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[172850_x_at]

Description Y71F9AL.3 /REP_DB=WormBase Gene ID /WP=CE24613 /TR=Q9N4H3 /GB=AAF36001.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 12      4grp_total > 03      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 427
1 2 3 4 range
A 82.5
(-3)
A 		82.2
(-3)
A 		114.5
(-2.3)
P 		363
(3)
M 		281
B 120.9
(1.9)
A 		95.2
(-2.7)
A 		93.3
(-3)
A 		127.1
(3)
A 		34
C 155
(-2.1)
A 		124.2
(-2.5)
A 		92.4
(-3)
M 		509.5
(3)
P 		417
avr 119.5
(-2.5) 		100.5
(-3) 		100.1
(-3) 		333.2
(3) 		233

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 113
1 2 3 4 5 6 range
A 94.5
(1.4)
A 		125
(3)
A 		71.3
(0.1)
A 		60
(-0.5)
A 		36.5
(-1.7)
A 		12.4
(-3)
A 		113
B 65.1
(-0.5)
M 		112.4
(3)
A 		80.5
(0.6)
A 		45.2
(-2)
A 		39.7
(-2.4)
A 		31.8
(-3)
A 		81
C 83.8
(2.2)
A 		94
(3)
A 		51.7
(-0.2)
A 		30.1
(-1.8)
A 		14.8
(-3)
A 		29.5
(-1.9)
A 		79
avr 81.1
(0.9) 		110.5
(3) 		67.8
(0) 		45.1
(-1.6) 		30.3
(-2.6) 		24.6
(-3) 		86
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 30
(-0.9)
A 		17.8
(-3)
A 		29.9
(-0.9)
P 		53.1
(3)
M 		35
B 38.6
(3)
A 		23.5
(-2.3)
A 		21.6
(-3)
A 		27.1
(-1.1)
A 		17
C 51.3
(-0.9)
A 		35.7
(-2.6)
A 		32.2
(-3)
M 		85.9
(3)
P 		54
avr 40
(-0.1) 		25.7
(-3) 		27.9
(-2.6) 		55.4
(3) 		30

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 17.4
(-0.9)
A 		44.4
(3)
A 		15.5
(-1.2)
A 		15.2
(-1.2)
A 		11
(-1.8)
A 		3
(-3)
A 		41
B 22.6
(-0.5)
M 		37.4
(3)
A 		19.5
(-1.2)
A 		12
(-3)
A 		16.1
(-2)
A 		11.9
(-3)
A 		26
C 31
(3)
A 		28.7
(2.5)
A 		13.2
(-1.1)
A 		6
(-2.7)
A 		4.8
(-3)
A 		9.9
(-1.8)
A 		26
avr 23.7
(0.2) 		36.8
(3) 		16.1
(-1.4) 		11.1
(-2.4) 		10.6
(-2.5) 		8.3
(-3) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172850_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.133
Sequence Type Exemplar sequence
Representative Public ID Y71F9AL.3 NCBI
Target Description Y71F9AL.3 /REP_DB=WormBase Gene ID /WP=CE24613 /TR=Q9N4H3 /GB=AAF36001.1 /SUBMIT=ST.LOUIS /CHR=1 /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_077119(9), NM_064793(11), NM_066128(10), NM_058672(11), NM_059054(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077119 NCBI Caenorhabditis elegans C24A3.7 (C24A3.7) mRNA, complete cds. 9/11 A 
NM_064793 NCBI Caenorhabditis elegans K10F12.5 (K10F12.5) mRNA, complete cds. 11/11 A 
NM_066128 NCBI Caenorhabditis elegans C06E8.4 (C06E8.4) mRNA, complete cds. 10/11 A 
NM_058672 NCBI Caenorhabditis elegans Y71F9AL.3 (Y71F9AL.3) mRNA, complete cds. 11/11 A 
NM_059054 NCBI Caenorhabditis elegans F54D7.1 (F54D7.1) mRNA, complete cds. 10/11 A 
GENEFINDER00000005898 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:2908726:2909997:1 11/11 None
SNAP00000043540 ENSEMBL cdna:SNAP chromosome:CEL140:I:8627388:8630837:1 11/11 None
SNAP00000039702 ENSEMBL cdna:SNAP chromosome:CEL140:I:4814842:4816113:1 10/11 None
GENEFINDER00000039704 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4814842:4816113:1 10/11 None
SNAP00000030989 ENSEMBL cdna:SNAP chromosome:CEL140:III:6998056:7001331:-1 10/11 None
SNAP00000031879 ENSEMBL cdna:SNAP chromosome:CEL140:III:393244:396437:-1 11/11 None
GENEFINDER00000031882 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:393244:398577:-1 11/11 None
SNAP00000006732 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4559813:4562185:-1 11/11 None
GENEFINDER00000006742 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4559813:4562230:-1 11/11 None
SNAP00000028592 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11418784:11421348:-1 9/11 None
GENEFINDER00000028599 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11415538:11421767:-1 9/11 None
SNAP00000043497 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7874370:7875209:-1 9/11 None
GENEFINDER00000043506 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7874370:7875209:-1 9/11 None
GENEFINDER00000009534 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:15395029:15400692:1 11/11 None
SNAP00000009529 ENSEMBL cdna:SNAP chromosome:CEL140:X:15397499:15400692:1 11/11 None
SNAP00000035247 ENSEMBL cdna:SNAP chromosome:CEL140:X:8999615:9000886:-1 9/11 None
GENEFINDER00000035253 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:8999615:9000961:-1 9/11 None
SNAP00000022302 ENSEMBL cdna:SNAP chromosome:CEL140:X:61165:73142:-1 11/11 None
GENEFINDER00000022354 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:61165:72240:-1 9/11 None
Y71F9AL.3 ENSEMBL cdna:known chromosome:CEL140:I:2908726:2909997:1 gene:Y71F9AL.3 11/11 A 
F54D7.1 ENSEMBL cdna:known chromosome:CEL140:I:4814236:4816113:1 gene:F54D7.1 10/11 A 
K10F12.5 ENSEMBL cdna:known chromosome:CEL140:III:393244:395661:-1 gene:K10F12.5 11/11 A 
C06E8.4 ENSEMBL cdna:known chromosome:CEL140:III:6998056:6999717:-1 gene:C06E8.4 10/11 A 
C24A3.7 ENSEMBL cdna:known chromosome:CEL140:X:8999615:9000961:-1 gene:C24A3.7 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_078379 8/11 Cross Hyb Matching Probes A 
NM_071125 5/11 Cross Hyb Matching Probes None
NM_075970 8/11 Cross Hyb Matching Probes A 
NM_078455 8/11 Cross Hyb Matching Probes A 
NM_061681 8/11 Cross Hyb Matching Probes A 
GENEFINDER00000043553 6/11 Cross Hyb Matching Probes None
SNAP00000012049 8/11 Cross Hyb Matching Probes None
GENEFINDER00000012051 8/11 Cross Hyb Matching Probes None
SNAP00000043894 7/11 Cross Hyb Matching Probes None
GENEFINDER00000043904 5/11 Cross Hyb Matching Probes None
SNAP00000008916 1/11 Cross Hyb Matching Probes None
GENEFINDER00000030995 6/11 Cross Hyb Matching Probes None
SNAP00000000198 8/11 Cross Hyb Matching Probes None
GENEFINDER00000000200 6/11 Cross Hyb Matching Probes None
SNAP00000033705 7/11 Cross Hyb Matching Probes None
GENEFINDER00000033772 5/11 Cross Hyb Matching Probes None
SNAP00000037693 5/11 Cross Hyb Matching Probes None
GENEFINDER00000037709 5/11 Cross Hyb Matching Probes None
SNAP00000039289 7/11 Cross Hyb Matching Probes None
GENEFINDER00000039297 7/11 Cross Hyb Matching Probes None
SNAP00000001526 8/11 Cross Hyb Matching Probes None
GENEFINDER00000001539 8/11 Cross Hyb Matching Probes None
SNAP00000003414 4/11 Cross Hyb Matching Probes None
GENEFINDER00000003424 4/11 Cross Hyb Matching Probes None
SNAP00000028144 5/11 Cross Hyb Matching Probes None
GENEFINDER00000028157 5/11 Cross Hyb Matching Probes None
SNAP00000032429 8/11 Cross Hyb Matching Probes None
GENEFINDER00000032435 8/11 Cross Hyb Matching Probes None
SNAP00000012632 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034063 4/11 Cross Hyb Matching Probes None
SNAP00000034055 8/11 Cross Hyb Matching Probes None
SNAP00000007929 8/11 Cross Hyb Matching Probes None
GENEFINDER00000007942 3/11 Cross Hyb Matching Probes None
SNAP00000043287 8/11 Cross Hyb Matching Probes None
GENEFINDER00000043303 8/11 Cross Hyb Matching Probes None
SNAP00000003534 7/11 Cross Hyb Matching Probes None
GENEFINDER00000003544 7/11 Cross Hyb Matching Probes None
SNAP00000022319 3/11 Cross Hyb Matching Probes None
C08F1.9 8/11 Cross Hyb Matching Probes A 
Y53C12A.5 5/11 Cross Hyb Matching Probes None
Y105C5A.7 7/11 Cross Hyb Matching Probes None
Y32G9A.9 5/11 Cross Hyb Matching Probes None
F44G3.3 4/11 Cross Hyb Matching Probes A 
Y102A11A.4 8/11 Cross Hyb Matching Probes A 
B0302.3 8/11 Cross Hyb Matching Probes A 
C33E10.4 7/11 Cross Hyb Matching Probes None
F20B4.7 8/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Ensembl Y71F9AL.3
F54D7.1
K10F12.5
C06E8.4
C24A3.7
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_509520 C24A3.7 [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 AAB71003 Hypothetical protein K10F12.5 [Caenorhabditis elegans] ref|NP_497194.1| K10F12.5 [Caenorhabditis elegans] 0.0
blast AAC72298 reverse transcriptase [Caenorhabditis elegans] 0.0
blast C87861 protein F43G9.7 [imported] - Caenorhabditis elegans 0.0
blast NP_498529 C06E8.4 [Caenorhabditis elegans] 0.0
blast 2206357A Rte-1 element 0.0
blast NP_491073 Y71F9AL.3 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 1.3E-22
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.4E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.7E-52
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.4E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.2E-41
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 7.6E-61
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 6.7E-33
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.7E-61
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 6.7E-33
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.7E-61
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 2.7E-7
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.7E-61
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 2.7E-7
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.3E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.3E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.4E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.4E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.8E-12
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 6.7E-33
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.3E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.3E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.2E-42
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 1.5E-29
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 7.9E-44
Pfam IPR001585 EMBL-EBI Transaldolase 2.6E-9
Pfam IPR001585 EMBL-EBI Transaldolase 8.9E-94
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 1.5E-29
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.2E-40
Pfam IPR001585 EMBL-EBI Transaldolase 1.4E-87
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 3.1E-33
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.6E-61
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.1E-41
Sequence
Target Sequence 
>C. ELEGANS:172850_X_AT
cgacgtcgacgagtacatctacctcggtcgtcaaatcaacgcccaaaacaacttgatgcc
ggaaatccaccgaagacgtcgagcagcctgggctgcattcaatggaatcaagaacaccgc
cgactccatcaccgacaagaagattcgtgcgaatctgttcgactcaattgtccttccagc
gctcacctacggttcagaagcctggacattcaccaaagctttatccgaacgagtacgaat
cacacatgcctccctagaaagacggcttgttgggataacactcacccaacaacgagagcg
agatctccatcgagaagacattcgtacgatgtctctagtcagggatccgctcaatttcgt
gaaaaagaggaagctaggatgggctggacacgttgcgagaaggaaagacggaagatggac
cacgttgatgacagaatggcgcccatatggatggaaaaggcctgttggaaggccgccgat
gcgatggactgattcgctgcgaaaggagatcaccactcgtgacgcagacggaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGACGTCGACGAGTACATCTACCTC 453 251 669 Antisense
CTACCTCGGTCGTCAAATCAACGCC 530 225 687 Antisense
CAGCCTGGGCTGCATTCAATGGAAT 339 203 752 Antisense
ATCTGTTCGACTCAATTGTCCTTCC 185 35 821 Antisense
GCTCACCTACGGTTCAGAAGCCTGG 202 301 849 Antisense
GAACGAGTACGAATCACACATGCCT 572 347 895 Antisense
ATTCGTACGATGTCTCTAGTCAGGG 126 3 988 Antisense
TAGTCAGGGATCCGCTCAATTTCGT 599 653 1004 Antisense
GCTAGGATGGGCTGGACACGTTGCG 443 299 1041 Antisense
GGCCGCCGATGCGATGGACTGATTC 95 543 1139 Antisense
TCACCACTCGTGACGCAGACGGAGA 154 625 1178 Antisense
Sequence Source Affymetrix Proprietary Database