgccttcagggtaaactatcagcaaacaagggagaaatcggagatg
ctacaccattcaacgatacagtcaacgtacaaaagatctctggcctactatgtgagtatg
gttatcatttgcgtggtaacgaagtgatgtacaacggacatactggaaaaaagttgacaa
ctcaaatcttctttggaccaacttattatcaacgtctcaagcatatggtcgatgacaaga
ttcactcacgtgcacgcggtccaattcagatgatgaatcgacagcctatggaaggaagag
ctcgtgacggaggtctccgtttcggagaaatggaacgagattgtcaaatttcccacggag
ctactcaatttttgcgagaacgtctttttgaggtgtcagatccatatcatgtgtacgtgt
gcaacaactgtggtcttattgtcgtcgccaacttgagaacgaacagtttcgagtgcaagg
cttgtcgcaacaagacccaagtatccgctgttcgtattccatacgcttgtaagctgctct
tccaggagttaatgtcaatgtctattgctccaagactcatggtcaagcctcgacaatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCACTTGATCGAATGCCTTCAGGG 500 465 2966 Antisense
CGGAGATGCTACACCATTCAACGAT 601 243 3018 Antisense
CAAAAGATCTCTGGCCTACTATGTG 565 189 3055 Antisense
TGACAAGATTCACTCACGTGCACGC 638 571 3198 Antisense
GAAGAGCTCGTGACGGAGGTCTCCG 475 337 3260 Antisense
AGATTGTCAAATTTCCCACGGAGCT 452 65 3303 Antisense
CAACTGTGGTCTTATTGTCGTCGCC 583 187 3390 Antisense
GCAACAAGACCCAAGTATCCGCTGT 352 317 3452 Antisense
TATCCGCTGTTCGTATTCCATACGC 212 659 3467 Antisense
TCCATACGCTTGTAAGCTGCTCTTC 229 591 3483 Antisense
GACTCATGGTCAAGCCTCGACAATC 211 371 3539 Antisense
Sequence Source Affymetrix Proprietary Database