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[174289_s_at]

Description C36163_rc /REP_DB=TREMBL Accession /GB=C36163 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk455d6 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 85      4grp_highest_8_8 > 12      4grp_high_8_8 > 39      6grp_highest_nonorm > 78      6grp_total > 75      4grp_total > 40      6grp_highest_sub > In      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 624
1 2 3 4 range
A 1109.6
(-3)
P 		1380.7
(1.3)
P 		1487.1
(3)
P 		1316.7
(0.3)
P 		378
B 1254.2
(-3)
P 		1442.4
(-0.6)
P 		1733.1
(3)
P 		1424
(-0.9)
P 		479
C 1229
(-3)
P 		1428.3
(1.5)
P 		1426.1
(1.5)
P 		1494.6
(3)
P 		266
avr 1197.6
(-3) 		1417.1
(0.7) 		1548.8
(3) 		1411.8
(0.7) 		351

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1436
1 2 3 4 5 6 range
A 1106.7
(-3)
P 		1274
(-1.5)
P 		1692.9
(2.1)
P 		1601.9
(1.3)
P 		1342.1
(-0.9)
P 		1789.8
(3)
P 		683
B 1207.1
(-2.5)
P 		1149.5
(-3)
P 		1551.7
(0.5)
P 		1682.3
(1.6)
P 		1782.5
(2.5)
P 		1838.7
(3)
P 		689
C 1039.3
(-3)
P 		1240.4
(-2.2)
P 		1244.4
(-2.1)
P 		1304.4
(-1.9)
P 		1550.6
(-0.9)
P 		2475
(3)
P 		1436
avr 1117.7
(-3) 		1221.3
(-2.3) 		1496.3
(-0.5) 		1529.5
(-0.3) 		1558.4
(-0.1) 		2034.5
(3) 		917
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 304
1 2 3 4 range
A 404
(3)
P 		299.7
(0)
P 		388.8
(2.6)
P 		192.7
(-3)
P 		211
B 399.9
(2.9)
P 		356.2
(0.2)
P 		401.6
(3)
P 		303.5
(-3)
P 		98
C 406.8
(0.8)
P 		410.7
(0.9)
P 		497
(3)
P 		252
(-3)
P 		245
avr 403.6
(2.1) 		355.5
(0.5) 		429.1
(3) 		249.4
(-3) 		180

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 625
1 2 3 4 5 6 range
A 204
(-3)
P 		453.1
(3)
P 		368.7
(1)
P 		406.3
(1.9)
P 		405
(1.8)
P 		435.8
(2.6)
P 		249
B 420
(-2.3)
P 		382.6
(-2.9)
P 		376.8
(-3)
P 		445.6
(-1.8)
P 		724.2
(3)
P 		685.7
(2.3)
P 		347
C 385.2
(-1.7)
P 		378.5
(-1.8)
P 		316.7
(-2.4)
P 		262.3
(-3)
P 		501.8
(-0.5)
P 		828.5
(3)
P 		566
avr 336.4
(-3) 		404.7
(-1.7) 		354.1
(-2.7) 		371.4
(-2.3) 		543.7
(1) 		650
(3) 		314
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174289_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20802
Sequence Type Exemplar sequence
Representative Public ID C36163 NCBI
Target Description C36163_rc /REP_DB=TREMBL Accession /GB=C36163 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk455d6 : 3prime 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_063143(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063143 NCBI Caenorhabditis elegans F43E2.2 (F43E2.2) mRNA, complete cds. 11/11 None
SNAP00000044496 ENSEMBL cdna:SNAP chromosome:CEL140:II:7372231:7375004:1 11/11 None
GENEFINDER00000044505 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7374435:7375004:1 11/11 None
F43E2.2 ENSEMBL cdna:known chromosome:CEL140:II:7371745:7375114:1 gene:F43E2.2 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
chrII:7374760-7375037(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F43E2.2
Entrez Gene 174208 Entrez gene
SwissProt O02092 EMBL-EBI
WormBase CE28327 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:250510_AT RNA polymerase II 15.9 kDa subunit (RPB15.9) at
CANINE_2:CFA.18522.1.S1_AT similar to polymerase (RNA) II (DNA directed) polypeptide D isoform 1 cfa
CANINE_2:CFA.19099.1.S1_AT similar to polymerase (RNA) II (DNA directed) polypeptide D isoform 1 cfa
CANINE_2:CFA.19099.1.S1_X_AT similar to polymerase (RNA) II (DNA directed) polypeptide D isoform 1 cfa
CANINE_2:CFAAFFX.7382.1.S1_S_AT similar to polymerase (RNA) II (DNA directed) polypeptide D isoform 1 cfa
CHICKEN:GGA.4766.2.S1_A_AT polymerase (RNA) II (DNA directed) polypeptide D gga
HG-U133_PLUS_2:203664_S_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133A:203664_S_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HG-FOCUS:203664_S_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133A_2:203664_S_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HU35KSUBA:U85510_AT polymerase (RNA) II (DNA directed) polypeptide D hs
U133_X3P:G4758573_3P_S_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U95AV2:33726_AT polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133_PLUS_2:214144_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133A_2:214144_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133A:214144_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HU35KSUBC:RC_AA478541_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HU35KSUBD:RC_H70627_S_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
U133_X3P:HS.194638.1.A1_3P_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
U133_X3P:HS.108336.0.A1_3P_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133_PLUS_2:228650_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133B:228650_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U95B:56881_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U95C:63651_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133_PLUS_2:243789_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
HG-U133B:243789_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
U133_X3P:HS.257464.0.A1_3P_AT Polymerase (RNA) II (DNA directed) polypeptide D hs
MU11KSUBB:MSA.14654.0_S_AT polymerase (RNA) II (DNA directed) polypeptide D mm
MG-U74AV2:97315_AT polymerase (RNA) II (DNA directed) polypeptide D mm
MOE430A:1424258_AT polymerase (RNA) II (DNA directed) polypeptide D mm
MOUSE430A_2:1424258_AT polymerase (RNA) II (DNA directed) polypeptide D mm
MOUSE430_2:1424258_AT polymerase (RNA) II (DNA directed) polypeptide D mm
MU19KSUBC:TC36857_AT Polymerase (RNA) II (DNA directed) polypeptide D (Polr2d), transcript variant 1, mRNA mm
RAE230B:1379832_AT polymerase (RNA) II (DNA directed) polypeptide D (predicted) rn
RAT230_2:1379832_AT polymerase (RNA) II (DNA directed) polypeptide D (predicted) rn
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
3899 DNA-directed RNA polymerase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC71124 Hypothetical protein F43E2.2 [Caenorhabditis elegans] ref|NP_495544.1| F43E2.2 [Caenorhabditis elegans] 1.0E-108
blast AAC71124 Hypothetical protein F43E2.2 [Caenorhabditis elegans] ref|NP_495544.1| F43E2.2 [Caenorhabditis elegans] 1.0E-95
blast CAE67606 Hypothetical protein CBG13151 [Caenorhabditis briggsae] 2.0E-62
blast CAE67606 Hypothetical protein CBG13151 [Caenorhabditis briggsae] 4.0E-62
blast T34046 hypothetical protein F43E2.1 - Caenorhabditis elegans 9.0E-62
blast T34046 hypothetical protein F43E2.1 - Caenorhabditis elegans 1.0E-61
blast AAC71124 Hypothetical protein F43E2.2 [Caenorhabditis elegans] ref|NP_495544.1| F43E2.2 [Caenorhabditis elegans] 3.0E-60
Protein Domains
Database ID Description E-Value
Pfam IPR005574 EMBL-EBI RNA polymerase Rpb4 3.7E-55
Pfam IPR005574 EMBL-EBI RNA polymerase Rpb4 1.2E-51
Pfam IPR005574 EMBL-EBI RNA polymerase Rpb4 3.7E-55
Sequence
Target Sequence 
>C. ELEGANS:174289_S_AT
ctcgccgcatgtctcgattcaaaaatcgcgaaactatccgtgcagttcgagcgattttct
ccgagaagcatcttcacaaattcgaagttgcgcagattgccaatctctgccctgaaaatg
ccgaagaagccaaagcactagttccttctttggaaaacaaaatcgaggagtctgaactag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCGCCGCATGTCTCGATTCAAAAA 178 233 30 Antisense
AAAATCGCGAAACTATCCGTGCAGT 705 131 51 Antisense
ACTATCCGTGCAGTTCGAGCGATTT 162 103 62 Antisense
GCAGTTCGAGCGATTTTCTCCGAGA 189 311 71 Antisense
TTTTCTCCGAGAAGCATCTTCACAA 301 677 84 Antisense
AAATTCGAAGTTGCGCAGATTGCCA 231 115 107 Antisense
TTGCGCAGATTGCCAATCTCTGCCC 406 703 117 Antisense
CCAATCTCTGCCCTGAAAATGCCGA 461 277 129 Antisense
AAGCCAAAGCACTAGTTCCTTCTTT 319 147 156 Antisense
GCACTAGTTCCTTCTTTGGAAAACA 460 315 164 Antisense
AACAAAATCGAGGAGTCTGAACTAG 331 133 185 Antisense
Sequence Source Affymetrix Proprietary Database