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[193308_at] RNA polymerases L / 13 to 16 Kd subunit

Description W01G7.3 /REP_DB=WormBase Gene ID /WP=CE18986 /TR=SW:Q9XVH6 /GB=CAB03455.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=RNA polymerases L - 13 to 16 Kd subunit
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 77      4grp_highest_8_8 > 19      4grp_high_8_8 > 63      6grp_highest_nonorm > 97      6grp_total > 77      4grp_total > 48      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 513
1 2 3 4 range
A 561.9
(-3)
P 		815.7
(0.9)
P 		953.3
(3)
P 		631.1
(-1.9)
P 		391
B 660.1
(-2.3)
P 		650.1
(-2.4)
P 		1074.5
(3)
P 		601.7
(-3)
P 		473
C 594.2
(-2.8)
P 		753.9
(0)
P 		924
(3)
P 		583.5
(-3)
P 		341
avr 605.4
(-3) 		739.9
(-0.9) 		983.9
(3) 		605.4
(-3) 		379

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1151
1 2 3 4 5 6 range
A 1000.4
(1.4)
P 		679.9
(-3)
P 		871.7
(-0.3)
P 		716.8
(-2.5)
P 		788
(-1.5)
P 		1112.1
(3)
P 		432
B 691.8
(-3)
P 		688.7
(-3)
P 		845.5
(-2.2)
P 		799.9
(-2.4)
P 		1115.3
(-0.7)
P 		1811.9
(3)
P 		1123
C 685.2
(-2.8)
P 		660.5
(-3)
P 		695.4
(-2.7)
P 		968.9
(-0.7)
P 		806.8
(-1.9)
P 		1457.4
(3)
P 		797
avr 792.5
(-2.1) 		676.4
(-3) 		804.2
(-2) 		828.5
(-1.8) 		903.4
(-1.3) 		1460.5
(3) 		784
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 204.6
(1.3)
P 		177.1
(0.2)
P 		249.2
(3)
P 		92.4
(-3)
P 		157
B 210.5
(1.1)
P 		160.6
(-1.4)
P 		249
(3)
P 		128.2
(-3)
P 		121
C 196.7
(-0.4)
P 		216.7
(0.2)
P 		322
(3)
P 		98.4
(-3)
P 		224
avr 203.9
(0.5) 		184.8
(-0.2) 		273.4
(3) 		106.3
(-3) 		167

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 499
1 2 3 4 5 6 range
A 184.4
(-2.8)
P 		241.8
(1)
P 		189.8
(-2.5)
P 		181.8
(-3)
P 		237.8
(0.8)
P 		270.8
(3)
P 		89
B 240.7
(-2.5)
P 		229.2
(-2.7)
P 		205.3
(-3)
P 		211.9
(-2.9)
P 		453.1
(0.2)
P 		675.7
(3)
P 		470
C 254
(-1.5)
P 		201.5
(-2.5)
P 		177
(-3)
P 		194.9
(-2.7)
P 		261.1
(-1.4)
P 		487.9
(3)
P 		311
avr 226.4
(-2.3) 		224.2
(-2.3) 		190.7
(-3) 		196.2
(-2.9) 		317.3
(-0.4) 		478.1
(3) 		287
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193308_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3058
Sequence Type Exemplar sequence
Representative Public ID W01G7.3 NCBI
Target Description W01G7.3 /REP_DB=WormBase Gene ID /WP=CE18986 /TR=SW:Q9XVH6 /GB=CAB03455.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=RNA polymerases L - 13 to 16 Kd subunit
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_064541(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064541 NCBI Caenorhabditis elegans W01G7.3 (W01G7.3) mRNA, complete cds. 11/11 None
GENEFINDER00000032224 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14059981:14060452:1 11/11 None
W01G7.3 ENSEMBL cdna:known chromosome:CEL140:II:14059976:14060513:1 gene:W01G7.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000032216 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:14059977-14060449(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA polymerases L / 13 to 16 Kd subunit
Ensembl W01G7.3
Entrez Gene 175056 Entrez gene
SwissProt Q9XVH6 EMBL-EBI
WormBase CE18986 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:252041_AT DNA-directed RNA polymerase II 13.6 kDa subunit (RPB13.6) at
DROSOPHILA_2:1638576_AT dm
DROSGENOME1:146402_AT dm
HG-U95AV2:1486_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HC-G110:1486_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HU35KSUBC:RC_H73947_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HUGENEFL:L37127_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
U133_X3P:HS.80475.3.A1_3P_S_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
U133_X3P:HS.80475.1.S1_3P_X_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HG-U133A_2:212782_X_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HG-U133_PLUS_2:212782_X_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HG-U133A:212782_X_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
HG-U95AV2:38055_AT polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa hs
MU11KSUBA:D85818_S_AT polymerase (RNA) II (DNA directed) polypeptide J mm
MU11KSUBB:MSA.7869.0_F_AT polymerase (RNA) II (DNA directed) polypeptide J mm
MG-U74AV2:100461_AT polymerase (RNA) II (DNA directed) polypeptide J mm
MOE430A:1417720_AT polymerase (RNA) II (DNA directed) polypeptide J mm
MOUSE430A_2:1417720_AT polymerase (RNA) II (DNA directed) polypeptide J mm
MOUSE430_2:1417720_AT polymerase (RNA) II (DNA directed) polypeptide J mm
RG-U34B:RC_AA925338_AT polymerase (RNA) II (DNA directed) polypeptide J (predicted) rn
RAE230A:1398914_AT polymerase (RNA) II (DNA directed) polypeptide J (predicted) rn
RAT230_2:1398914_AT polymerase (RNA) II (DNA directed) polypeptide J (predicted) rn
YEAST_2:1769942_AT RNA polymerase II subunit B12.5; part of central core; similar to Rpc19p and bacterial alpha subunit 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 CAB03455 Hypothetical protein W01G7.3 [Caenorhabditis elegans] ref|NP_496942.1| W01G7.3 [Caenorhabditis elegans] sp|Q9XVH6|RPB11_CAEEL Probable DNA-directed RNA polymerase II 13.3 kDa polypeptide (RPB11) 1.0E-64
blast CAE73393 Hypothetical protein CBG20834 [Caenorhabditis briggsae] 4.0E-60
blast NP_006225 DNA directed RNA polymerase II polypeptide J [Homo sapiens] ref|XP_593972.2| PREDICTED: similar to DNA-directed RNA polymerase II 13.3 kDa polypeptide (RPB11) isoform 1 [Bos taurus] gb|AAH65711.1| POLR2J protein [Homo sapiens] gb|AAH24165.1| DNA directed RNA polymerase II polypeptide J [Homo sapiens] gb|AAH42939.1| Polymerase (RNA) II (DNA directed) polypeptide J [Mus musculus] emb|CAA67075.1| RNA polymerase II subunit [Homo sapiens] emb|CAA57785.1| RNA polymerase II subunit [Homo sapiens] dbj|BAE34594.1| unnamed protein product [Mus musculus] ref|XP_213753.1| PREDICTED: similar to DNA-directed RNA polymerase II 13.3 kDa polypeptide (RPB11) [Rattus norvegicus] sp|P52435|RPB11_HUMAN DNA-directed RNA polymerase II 13.3 kDa polypeptide (RPB11) gb|AAD05361.1| RNA polymerase II [Homo sapiens] prf||2210288A RNA polymerase II 4.0E-37
Protein Domains
Database ID Description E-Value
Pfam IPR008193 EMBL-EBI DNA-directed RNA polymerase, 13 to 16 kDa subunit 3.7E-19
Sequence
Target Sequence 
>C. ELEGANS:193308_AT
atgaatgcgccagctgctttcgaatcatttttgcttctcgacgacaagaaattctacatt
gaaaaagacacaaaggttccaaatgcggcgatcttcacaatcatgaaggaggatcacacg
ctgggaaatatgctgaaaatccaacttctcaaggacccagaggtgctgttcgccggctac
aagaaccctcacccgttggagcacaagatcttgctccgaatccagacaaccaacaatacg
acgccagctgatgctctcacaacggccataaccgatttggtgggagaactctcgttgctc
gagcatcgaatcgacgcggccatcaaaaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGAATGCGCCAGCTGCTTTCGAAT 212 43 13 Antisense
GCTGCTTTCGAATCATTTTTGCTTC 455 297 25 Antisense
GGTTCCAAATGCGGCGATCTTCACA 320 507 87 Antisense
GAAGGAGGATCACACGCTGGGAAAT 536 331 117 Antisense
TCAAGGACCCAGAGGTGCTGTTCGC 257 631 161 Antisense
CCTCACCCGTTGGAGCACAAGATCT 459 267 199 Antisense
TTGCTCCGAATCCAGACAACCAACA 37 701 223 Antisense
ACAATACGACGCCAGCTGATGCTCT 601 113 245 Antisense
TGCTCTCACAACGGCCATAACCGAT 63 581 264 Antisense
GAACTCTCGTTGCTCGAGCATCGAA 28 349 298 Antisense
TCGAATCGACGCGGCCATCAAAAAG 345 601 318 Antisense
Sequence Source Affymetrix Proprietary Database