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[189330_at] RNA polymerase

Description H27M09.2 /REP_DB=WormBase Gene ID /WP=CE23831 /TR=Q9N5K2 /GB=AAF39906.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA polymerase
Cluster 6grp_highest_10_10 > 89      6grp_high1_10_10 > 99      4grp_highest_8_8 > 17      4grp_high_8_8 > 61      6grp_highest_nonorm > 77      6grp_total > 95      4grp_total > 59      6grp_highest_sub > In      6grp_total_sub > Increase      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1153
1 2 3 4 range
A 1622.2
(-0.8)
P 		1987.5
(1.5)
P 		2232.2
(3)
P 		1273.1
(-3)
P 		959
B 1862.1
(2)
P 		1990.8
(2.8)
P 		2021.1
(3)
P 		1078.8
(-3)
P 		942
C 1609.2
(0.2)
P 		1556.7
(-0.1)
P 		2042
(3)
P 		1108.1
(-3)
P 		934
avr 1697.8
(0.5) 		1845
(1.4) 		2098.4
(3) 		1153.3
(-3) 		945

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 462
1 2 3 4 5 6 range
A 1420.1
(0.2)
P 		1332.9
(-3)
P 		1399.9
(-0.6)
P 		1345.9
(-2.5)
P 		1497.9
(3)
P 		1466.1
(1.8)
P 		165
B 1415.2
(-2.7)
P 		1530.1
(-0.7)
P 		1398.9
(-3)
P 		1573.9
(0.1)
P 		1738.1
(3)
P 		1629.1
(1.1)
P 		339
C 1336.1
(-1.9)
P 		1275.8
(-3)
P 		1321.6
(-2.2)
P 		1499.3
(1)
P 		1441.2
(-0.1)
P 		1613.4
(3)
P 		338
avr 1390.5
(-2.5) 		1379.6
(-2.8) 		1373.5
(-3) 		1473
(0) 		1559.1
(2.7) 		1569.5
(3) 		196
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 525
1 2 3 4 range
A 590.6
(3)
P 		431.4
(0.6)
P 		583.5
(2.9)
P 		186.4
(-3)
P 		404
B 593.8
(3)
P 		491.7
(1.3)
P 		468.3
(0.9)
P 		229.9
(-3)
P 		364
C 532.7
(1)
P 		447.6
(-0)
P 		711.7
(3)
P 		186.9
(-3)
P 		525
avr 572.4
(2.8) 		456.9
(1) 		587.8
(3) 		201.1
(-3) 		387

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 444
1 2 3 4 5 6 range
A 261.8
(-3)
P 		474
(3)
P 		304.9
(-1.8)
P 		341.4
(-0.7)
P 		452
(2.4)
P 		357
(-0.3)
P 		212
B 492.4
(-0.5)
P 		509.3
(-0.2)
P 		339.7
(-3)
P 		416.9
(-1.7)
P 		706.2
(3)
P 		607.5
(1.4)
P 		367
C 495.2
(1.9)
P 		389.3
(-0.8)
P 		336.4
(-2.1)
P 		301.5
(-3)
P 		466.4
(1.1)
P 		540.1
(3)
P 		239
avr 416.5
(-0.5) 		457.5
(0.7) 		327
(-3) 		353.3
(-2.3) 		541.5
(3) 		501.5
(1.9) 		215
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189330_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.919
Sequence Type Exemplar sequence
Representative Public ID H27M09.2 NCBI
Target Description H27M09.2 /REP_DB=WormBase Gene ID /WP=CE23831 /TR=Q9N5K2 /GB=AAF39906.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=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_059560(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059560 NCBI Caenorhabditis elegans H27M09.2 (H27M09.2) mRNA, complete cds. 11/11 None
SNAP00000019137 ENSEMBL cdna:SNAP chromosome:CEL140:I:6858556:6859281:1 11/11 None
GENEFINDER00000019144 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6858556:6859281:1 11/11 None
H27M09.2 ENSEMBL cdna:known chromosome:CEL140:I:6858552:6859344:1 gene:H27M09.2 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:6858486-6859212(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA polymerase
Ensembl H27M09.2
Entrez Gene 172412 Entrez gene
SwissProt Q9N5K2 EMBL-EBI
WormBase CE23831 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:258453_AT DNA-directed RNA polymerase, putative at
DROSOPHILA_2:1632142_AT dm
DROSGENOME1:146974_AT dm
CHICKEN:GGA.7881.1.S1_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa gga
HG-U133A:217854_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133_PLUS_2:217854_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-FOCUS:217854_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133A_2:217854_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133_PLUS_2:213887_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133A_2:213887_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133A:213887_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HUGENEFL:D38251_S_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
U133_X3P:G4505944_3P_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
U133_X3P:HS.24301.1.S1_3P_A_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U95AV2:41332_AT polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133_PLUS_2:217614_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133A_2:217614_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U133A:217614_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
HG-U95D:84752_R_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
U133_X3P:217614_3P_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
U133_X3P:HS.165728.0.A1_3P_X_AT Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa hs
MG-U74AV2:93325_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MG-U74CV2:165866_F_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOE430A:1451093_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOUSE430A_2:1451093_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOUSE430_2:1451093_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOE430A:1417138_S_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOUSE430A_2:1417138_S_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOUSE430_2:1417138_S_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOE430B:1458326_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MOUSE430_2:1458326_AT polymerase (RNA) II (DNA directed) polypeptide E mm
MG-U74BV2:165236_F_AT Polymerase (RNA) II (DNA directed) polypeptide E, mRNA (cDNA clone MGC:46792 IMAGE:3156885) mm
MU19KSUBA:TC17040_AT Polymerase (RNA) II (DNA directed) polypeptide E, mRNA (cDNA clone MGC:46792 IMAGE:3156885) mm
MU19KSUBA:TC17040_G_AT Polymerase (RNA) II (DNA directed) polypeptide E, mRNA (cDNA clone MGC:46792 IMAGE:3156885) mm
MU19KSUBC:TC38412_AT Polymerase (RNA) II (DNA directed) polypeptide E, mRNA (cDNA clone MGC:46792 IMAGE:3156885) mm
RG-U34B:RC_AA944792_S_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RG-U34C:RC_AA819798_G_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RG-U34C:RC_AA819798_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RG-U34C:RC_AI170699_R_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RG-U34C:RC_AI170699_I_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RAE230A:1367471_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RAE230B:1367471_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
RAT230_2:1367471_AT polymerase (RNA) II (DNA directed) polypeptide E (predicted) rn
YEAST_2:1771706_AT RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III; contacts DNA and affects transactivation 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 AAF39906 Hypothetical protein H27M09.2 [Caenorhabditis elegans] ref|NP_491961.1| H27M09.2 [Caenorhabditis elegans] sp|Q9N5K2|RPB5_CAEEL DNA-directed RNA polymerases II 24 kDa polypeptide (RNA polymerase II subunit 5) 1.0E-116
blast CAE67293 Hypothetical protein CBG12745 [Caenorhabditis briggsae] 1.0E-114
blast BAA07406.1 RPB5 [Homo sapiens] 2.0E-93
Protein Domains
Database ID Description E-Value
Pfam IPR005571 EMBL-EBI RNA polymerase Rpb5, N-terminal domain 4.2E-58
Pfam IPR000783 EMBL-EBI RNA polymerase H/23 kD subunit 1.2E-45
Sequence
Target Sequence 
>C. ELEGANS:189330_AT
gatcgtggttatctcgtagctcaagatgaattagatcaaccattggaaacattcaaagtg
cagtacggagatcgtccctctgaaaaaaagccggctcgctcagatctgacaattctcgtg
gctcacaacgacgatccagccgatcaaatgtttgttttcttcccagaggacgccaaaatt
ggaatcaaaactattaaagctatctgccagcaaatgcaagaacagaatatctcccgtgct
atcattgtcgtacaaaccggaatgactccaagcgccaaacaatccattggcgacatggcc
ccaaagtacatgttggagcactttttagaggctgagctcatggtaaacatcacagaacat
gagttggtaccagaacatgtcgtcatgacagccgaagagaaagcagaactacttgctaga
tacaaacttaaggattctcagttgccacgtatccaacaatgtgatccggtcgctcgttat
tttggtctccgccgtggacaagttgtcaaaatcattcggccatcggaaactgctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCGTGGTTATCTCGTAGCTCAAG 197 415 82 Antisense
AAGTGCAGTACGGAGATCGTCCCTC 263 159 137 Antisense
AAAAAAAGCCGGCTCGCTCAGATCT 692 127 164 Antisense
GCTCAGATCTGACAATTCTCGTGGC 507 301 179 Antisense
TTCTCGTGGCTCACAACGACGATCC 21 691 194 Antisense
TTGTTTTCTTCCCAGAGGACGCCAA 532 703 233 Antisense
GAACAGAATATCTCCCGTGCTATCA 692 351 301 Antisense
CAAACCGGAATGACTCCAAGCGCCA 533 191 334 Antisense
GATTCTCAGTTGCCACGTATCCAAC 568 431 514 Antisense
GTATCCAACAATGTGATCCGGTCGC 5 455 530 Antisense
ATCATTCGGCCATCGGAAACTGCTG 698 29 592 Antisense
Sequence Source Affymetrix Proprietary Database