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[173320_s_at]

Description CEK009D1R_rc /REP_DB=TREMBL Accession /GB=D27127 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk9d1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 66      4grp_highest_8_8 > 34      4grp_high_8_8 > 57      6grp_highest_nonorm > 83      6grp_total > 57      4grp_total > 63      6grp_highest_sub > Cu      6grp_high1_sub > Da      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 389
1 2 3 4 range
A 664.5
(3)
P 		583.4
(0.1)
P 		600.7
(0.7)
P 		496.7
(-3)
P 		168
B 772.9
(3)
P 		508.2
(-2.9)
P 		672.8
(0.8)
P 		502.1
(-3)
P 		271
C 683.3
(3)
P 		528.2
(-0.1)
P 		623.2
(1.8)
P 		384.2
(-3)
P 		299
avr 706.9
(3) 		539.9
(-1.1) 		632.2
(1.2) 		461
(-3) 		246

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 356
1 2 3 4 5 6 range
A 394.1
(-2)
P 		448.9
(-1.1)
P 		438.4
(-1.3)
P 		436.5
(-1.3)
P 		338.1
(-3)
P 		682.2
(3)
P 		344
B 471.6
(-0.1)
P 		376.4
(-2.1)
P 		389.3
(-1.9)
P 		380.3
(-2.1)
P 		335.1
(-3)
P 		621.2
(3)
P 		286
C 547.2
(0.1)
P 		396.9
(-2.9)
P 		391.3
(-3)
P 		391
(-3)
P 		398.8
(-2.8)
P 		690.8
(3)
P 		300
avr 471
(-0.8) 		407.4
(-2) 		406.3
(-2) 		402.6
(-2.1) 		357.3
(-3) 		664.7
(3) 		307
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 182
1 2 3 4 range
A 241.9
(3)
P 		126.6
(-1.1)
P 		157
(-0)
P 		72.7
(-3)
P 		169
B 246.5
(3)
P 		125.5
(-2.2)
P 		155.9
(-0.9)
P 		107
(-3)
P 		140
C 226.2
(3)
P 		151.8
(0.2)
P 		217.2
(2.7)
P 		64.8
(-3)
P 		161
avr 238.2
(3) 		134.6
(-1) 		176.7
(0.6) 		81.5
(-3) 		157

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 159
1 2 3 4 5 6 range
A 72.7
(-3)
P 		159.7
(2.6)
P 		95.5
(-1.5)
P 		110.7
(-0.6)
P 		102
(-1.1)
P 		166.1
(3)
P 		93
B 164.1
(0)
P 		125.3
(-1.7)
P 		94.5
(-3)
P 		100.7
(-2.7)
P 		136.2
(-1.2)
P 		231.6
(3)
P 		137
C 202.8
(1.9)
P 		121.1
(-1.3)
P 		99.6
(-2.2)
P 		78.6
(-3)
P 		129
(-1)
P 		231.3
(3)
P 		153
avr 146.5
(-0.3) 		135.4
(-0.9) 		96.5
(-3) 		96.7
(-3) 		122.4
(-1.6) 		209.7
(3) 		113
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173320_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27869
Sequence Type Exemplar sequence
Representative Public ID CEK009D1R NCBI
Target Description CEK009D1R_rc /REP_DB=TREMBL Accession /GB=D27127 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk9d1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_065791(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065791 NCBI Caenorhabditis elegans F09F7.3 (F09F7.3) mRNA, complete cds. 11/11 A 
SNAP00000025398 ENSEMBL cdna:SNAP chromosome:CEL140:III:5555408:5564633:1 11/11 None
F09F7.3.1 ENSEMBL cdna:known chromosome:CEL140:III:5557298:5564785:1 gene:F09F7.3 11/11 None
F09F7.3.2 ENSEMBL cdna:known chromosome:CEL140:III:5557319:5564783:1 gene:F09F7.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000025410 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:5562796-5564761(+) 98.9 98.89
Public Domain and Genome References
Gene Title
Ensembl F09F7.3
Entrez Gene 175767 Entrez gene
SwissProt Q27492 EMBL-EBI
WormBase CE30653 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:248984_AT DNA-directed RNA polymerase, putative at
CANINE:1585129_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) cfa
CANINE_2:CFA.7262.1.A1_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) cfa
CANINE_2:CFAAFFX.3707.1.S1_S_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) cfa
DROSOPHILA_2:1628131_AT RNA polymerase III 128kD subunit dm
DROSGENOME1:153813_AT RNA polymerase III 128kD subunit dm
CHICKEN:GGA.11068.1.S1_S_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) gga
CHICKEN:GGAAFFX.23964.2.S1_S_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) gga
CHICKEN:GGAAFFX.23964.7.S1_S_AT similar to DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) gga
HU35KSUBB:RC_R59312_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HU35KSUBB:RC_AA121153_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HU35KSUBD:RC_N75936_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U133A:219459_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U133_PLUS_2:219459_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U133A_2:219459_AT polymerase (RNA) III (DNA directed) polypeptide B hs
U133_X3P:G8922398_3P_AT polymerase (RNA) III (DNA directed) polypeptide B hs
U133_X3P:HS2.407481.1.S1_3P_S_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U133_PLUS_2:1556803_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U133_PLUS_2:1556804_S_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U95C:62810_AT polymerase (RNA) III (DNA directed) polypeptide B hs
HG-U95B:41938_AT Polymerase (RNA) III (DNA directed) polypeptide B hs
HU35KSUBB:RC_AA042871_AT Polymerase (RNA) III (DNA directed) polypeptide B hs
MG-U74CV2:132659_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOE430B:1452949_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOUSE430_2:1452949_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOE430B:1443466_S_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOUSE430_2:1443466_S_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOE430B:1443494_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOUSE430_2:1443494_AT polymerase (RNA) III (DNA directed) polypeptide B mm
MOE430B:1457345_AT Polymerase (RNA) III (DNA directed) polypeptide B (Polr3b), mRNA mm
MOUSE430_2:1457345_AT Polymerase (RNA) III (DNA directed) polypeptide B (Polr3b), mRNA mm
RAE230A:1388984_AT similar to RNA polymerase III subunit RPC2 rn
RAT230_2:1388984_AT similar to RNA polymerase III subunit RPC2 rn
YEAST_2:1775098_AT Second-largest subunit of RNA polymerase III, which is responsible for the transcription of tRNA and 5S RNA genes, and other low molecular weight RNAs 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 NP_498192 F09F7.3 [Caenorhabditis elegans] gb|AAA50695.2| Hypothetical protein F09F7.3 [Caenorhabditis elegans] 0.0
blast CAE56370 Hypothetical protein CBG24045 [Caenorhabditis briggsae] 0.0
blast NP_081699 RNA polymerase III subunit RPC2 [Mus musculus] gb|AAH68143.1| RNA polymerase III subunit RPC2 [Mus musculus] sp|P59470|RPC2_MOUSE DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (RNA polymerase III subunit 2) (RPC2) 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 1.1E-63
Pfam IPR001753 EMBL-EBI Enoyl-CoA hydratase/isomerase 7.1E-12
Pfam IPR001753 EMBL-EBI Enoyl-CoA hydratase/isomerase 9.5E-8
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 1.2E-13
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 1.7E-10
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 7.2E-29
Pfam IPR007646 EMBL-EBI RNA polymerase Rpb2, domain 4 4.1E-27
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 2.4E-19
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-126
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 3.1E-47
Pfam IPR007644 EMBL-EBI RNA polymerase beta subunit 1.1E-63
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 1.2E-13
Pfam IPR007642 EMBL-EBI RNA polymerase Rpb2, domain 2 1.7E-10
Pfam IPR007645 EMBL-EBI RNA polymerase Rpb2, domain 3 7.2E-29
Pfam IPR007646 EMBL-EBI RNA polymerase Rpb2, domain 4 4.1E-27
Pfam IPR007647 EMBL-EBI RNA polymerase Rpb2, domain 5 2.4E-19
Pfam IPR007120 EMBL-EBI RNA polymerase Rpb2, domain 6 1.0E-126
Pfam IPR007641 EMBL-EBI RNA polymerase Rpb2, domain 7 3.1E-47
Sequence
Target Sequence 
>C. ELEGANS:173320_S_AT
aaggtcgacgtgtgcactggatgcggagtaatcggctcgaagggttggtgccaaaagtgt
cgttcgagcaagtcaatggcgaacattaagattccgtatgcgtgtaagctgctcttccag
gaacttcaatccatgaacattgtcccgaggctggacttggccagatacaccgaataa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGGTCGACGTGTGCACTGGATGCG 332 159 69 Antisense
ACTGGATGCGGAGTAATCGGCTCGA 595 95 84 Antisense
AATCGGCTCGAAGGGTTGGTGCCAA 541 169 98 Antisense
GGTTGGTGCCAAAAGTGTCGTTCGA 42 499 111 Antisense
GTGTCGTTCGAGCAAGTCAATGGCG 259 485 125 Antisense
GGCGAACATTAAGATTCCGTATGCG 699 539 146 Antisense
TCCGTATGCGTGTAAGCTGCTCTTC 517 595 161 Antisense
GCTGCTCTTCCAGGAACTTCAATCC 544 297 176 Antisense
AATCCATGAACATTGTCCCGAGGCT 200 167 196 Antisense
CATTGTCCCGAGGCTGGACTTGGCC 149 217 206 Antisense
GGACTTGGCCAGATACACCGAATAA 411 523 221 Antisense
Sequence Source Affymetrix Proprietary Database