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[190406_s_at]

Description R11E3.3 /REP_DB=WormBase Gene ID /WP=CE19545 /TR=Q9TYX8 /GB=AAK39265.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 39      4grp_total > 04      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 228
1 2 3 4 range
A 75.5
(-0.7)
A 		13.6
(-3)
A 		44.4
(-1.9)
A 		178.3
(3)
P 		165
B 60.2
(-0.8)
A 		39.3
(-3)
A 		54.8
(-1.4)
A 		95.9
(3)
A 		57
C 87.5
(-1.4)
A 		36.1
(-2.9)
A 		30.9
(-3)
A 		241.9
(3)
P 		211
avr 74.4
(-1.1) 		29.7
(-3) 		43.4
(-2.4) 		172
(3) 		142

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 65
1 2 3 4 5 6 range
A 24
(-3)
A 		61.2
(1.9)
A 		34.8
(-1.6)
A 		40.4
(-0.8)
A 		37.6
(-1.2)
A 		69.4
(3)
A 		45
B 44.7
(3)
A 		25.8
(-0.1)
A 		11.6
(-2.5)
A 		8.5
(-3)
A 		37.4
(1.8)
A 		34.8
(1.4)
A 		36
C 45.2
(1.3)
A 		61.2
(3)
A 		7.5
(-2.6)
A 		4
(-3)
A 		37.9
(0.6)
A 		15.3
(-1.8)
A 		57
avr 38
(0.8) 		49.4
(3) 		18
(-2.9) 		17.6
(-3) 		37.6
(0.8) 		39.8
(1.2) 		32
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38
1 2 3 4 range
A 27.5
(3)
A 		3
(-3)
A 		11.6
(-0.9)
A 		26.1
(2.7)
P 		25
B 19.2
(2.3)
A 		9.7
(-3)
A 		12.7
(-1.3)
A 		20.4
(3)
A 		11
C 29
(0.7)
A 		10.4
(-3)
A 		10.8
(-2.9)
A 		40.8
(3)
P 		30
avr 25.2
(1.9) 		7.7
(-3) 		11.7
(-1.9) 		29.1
(3) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 21
1 2 3 4 5 6 range
A 4.4
(-3)
A 		21.8
(3)
A 		7.6
(-1.9)
A 		10.2
(-1)
A 		11.4
(-0.6)
A 		16.9
(1.3)
A 		17
B 15.5
(3)
A 		8.6
(-0.1)
A 		2.8
(-2.8)
A 		2.3
(-3)
A 		15.2
(2.9)
A 		13
(1.9)
A 		13
C 16.8
(2.4)
A 		18.7
(3)
A 		1.9
(-2.6)
A 		0.8
(-3)
A 		12.3
(0.9)
A 		5.1
(-1.6)
A 		18
avr 12.2
(1) 		16.4
(3) 		4.1
(-3) 		4.4
(-2.9) 		13
(1.3) 		11.7
(0.7) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190406_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11015
Sequence Type Exemplar sequence
Representative Public ID R11E3.3 NCBI
Target Description R11E3.3 /REP_DB=WormBase Gene ID /WP=CE19545 /TR=Q9TYX8 /GB=AAK39265.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=reverse transcriptase
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_068239(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068239 NCBI Caenorhabditis elegans R11E3.3 (R11E3.3) mRNA, complete cds. 11/11 None
SNAP00000002045 ENSEMBL cdna:SNAP chromosome:CEL140:II:13645677:13648746:1 11/11 None
GENEFINDER00000002055 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13645677:13654779:1 11/11 None
SNAP00000009822 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4768670:4771465:1 11/11 None
GENEFINDER00000009843 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4768670:4771465:1 11/11 None
R11E3.3 ENSEMBL cdna:known chromosome:CEL140:IV:4768670:4771465:1 gene:R11E3.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000007446 8/11 Cross Hyb Matching Probes None
GENEFINDER00000007449 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:13646305-13647990(+) 58.91 58.91
chrIV:4768675-4771471(+) 100.0 100.0
Public Domain and Genome References
Ensembl R11E3.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK39265 Hypothetical protein R11E3.3 [Caenorhabditis elegans] ref|NP_500640.1| R11E3.3 [Caenorhabditis elegans] 0.0
blast T19605 hypothetical protein C31C9.5 - Caenorhabditis elegans 0.0
blast CAB05696 Hypothetical protein C31C9.4 [Caenorhabditis elegans] ref|NP_496870.2| C31C9.4 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.0E-60
Pfam IPR002900 EMBL-EBI Protein of unknown function DUF38 3.3E-32
Pfam IPR001810 EMBL-EBI Cyclin-like F-box 1.5E-8
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.5E-53
Pfam IPR002900 EMBL-EBI Protein of unknown function DUF38 3.3E-32
Pfam IPR002900 EMBL-EBI Protein of unknown function DUF38 3.8E-9
Pfam IPR001810 EMBL-EBI Cyclin-like F-box 5.3E-8
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 5.6E-63
Sequence
Target Sequence 
>C. ELEGANS:190406_S_AT
acggaccacatctaccaagagtgcagagttctccctttgaaagaagaatataagctggcg
acgcaacagatgtacttggcagcgatcaagtcgaacacgcacccgtgcagagacctgaaa
gcaaagggccaactggaacgaacctcaaaaccgccaaggatcccgccgctgaagctatcg
gactctgaaaagctcagactcgacaacatcccaggcgacaagacggagacccaaaagaag
aatcacacgaagctggtagcggacttcatcaggaatgcgccaaacaacagaatcctcaac
aaacctccaccaagagtgaattacagggacgaaaggacgctgccaaaggagactcgatgt
gaactggcacggctaagatgcggtcactcactcctcgtcgagaagtacaaagcccggctg
gaagaaaggcaaataaagaaatgtttgaattgtggagatgaagaaggagatgtgcaacac
ctactaagttgcctccaaactccagtccccctagaggaactctggacttctccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGGACCACATCTACCAAGAGTGCA 29 97 2209 Antisense
AAGAGTGCAGAGTTCTCCCTTTGAA 71 155 2225 Antisense
CGCACCCGTGCAGAGACCTGAAAGC 431 253 2306 Antisense
CGCCGCTGAAGCTATCGGACTCTGA 98 257 2372 Antisense
TGAAAAGCTCAGACTCGACAACATC 532 573 2394 Antisense
CGACAACATCCCAGGCGACAAGACG 613 251 2409 Antisense
GCGGACTTCATCAGGAATGCGCCAA 699 291 2467 Antisense
AGGACGCTGCCAAAGGAGACTCGAT 112 53 2542 Antisense
CACGGCTAAGATGCGGTCACTCACT 318 199 2576 Antisense
TACTAAGTTGCCTCCAAACTCCAGT 584 645 2690 Antisense
CTAGAGGAACTCTGGACTTCTCCAC 563 225 2719 Antisense
Sequence Source Affymetrix Proprietary Database