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[172646_x_at]

Description F52C9.6 /REP_DB=WormBase Gene ID /WP=CE01964 /TR=SW:Q10126 /GB=AAA81063.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 12      4grp_total > 19      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 348
1 2 3 4 range
A 89.9
(-2.6)
A 		128.6
(-1.8)
A 		70.5
(-3)
A 		358.5
(3)
A 		288
B 168.1
(-0.5)
A 		287.3
(3)
A 		113.3
(-2.1)
A 		83.2
(-3)
A 		204
C 150.3
(-1.6)
A 		115.7
(-2.2)
A 		69.6
(-3)
A 		418
(3)
M 		348
avr 136.1
(-1.5) 		177.2
(-0.2) 		84.5
(-3) 		286.6
(3) 		202

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 124
1 2 3 4 5 6 range
A 63.6
(0.2)
A 		95
(2.3)
A 		105
(3)
A 		78
(1.2)
A 		27.4
(-2.3)
A 		16.8
(-3)
A 		88
B 117.4
(3)
A 		99.3
(1.8)
A 		45.7
(-1.9)
A 		28.7
(-3)
A 		44.9
(-1.9)
A 		40.9
(-2.2)
A 		89
C 77.7
(-0.8)
A 		140.5
(3)
A 		64
(-1.6)
A 		54.5
(-2.2)
A 		60.6
(-1.8)
A 		40.6
(-3)
A 		100
avr 86.2
(1.1) 		111.6
(3) 		71.6
(-0) 		53.7
(-1.4) 		44.3
(-2.1) 		32.8
(-3) 		79
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 32.7
(-0.5)
A 		27.9
(-1.3)
A 		18.4
(-3)
A 		52.5
(3)
A 		34
B 53.6
(1)
A 		71
(3)
A 		26.2
(-2)
A 		17.7
(-3)
A 		53
C 49.7
(0.3)
A 		33.3
(-1.8)
A 		24.3
(-3)
A 		70.5
(3)
M 		46
avr 45.3
(2.6) 		44.1
(2.3) 		23
(-3) 		46.9
(3) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 11.7
(-1.5)
A 		33.8
(3)
A 		22.9
(0.8)
A 		19.8
(0.2)
A 		8.3
(-2.2)
A 		4.1
(-3)
A 		30
B 40.9
(3)
A 		33.1
(1.6)
A 		11.1
(-2.4)
A 		7.6
(-3)
A 		18.3
(-1.1)
A 		15.3
(-1.6)
A 		33
C 28.8
(0.3)
A 		42.9
(3)
A 		16.3
(-2)
A 		11
(-3)
A 		19.6
(-1.4)
A 		13.6
(-2.5)
A 		32
avr 27.1
(0.8) 		36.6
(3) 		16.8
(-1.6) 		12.8
(-2.6) 		15.4
(-2) 		11
(-3) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172646_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7043
Sequence Type Exemplar sequence
Representative Public ID F52C9.6 NCBI
Target Description F52C9.6 /REP_DB=WormBase Gene ID /WP=CE01964 /TR=SW:Q10126 /GB=AAA81063.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=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_065740(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065740 NCBI Caenorhabditis elegans F52C9.6 (F52C9.6) mRNA, complete cds. 11/11 None
GENEFINDER00000014760 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5336513:5338391:-1 9/11 None
SNAP00000014756 ENSEMBL cdna:SNAP chromosome:CEL140:III:5337165:5338257:-1 11/11 None
F52C9.6 ENSEMBL cdna:known chromosome:CEL140:III:5337165:5338004:-1 gene:F52C9.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_078379 2/11 Cross Hyb Matching Probes A 
NM_077119 1/11 Cross Hyb Matching Probes A 
NM_064793 3/11 Cross Hyb Matching Probes A 
NM_066128 3/11 Cross Hyb Matching Probes A 
NM_075970 3/11 Cross Hyb Matching Probes A 
NM_078455 2/11 Cross Hyb Matching Probes A 
NM_058672 2/11 Cross Hyb Matching Probes A 
NM_061681 3/11 Cross Hyb Matching Probes A 
NM_059054 3/11 Cross Hyb Matching Probes A 
GENEFINDER00000005898 2/11 Cross Hyb Matching Probes None
GENEFINDER00000043553 1/11 Cross Hyb Matching Probes None
SNAP00000043540 3/11 Cross Hyb Matching Probes None
SNAP00000039702 3/11 Cross Hyb Matching Probes None
GENEFINDER00000039704 3/11 Cross Hyb Matching Probes None
SNAP00000012049 3/11 Cross Hyb Matching Probes None
GENEFINDER00000012051 3/11 Cross Hyb Matching Probes None
SNAP00000043894 2/11 Cross Hyb Matching Probes None
GENEFINDER00000043904 1/11 Cross Hyb Matching Probes None
SNAP00000030989 3/11 Cross Hyb Matching Probes None
GENEFINDER00000030995 1/11 Cross Hyb Matching Probes None
SNAP00000031879 3/11 Cross Hyb Matching Probes None
GENEFINDER00000031882 3/11 Cross Hyb Matching Probes None
SNAP00000000198 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000200 1/11 Cross Hyb Matching Probes None
SNAP00000006732 3/11 Cross Hyb Matching Probes None
GENEFINDER00000006742 3/11 Cross Hyb Matching Probes None
SNAP00000028592 2/11 Cross Hyb Matching Probes None
GENEFINDER00000028599 2/11 Cross Hyb Matching Probes None
SNAP00000033705 1/11 Cross Hyb Matching Probes None
GENEFINDER00000033772 1/11 Cross Hyb Matching Probes None
SNAP00000039289 5/11 Cross Hyb Matching Probes None
GENEFINDER00000039297 5/11 Cross Hyb Matching Probes None
SNAP00000043497 2/11 Cross Hyb Matching Probes None
GENEFINDER00000043506 2/11 Cross Hyb Matching Probes None
SNAP00000001526 2/11 Cross Hyb Matching Probes None
GENEFINDER00000001539 2/11 Cross Hyb Matching Probes None
SNAP00000003414 2/11 Cross Hyb Matching Probes None
GENEFINDER00000003424 2/11 Cross Hyb Matching Probes None
SNAP00000032429 3/11 Cross Hyb Matching Probes None
GENEFINDER00000032435 3/11 Cross Hyb Matching Probes None
SNAP00000012632 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034063 1/11 Cross Hyb Matching Probes None
SNAP00000034055 2/11 Cross Hyb Matching Probes None
SNAP00000007929 2/11 Cross Hyb Matching Probes None
GENEFINDER00000007942 1/11 Cross Hyb Matching Probes None
GENEFINDER00000009534 2/11 Cross Hyb Matching Probes None
SNAP00000009529 2/11 Cross Hyb Matching Probes None
SNAP00000043287 3/11 Cross Hyb Matching Probes None
GENEFINDER00000043303 3/11 Cross Hyb Matching Probes None
SNAP00000003534 3/11 Cross Hyb Matching Probes None
GENEFINDER00000003544 3/11 Cross Hyb Matching Probes None
SNAP00000035247 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035253 1/11 Cross Hyb Matching Probes None
SNAP00000022302 3/11 Cross Hyb Matching Probes None
GENEFINDER00000022354 2/11 Cross Hyb Matching Probes None
Y71F9AL.3 2/11 Cross Hyb Matching Probes A 
F54D7.1 3/11 Cross Hyb Matching Probes A 
C08F1.9 3/11 Cross Hyb Matching Probes A 
Y53C12A.5 1/11 Cross Hyb Matching Probes None
K10F12.5 3/11 Cross Hyb Matching Probes A 
C06E8.4 3/11 Cross Hyb Matching Probes A 
Y105C5A.7 1/11 Cross Hyb Matching Probes None
F44G3.3 2/11 Cross Hyb Matching Probes A 
Y102A11A.4 3/11 Cross Hyb Matching Probes A 
C24A3.7 1/11 Cross Hyb Matching Probes A 
B0302.3 2/11 Cross Hyb Matching Probes A 
C33E10.4 3/11 Cross Hyb Matching Probes None
F20B4.7 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Ensembl F52C9.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_494082 C08F1.9 [Caenorhabditis elegans] 0.0
blast H88671 protein F28E10.3 [imported] - Caenorhabditis elegans 0.0
blast T24639 hypothetical protein T07C12.2 - Caenorhabditis elegans 0.0
blast T24639 hypothetical protein T07C12.2 - Caenorhabditis elegans 1.0E-172
blast H88671 protein F28E10.3 [imported] - Caenorhabditis elegans 1.0E-172
blast NP_494082 C08F1.9 [Caenorhabditis elegans] 1.0E-172
blast NP_498141 F52C9.6 [Caenorhabditis elegans] sp|Q10126|YSM6_CAEEL Hypothetical protein F52C9.6 in chromosome III 1.0E-161
blast T22200 hypothetical protein F44G3.3 - Caenorhabditis elegans 1.0E-153
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.2E-14
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.3E-29
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.3E-29
Sequence
Target Sequence 
>C. ELEGANS:172646_X_AT
tacccagctcgatgacgtcgacgaatacatctacctcggccgtcaaatcaacgctcacaa
caacctgatgccggaaattcaccgaagacgtcgagcagcatgggcagcgttcaatggaag
caagaacaccaccgactccatcaccgacaagaagattcgtgtgaatctatttgattcaat
cgtccttcccgctctcacctacggttcagaagcctggacattcaacaaagctctatccga
acgagtaagaatcacacatgcctctctagaaagacggcttgtgggaatcacactcactca
acaacgagaacgagatctccatcgagaagacatccgagtgatgtctcaagtaagagatcc
gctcaacttcgtgaaaaagaggaagctaggatgggctggacatgttgcgagaagaaaaga
cggaagatggaccacgctgatgacagaatggcgcccctggaactggaaaaggtatgttgg
aaggacgccgatgcgatggactgattcgctgcgaaaggagatcaccactcgagacgcaga
cggagaagtcatcaccccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACCCAGCTCGATGACGTCGACGAA 346 649 225 Antisense
GTCGACGAATACATCTACCTCGGCC 97 475 241 Antisense
GAAGACGTCGAGCAGCATGGGCAGC 585 339 308 Antisense
CTATTTGATTCAATCGTCCTTCCCG 680 223 391 Antisense
CTCACCTACGGTTCAGAAGCCTGGA 280 229 418 Antisense
GTAAGAATCACACATGCCTCTCTAG 59 463 469 Antisense
GTGGGAATCACACTCACTCAACAAC 196 489 505 Antisense
GTAAGAGATCCGCTCAACTTCGTGA 437 461 574 Antisense
GAAGATGGACCACGCTGATGACAGA 143 339 647 Antisense
GTATGTTGGAAGGACGCCGATGCGA 694 455 696 Antisense
CGCAGACGGAGAAGTCATCACCCCC 565 253 759 Antisense
Sequence Source Affymetrix Proprietary Database