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[173795_at] DNA-directed RNA polymerase I

Description CEK004A6F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F14B4.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27184 /WB_GENE_ID=F14B4.3 /WP=CE05629 /CHR=1 /FEA=Genomic Cluster /DEF=DNA-directed RNA polymerase I; C.elegans cDNA clone yk4a6 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 68      4grp_highest_8_8 > 34      4grp_high_8_8 > 57      6grp_highest_nonorm > 81      6grp_total > 79      4grp_total > 62      6grp_highest_sub > Cu      6grp_high1_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 315
1 2 3 4 range
A 413.1
(3)
P 		246.3
(-0.3)
P 		324.7
(1.3)
P 		105.2
(-3)
P 		308
B 407.3
(3)
P 		266.6
(-2.7)
P 		354.7
(0.9)
P 		259.8
(-3)
P 		148
C 401.6
(2.7)
P 		275.7
(0.3)
P 		417.1
(3)
P 		102.4
(-3)
P 		315
avr 407.3
(3) 		262.9
(-0.4) 		365.5
(2) 		155.8
(-3) 		252

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 226
1 2 3 4 5 6 range
A 225.9
(-0.3)
P 		266.8
(1.2)
P 		213.3
(-0.7)
P 		150.6
(-3)
P 		315.4
(2.9)
P 		316.8
(3)
P 		166
B 225.5
(-2.3)
P 		245
(-1.6)
P 		233.9
(-2)
P 		205.1
(-3)
P 		212.7
(-2.7)
P 		376.6
(3)
P 		172
C 238.3
(-1.6)
P 		278
(-0)
P 		204.5
(-3)
P 		256.9
(-0.9)
P 		217.8
(-2.5)
P 		353.1
(3)
P 		149
avr 229.9
(-1.9) 		263.3
(-0.5) 		217.2
(-2.5) 		204.2
(-3) 		248.6
(-1.2) 		348.8
(3) 		145
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 135
1 2 3 4 range
A 150.4
(3)
P 		53.5
(-1.3)
P 		84.9
(0.1)
P 		15.4
(-3)
P 		135
B 129.9
(3)
P 		65.9
(-2.2)
P 		82.2
(-0.8)
P 		55.4
(-3)
P 		75
C 133
(2.4)
P 		79.3
(-0.1)
P 		145.4
(3)
P 		17.3
(-3)
P 		128
avr 137.8
(3) 		66.2
(-1) 		104.2
(1.1) 		29.4
(-3) 		108

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 41.6
(-2.6)
P 		94.9
(3)
P 		46.4
(-2.1)
P 		38.2
(-3)
P 		95.2
(3)
P 		77.1
(1.1)
P 		57
B 78.4
(-1.3)
P 		81.5
(-1.1)
P 		56.8
(-2.8)
P 		54.3
(-3)
P 		86.4
(-0.8)
P 		140.4
(3)
P 		86
C 88.3
(0.3)
P 		84.8
(-0)
P 		52
(-3)
P 		51.7
(-3)
P 		70.5
(-1.3)
P 		118.2
(3)
P 		67
avr 69.4
(-1) 		87.1
(0.7) 		51.7
(-2.7) 		48.1
(-3) 		84
(0.4) 		111.9
(3) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173795_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22578
Sequence Type Exemplar sequence
Representative Public ID CEK004A6F NCBI
Target Description CEK004A6F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F14B4.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27184 /WB_GENE_ID=F14B4.3 /WP=CE05629 /CHR=1 /FEA=Genomic Cluster /DEF=DNA-directed RNA polymerase I; C.elegans cDNA clone yk4a6 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_060075(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060075 NCBI Caenorhabditis elegans F14B4.3 (F14B4.3) mRNA, complete cds. 11/11 None
F14B4.3 ENSEMBL cdna:known chromosome:CEL140:I:9289086:9294685:-1 gene:F14B4.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000033145 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:9289043-9294617(-) 98.62 100.0
Public Domain and Genome References
Gene Title DNA-directed RNA polymerase I
Ensembl F14B4.3
Entrez Gene 172752 Entrez gene
SwissProt Q27493 EMBL-EBI
WormBase CE05629 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:260049_AT DNA-directed RNA polymerase family protein at
DROSOPHILA_2:1627924_AT RNA polymerase I 135kD subunit dm
DROSGENOME1:141487_AT RNA polymerase I 135kD subunit dm
CHICKEN:GGA.16760.1.S1_AT similar to RNA polymerase I polypeptide B; DNA-directed RNA polymerase I 135kDa polypeptide; RNA polymerase I subunit 2 gga
CHICKEN:GGA.16760.1.S1_S_AT similar to RNA polymerase I polypeptide B; DNA-directed RNA polymerase I 135kDa polypeptide; RNA polymerase I subunit 2 gga
CHICKEN:GGA.6256.2.S1_A_AT similar to RNA polymerase I polypeptide B; DNA-directed RNA polymerase I 135kDa polypeptide; RNA polymerase I subunit 2 gga
HG-U133_PLUS_2:220113_X_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133A:220113_X_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-FOCUS:220113_X_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133A_2:220113_X_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133_PLUS_2:233341_S_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133B:233341_S_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133B:223403_S_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133_PLUS_2:223403_S_AT polymerase (RNA) I polypeptide B, 128kDa hs
HU35KSUBC:RC_AA460359_AT polymerase (RNA) I polypeptide B, 128kDa hs
U133_X3P:G13436127_3P_A_AT polymerase (RNA) I polypeptide B, 128kDa hs
U133_X3P:HS2.212849.1.S1_3P_X_AT polymerase (RNA) I polypeptide B, 128kDa hs
U133_X3P:HS.86337.2.S1_3P_A_AT polymerase (RNA) I polypeptide B, 128kDa hs
U133_X3P:1557331_3P_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U133_PLUS_2:1557331_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U95C:62960_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U95E:83482_R_AT polymerase (RNA) I polypeptide B, 128kDa hs
HG-U95E:79008_AT Polymerase (RNA) I polypeptide B, 128kDa hs
MU11KSUBA:U58280_S_AT RNA polymerase 1-2 mm
MG-U74AV2:92225_F_AT RNA polymerase 1-2 mm
MOE430A:1416126_AT RNA polymerase 1-2 mm
MOUSE430A_2:1416126_AT RNA polymerase 1-2 mm
MOUSE430_2:1416126_AT RNA polymerase 1-2 mm
RG-U34A:AF025424_AT RNA polymerase 1-2 rn
RG-U34B:RC_AI011980_AT RNA polymerase 1-2 rn
RAE230A:1387268_AT RNA polymerase 1-2 rn
RAT230_2:1387268_AT RNA polymerase 1-2 rn
YEAST_2:1771463_AT RNA polymerase I subunit A135 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 CAA99827 Hypothetical protein F14B4.3 [Caenorhabditis elegans] ref|NP_492476.1| F14B4.3 [Caenorhabditis elegans] 0.0
blast CAE72324 Hypothetical protein CBG19469 [Caenorhabditis briggsae] 0.0
blast AAH97040 Hypothetical protein LOC393490 [Danio rerio] ref|NP_956812.2| hypothetical protein LOC393490 [Danio rerio] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 3.5E-21
Pfam IPR009674 EMBL-EBI RNA polymerase I, Rpa2 specific 9.9E-38
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 4.9E-26
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 1.3E-33
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 9.9E-12
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.2E-50
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-94
Sequence
Target Sequence 
>C. ELEGANS:173795_AT
attttttcaacatttccttcataatagaaatactgaaaacttcatgcagttctctaaact
ttgatttttaaaaaatttcttttacactacactttaatattctccgtcccctatcctaca
acaatctcacggtttttgtctattttttgttattttctctttgcaagttgttttattgtt
gaaccttttctgaaatttttgatttttagccgattttagcaatttttgttacttttttgt
ttaccctcatccaatttattctgtttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTTTTCAACATTTCCTTCATAAT 419 15 3405 Antisense
AACTTCATGCAGTTCTCTAAACTTT 325 139 3442 Antisense
CACTACACTTTAATATTCTCCGTCC 577 197 3489 Antisense
CCCTATCCTACAACAATCTCACGGT 9 261 3513 Antisense
CAATCTCACGGTTTTTGTCTATTTT 486 181 3526 Antisense
GTTATTTTCTCTTTGCAAGTTGTTT 482 447 3553 Antisense
GCAAGTTGTTTTATTGTTGAACCTT 322 303 3567 Antisense
TTTTGATTTTTAGCCGATTTTAGCA 404 675 3601 Antisense
GCCGATTTTAGCAATTTTTGTTACT 614 265 3613 Antisense
TTTTGTTTACCCTCATCCAATTTAT 513 673 3639 Antisense
ACCCTCATCCAATTTATTCTGTTTC 322 91 3647 Antisense
Sequence Source Affymetrix Proprietary Database