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[173956_s_at]

Description AV200614_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y54E10BR.C /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV200614 /WB_GENE_ID=Y54E10BR.C /WP=CE22465 /CHR=1 /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF59550.1; Caenorhabditis elegans cDNA clone:yk577h10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 90      6grp_high1_10_10 > 09      4grp_highest_8_8 > 11      4grp_high_8_8 > 55      6grp_highest_nonorm > 57      6grp_total > 19      4grp_total > 48      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1457
1 2 3 4 range
A 2116.7
(-3)
P 		2131.4
(-2.9)
P 		3414.9
(3)
P 		2493.5
(-1.3)
P 		1298
B 1958.3
(-3)
P 		2729
(3)
P 		2703.7
(2.8)
P 		2257.9
(-0.7)
P 		771
C 2200.7
(-2.1)
P 		2757.9
(1.6)
P 		2966.9
(3)
P 		2065.2
(-3)
P 		902
avr 2091.9
(-3) 		2539.4
(-0.1) 		3028.5
(3) 		2272.2
(-1.8) 		937

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1277
1 2 3 4 5 6 range
A 3465.1
(3)
P 		2344.1
(-2.6)
P 		2518.5
(-1.8)
P 		2743.3
(-0.6)
P 		2597.9
(-1.4)
P 		2271.6
(-3)
P 		1194
B 2818.9
(2)
P 		2475.3
(-0.7)
P 		2188.1
(-3)
P 		2808
(1.9)
P 		2950.8
(3)
P 		2581.7
(0.1)
P 		763
C 2481.8
(-1.4)
P 		2462.8
(-1.6)
P 		2326.8
(-3)
P 		2604.9
(-0.1)
P 		2909.6
(3)
P 		2530.7
(-0.9)
P 		583
avr 2921.9
(3) 		2427.4
(-2.1) 		2344.5
(-3) 		2718.7
(0.9) 		2819.4
(1.9) 		2461.3
(-1.8) 		577
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 686
1 2 3 4 range
A 770.7
(1.6)
P 		462.7
(-1.9)
P 		892.7
(3)
P 		365
(-3)
P 		528
B 624.5
(1.5)
P 		674
(3)
P 		626.5
(1.5)
P 		481.2
(-3)
P 		193
C 728.5
(0.3)
P 		792.9
(0.9)
P 		1034
(3)
P 		348.2
(-3)
P 		686
avr 707.9
(1.1) 		643.2
(0.2) 		851.1
(3) 		398.1
(-3) 		453

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 675
1 2 3 4 5 6 range
A 638.8
(-1.1)
P 		833.7
(3)
P 		548.5
(-3)
P 		695.8
(0.1)
P 		783.9
(2)
P 		553.1
(-2.9)
P 		285
B 980.8
(1)
P 		823.9
(-0.4)
P 		531.3
(-3)
P 		743.7
(-1.1)
P 		1198.9
(3)
P 		962.7
(0.9)
P 		668
C 919.9
(2.7)
P 		751.5
(0.3)
P 		592.2
(-2)
P 		523.9
(-3)
P 		941.5
(3)
P 		847.2
(1.6)
P 		418
avr 846.5
(1.2) 		803
(0.5) 		557.3
(-3) 		654.5
(-1.6) 		974.8
(3) 		787.7
(0.3) 		418
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173956_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22498
Sequence Type Exemplar sequence
Representative Public ID AV200614 NCBI
Target Description AV200614_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y54E10BR.C /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV200614 /WB_GENE_ID=Y54E10BR.C /WP=CE22465 /CHR=1 /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF59550.1; Caenorhabditis elegans cDNA clone:yk577h10 : 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_058692(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058692 NCBI Caenorhabditis elegans Y54E10BR.6 (Y54E10BR.6) mRNA, complete cds. 11/11 None
SNAP00000038971 ENSEMBL cdna:SNAP chromosome:CEL140:I:3031339:3031863:-1 10/11 None
GENEFINDER00000038978 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3031339:3031863:-1 10/11 None
Y54E10BR.6 ENSEMBL cdna:known chromosome:CEL140:I:3031278:3032939:-1 gene:Y54E10BR.6 11/11 None
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:3031288-3032940(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y54E10BR.6
Entrez Gene 171877 Entrez gene
SwissProt Q9N3C9 EMBL-EBI
WormBase CE22465 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12985_AT DNA-directed RNA polymerase II at
ATH1-121501:247763_AT DNA-directed RNA polymerase II at
CANINE:1584006_AT similar to polymerase (RNA) II (DNA directed) polypeptide G cfa
CANINE_2:CFA.8920.1.A1_AT similar to polymerase (RNA) II (DNA directed) polypeptide G cfa
CANINE_2:CFAAFFX.23745.1.S1_AT similar to polymerase (RNA) II (DNA directed) polypeptide G cfa
CANINE_2:CFAAFFX.23745.1.S1_S_AT similar to polymerase (RNA) II (DNA directed) polypeptide G cfa
DROSOPHILA_2:1629251_AT dm
HG-U95AV2:39747_AT polymerase (RNA) II (DNA directed) polypeptide G hs
HUGENEFL:U52427_RNA1_AT polymerase (RNA) II (DNA directed) polypeptide G hs
HG-U133A:202306_AT polymerase (RNA) II (DNA directed) polypeptide G hs
HG-U133_PLUS_2:202306_AT polymerase (RNA) II (DNA directed) polypeptide G hs
HG-FOCUS:202306_AT polymerase (RNA) II (DNA directed) polypeptide G hs
HG-U133A_2:202306_AT polymerase (RNA) II (DNA directed) polypeptide G hs
U133_X3P:G4505946_3P_AT polymerase (RNA) II (DNA directed) polypeptide G hs
MU11KSUBA:C76415_RC_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MU11KSUBA:C76415_RC_G_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MU11KSUBB:MSA.4085.0_S_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MG-U74AV2:94073_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MG-U74CV2:169848_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MG-U74CV2:169807_R_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MOE430A:1416270_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MOUSE430A_2:1416270_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MOUSE430_2:1416270_AT polymerase (RNA) II (DNA directed) polypeptide G mm
MU19KSUBA:TC18614_S_AT Polymerase (RNA) II (DNA directed) polypeptide G, mRNA (cDNA clone MGC:11735 IMAGE:3968561) mm
RG-U34A:Z71925_AT polymerase (RNA) II (DNA directed) polypeptide G rn
RAE230A:1367769_AT polymerase (RNA) II (DNA directed) polypeptide G rn
RAT230_2:1367769_AT polymerase (RNA) II (DNA directed) polypeptide G rn
YEAST_2:1770594_AT RNA polymerase II subunit B16; forms two subunit dissociable complex with Rpb4p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6350 transcription inferred from electronic annotation QuickGO AmiGO
6979 response to oxidative stress inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3899 DNA-directed RNA polymerase activity inferred from electronic annotation QuickGO AmiGO
4601 peroxidase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAF59550 Hypothetical protein Y54E10BR.6 [Caenorhabditis elegans] ref|NP_491093.1| Y54E10BR.6 [Caenorhabditis elegans] 1.0E-114
blast AAF59550 Hypothetical protein Y54E10BR.6 [Caenorhabditis elegans] ref|NP_491093.1| Y54E10BR.6 [Caenorhabditis elegans] 1.0E-100
blast CAE60566 Hypothetical protein CBG04195 [Caenorhabditis briggsae] 2.0E-98
blast XP_780458 PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide G [Strongylocentrotus purpuratus] 3.0E-78
Protein Domains
Database ID Description E-Value
Pfam IPR003029 EMBL-EBI RNA binding S1 1.2E-14
Pfam IPR005576 EMBL-EBI RNA polymerase Rpb7, N-terminal 8.1E-41
Pfam IPR003029 EMBL-EBI RNA binding S1 1.2E-14
Pfam IPR005576 EMBL-EBI RNA polymerase Rpb7, N-terminal 8.1E-41
Sequence
Target Sequence 
>C. ELEGANS:173956_S_AT
gttggcacgcaactggtgcgcttacgcttcggatgttcttccacttgtcactcgaccatg
aagtctgcctccatccgaaatatttcggtccaaacctgaacgaaaccatcaaaatgaagc
tgttcaacgaagtcgagggaacgtgcacaggaaagtacggattcgtcatcgcagtcacca
caatcgacacgatcggccacggcctgatccagcctggccgtggattcgtcatctacccgg
tccgttacaaggccatcgtgttccgcccgttcaaaggacaagtcgtcgatggagtcgtca
cacaggtcaataaagtcggcattttctgtgatatcggaccactttcatgcttcatcagtc
gtcattgtattccaccagacatggaattcgatccgaacagtgagaaaccgtgctacaaga
ccaatgatgaggcgaatgtgattcggaatgatgatgagatccgtgtgaagctcatcggaa
cacgtgtcgatgctaacgacatttttgccatcggaaccttgatggacgattttctcggac
tgtgcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTGGCACGCAACTGGTGCGCTTAC 623 435 51 Antisense
TTCCACTTGTCACTCGACCATGAAG 546 699 89 Antisense
AAGTACGGATTCGTCATCGCAGTCA 710 149 203 Antisense
TCGCAGTCACCACAATCGACACGAT 473 597 219 Antisense
TGTTCCGCCCGTTCAAAGGACAAGT 295 563 309 Antisense
GATGGAGTCGTCACACAGGTCAATA 581 407 338 Antisense
AAGTCGGCATTTTCTGTGATATCGG 705 157 363 Antisense
TGATATCGGACCACTTTCATGCTTC 587 563 379 Antisense
TCAGTCGTCATTGTATTCCACCAGA 119 623 405 Antisense
GACATTTTTGCCATCGGAACCTTGA 632 369 548 Antisense
TGGACGATTTTCTCGGACTGTGCCA 86 549 573 Antisense
Sequence Source Affymetrix Proprietary Database