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[191795_s_at] DNA-directed RNA polymerase I

Description F14B4.3 /REP_DB=WormBase Gene ID /WP=CE05629 /TR=Q27493 /GB=CAA99827.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=DNA-directed RNA polymerase I
Cluster 6grp_highest_10_10 > 65      6grp_high1_10_10 > 56      4grp_highest_8_8 > 40      4grp_high_8_8 > 50      6grp_highest_nonorm > 83      6grp_total > 56      4grp_total > 61      6grp_high1_sub > Cu      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 604
1 2 3 4 range
A 924
(3)
P 		584.2
(-0.5)
P 		701.8
(0.7)
P 		339.8
(-3)
P 		584
B 842.6
(3)
P 		684.5
(1.2)
P 		593.9
(0.1)
P 		320.1
(-3)
P 		523
C 778.1
(1.8)
P 		874.5
(3)
P 		683.5
(0.6)
P 		396.5
(-3)
P 		478
avr 848.2
(3) 		714.4
(1.4) 		659.7
(0.7) 		352.1
(-3) 		496

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 308
1 2 3 4 5 6 range
A 517
(0)
P 		481.8
(-1.2)
P 		433.1
(-2.9)
P 		435.1
(-2.8)
P 		429.4
(-3)
P 		602.6
(3)
P 		173
B 454.2
(-0.9)
P 		511.6
(0.3)
P 		453
(-0.9)
P 		468.2
(-0.6)
P 		344.3
(-3)
P 		652.7
(3)
P 		308
C 502.4
(0.4)
P 		542.4
(1.5)
P 		433.5
(-1.4)
P 		475.6
(-0.3)
P 		370.5
(-3)
P 		601.2
(3)
P 		231
avr 491.2
(-0.2) 		511.9
(0.3) 		439.9
(-1.5) 		459.6
(-1) 		381.4
(-3) 		618.8
(3) 		237
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 287
1 2 3 4 range
A 336.4
(3)
P 		126.8
(-1.4)
P 		183.5
(-0.2)
P 		49.7
(-3)
P 		287
B 268.7
(3)
P 		169
(0)
P 		137.6
(-0.9)
P 		68.2
(-3)
P 		201
C 257.6
(3)
P 		251.4
(2.8)
P 		238.2
(2.4)
P 		66.9
(-3)
P 		191
avr 287.6
(3) 		182.4
(0.2) 		186.4
(0.3) 		61.6
(-3) 		226

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 149
1 2 3 4 5 6 range
A 95.3
(-2.9)
P 		171.4
(3)
P 		94.3
(-3)
P 		110.4
(-1.7)
P 		129.6
(-0.3)
P 		146.7
(1.1)
P 		77
B 158.1
(-0.8)
P 		170.3
(-0.3)
P 		110
(-3)
P 		124
(-2.4)
P 		139.9
(-1.7)
P 		243.4
(3)
P 		133
C 186.2
(2.1)
P 		165.5
(1)
P 		110.3
(-2.2)
P 		95.6
(-3)
P 		119.9
(-1.6)
P 		201.3
(3)
P 		106
avr 146.5
(-0.3) 		169.1
(1.2) 		104.9
(-3) 		110
(-2.7) 		129.8
(-1.4) 		197.1
(3) 		92
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191795_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.424
Sequence Type Exemplar sequence
Representative Public ID F14B4.3 NCBI
Target Description F14B4.3 /REP_DB=WormBase Gene ID /WP=CE05629 /TR=Q27493 /GB=CAA99827.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=DNA-directed RNA polymerase I
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_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
GENEFINDER00000033145 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9289100:9294685:-1 10/11 None
SNAP00000033142 ENSEMBL cdna:SNAP chromosome:CEL140:I:9289432:9294685:-1 11/11 None
F14B4.3 ENSEMBL cdna:known chromosome:CEL140:I:9289086:9294685:-1 gene:F14B4.3 11/11 A 
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:9289362-9294616(-) 100.0 100.0
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
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 2.3E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000033145 1 1174-1196
Sequence
Target Sequence 
>C. ELEGANS:191795_S_AT
tatgatgcatcgccatttgttttcaatgaagacaacacagcaatcaaccattttggagaa
ttactcacaaaagcaggttataattactacggtaacgaaacattttattcgggagttgat
ggacgtcaaatggagatgcaaatcttctttggaattgtttattatcaaagacttcgtcat
atgattgctgataaattccaagtgagagccactggaccaattgatccaattactcatcaa
ccagtaaaaggaagaaaaaagggaggaggtattcgatttggagaaatggaaagagatgct
attattgcacatggaacatctttcgtgttgcaggaccgtcttctcaactgttcggatcgt
gacgtagcatacgcttgtcgtcgttgtggatccctattgtccgtgttgatgtccagtcgt
gcaggatcacatttattgaaaaagaaaaggaaagacgacgaaccattggactacacggaa
actcaacgatgtcgtacgtgtgataaagatgatcaagttttcctgcttcaagttcctcgt
gtcttccgttatttgactgccgagttagctgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATGATGCATCGCCATTTGTTTTCA 352 657 2767 Antisense
GAGAGCCACTGGACCAATTGATCCA 329 395 2970 Antisense
GGAACATCTTTCGTGTTGCAGGACC 480 529 3079 Antisense
GACCGTCTTCTCAACTGTTCGGATC 497 381 3100 Antisense
GTAGCATACGCTTGTCGTCGTTGTG 460 457 3130 Antisense
GATCCCTATTGTCCGTGTTGATGTC 133 417 3155 Antisense
GATGTCCAGTCGTGCAGGATCACAT 164 409 3174 Antisense
GACGACGAACCATTGGACTACACGG 63 379 3220 Antisense
GATCAAGTTTTCCTGCTTCAAGTTC 641 421 3277 Antisense
TTCCTCGTGTCTTCCGTTATTTGAC 53 699 3299 Antisense
GTTATTTGACTGCCGAGTTAGCTGC 469 447 3314 Antisense
Sequence Source Affymetrix Proprietary Database