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[171809_s_at] transcritpion factor

Description C39138_rc /REP_DB=TREMBL Accession /GB=C39138 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk506c12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 55      6grp_high1_10_10 > 75      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 68      6grp_total > 66      4grp_total > 46      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1093
1 2 3 4 range
A 1938.4
(3)
P 		1587.6
(0.6)
P 		1057.7
(-3)
P 		1449.5
(-0.3)
P 		881
B 1790.3
(3)
P 		1324.6
(-3)
P 		1596.8
(0.5)
P 		1408.9
(-1.9)
P 		466
C 2150.7
(3)
P 		1636.2
(-0.3)
P 		1203.3
(-3)
P 		1269.9
(-2.6)
P 		947
avr 1959.8
(3) 		1516.1
(-1) 		1285.9
(-3) 		1376.1
(-2.2) 		674

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1501
1 2 3 4 5 6 range
A 1311.6
(-3)
P 		2675.3
(2.5)
P 		1329.4
(-2.9)
P 		2061.2
(-0)
P 		1577.7
(-1.9)
P 		2812.8
(3)
P 		1501
B 1618.7
(-2.9)
P 		2103.7
(-0)
P 		2512.3
(2.4)
P 		2611
(3)
P 		1606.1
(-3)
P 		2071.5
(-0.2)
P 		1005
C 1908.9
(-2.6)
P 		2117.9
(-0.8)
P 		2116.9
(-0.8)
P 		1856.9
(-3)
P 		1995.1
(-1.8)
P 		2564.2
(3)
P 		707
avr 1613.1
(-3) 		2299
(1.7) 		1986.2
(-0.4) 		2176.4
(0.9) 		1726.3
(-2.2) 		2482.8
(3) 		870
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 500
1 2 3 4 range
A 705.8
(3)
P 		344.6
(-1.4)
P 		276.5
(-2.2)
P 		212.2
(-3)
P 		494
B 570.9
(3)
P 		327.2
(-2.4)
P 		370
(-1.5)
P 		300.2
(-3)
P 		271
C 711.9
(3)
P 		470.4
(0.1)
P 		419.4
(-0.5)
P 		214.1
(-3)
P 		498
avr 662.9
(3) 		380.7
(-1) 		355.3
(-1.4) 		242.2
(-3) 		421

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 710
1 2 3 4 5 6 range
A 241.8
(-3)
P 		951.5
(3)
P 		289.5
(-2.6)
P 		522.8
(-0.6)
P 		476.1
(-1)
P 		684.8
(0.7)
P 		710
B 563.2
(-3)
P 		700.2
(0.9)
P 		610.1
(-1.7)
P 		691.6
(0.7)
P 		652.5
(-0.4)
P 		772.5
(3)
P 		209
C 707.5
(1.1)
P 		646.2
(0.4)
P 		538.8
(-1)
P 		373.4
(-3)
P 		645.6
(0.4)
P 		858.4
(3)
P 		485
avr 504.2
(-2.5) 		766
(2.9) 		479.5
(-3) 		529.3
(-2) 		591.4
(-0.7) 		771.9
(3) 		292
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171809_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27855
Sequence Type Exemplar sequence
Representative Public ID C39138 NCBI
Target Description C39138_rc /REP_DB=TREMBL Accession /GB=C39138 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk506c12 : 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_060420(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060420 NCBI Caenorhabditis elegans F55A3.3 (F55A3.3) mRNA, complete cds. 11/11 A 
SNAP00000019262 ENSEMBL cdna:SNAP chromosome:CEL140:I:10797258:10801022:1 11/11 None
GENEFINDER00000019267 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10797258:10801022:1 11/11 None
F55A3.3 ENSEMBL cdna:known chromosome:CEL140:I:10797251:10801268:1 gene:F55A3.3 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:10800806-10801109(+) 92.08 92.08
Public Domain and Genome References
Gene Title transcritpion factor
Ensembl F55A3.3
Entrez Gene 172984 Entrez gene
SwissProt Q9N5R9 EMBL-EBI
WormBase CE17113 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12578_AT transcriptional regulator-related at
ATH1-121501:254992_AT transcriptional regulator-related at
CANINE:1602302_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE:1598080_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE:1588193_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE_2:CFA.7705.1.A1_A_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE_2:CFA.7705.1.A1_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE_2:CFA.7705.2.A1_S_AT similar to chromatin-specific transcription elongation factor large subunit cfa
CANINE_2:CFAAFFX.9353.1.S1_S_AT similar to chromatin-specific transcription elongation factor large subunit cfa
DROSOPHILA_2:1630638_AT dm
DROSOPHILA_2:1632743_A_AT dm
DROSGENOME1:143225_AT dm
HG-U133A:217815_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:217815_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-FOCUS:217815_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U133A_2:217815_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:233827_S_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U133B:233827_S_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HU35KSUBB:RC_N30795_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
U133_X3P:G6005756_3P_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
U133_X3P:HS.14963.1.S1_3P_A_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U95B:57040_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U95C:60675_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U95E:68143_AT suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U95D:89518_AT Suppressor of Ty 16 homolog (S. cerevisiae) hs
HG-U95D:90470_R_AT Suppressor of Ty 16 homolog (S. cerevisiae) hs
MG-U74CV2:165821_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOE430A:1449578_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOUSE430A_2:1449578_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOUSE430_2:1449578_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOE430A:1419741_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOUSE430A_2:1419741_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MOUSE430_2:1419741_AT suppressor of Ty 16 homolog (S. cerevisiae) mm
MG-U74CV2:168261_AT Suppressor of Ty 16 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3710708) mm
RG-U34B:RC_AA946038_AT suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RG-U34C:AA850372_AT suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAE230A:1398980_AT suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAT230_2:1398980_AT suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAE230A:1375407_AT Suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAT230_2:1375407_AT Suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAE230A:1377281_AT Suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
RAT230_2:1377281_AT Suppressor of Ty 16 homolog (S. cerevisiae) (predicted) rn
YEAST_2:1774676_AT Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure Sc
Protein Similarities
Method ID Description E-Value
blast AAF39835 Hypothetical protein F55A3.3 [Caenorhabditis elegans] ref|NP_492821.1| F55A3.3 [Caenorhabditis elegans] 0.0
blast CAE66834 Hypothetical protein CBG12204 [Caenorhabditis briggsae] 0.0
blast NP_009123 chromatin-specific transcription elongation factor large subunit [Homo sapiens] gb|AAD43978.1| chromatin-specific transcription elongation factor FACT 140 kDa subunit [Homo sapiens] 0.0
Sequence
Target Sequence 
>C. ELEGANS:171809_S_AT
atttggaggaagaagcagcgaatgctgataagagacgtgaagtcgaagaaccttcacgtg
ttcgtgatcgtaagagaccacattcgagcaagtctggaccatcgcacaaacgcagaaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTGGAGGAAGAAGCAGCGAATGC 605 17 39 Antisense
CAGCGAATGCTGATAAGAGACGTGA 709 135 54 Antisense
AGAGACGTGAAGTCGAAGAACCTTC 328 69 69 Antisense
TCGTGATCGTAAGAGACCACATTCG 468 603 100 Antisense
CGTAAGAGACCACATTCGAGCAAGT 545 245 107 Antisense
GACCACATTCGAGCAAGTCTGGACC 671 383 114 Antisense
CACATTCGAGCAAGTCTGGACCATC 304 195 117 Antisense
TCGAGCAAGTCTGGACCATCGCACA 543 601 122 Antisense
AGCAAGTCTGGACCATCGCACAAAC 46 77 125 Antisense
CAAGTCTGGACCATCGCACAAACGC 183 185 127 Antisense
GGACCATCGCACAAACGCAGAAAGT 496 521 134 Antisense
Sequence Source Affymetrix Proprietary Database