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[172727_x_at]

Description R05F9.4 /REP_DB=WormBase Gene ID /WP=CE04806 /GB=AAA83167.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 20      4grp_total > 02      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 651
1 2 3 4 range
A 15.7
(-2.9)
A 		11.9
(-3)
A 		11.7
(-3)
A 		268
(3)
A 		256
B 9.6
(-2.4)
A 		4.4
(-3)
A 		17
(-1.6)
A 		59.5
(3)
A 		55
C 7.3
(-3)
A 		17
(-2.9)
A 		4.5
(-3)
A 		655.6
(3)
P 		651
avr 10.9
(-3) 		11.1
(-3) 		11.1
(-3) 		327.7
(3) 		317

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 11.5
(-2.2)
A 		21.3
(-0.3)
A 		38.4
(3)
A 		7.5
(-3)
A 		11.6
(-2.2)
A 		10
(-2.5)
A 		31
B 10.4
(3)
A 		8.9
(1.5)
A 		4.3
(-3)
A 		4.5
(-2.8)
A 		8.6
(1.2)
A 		5.7
(-1.6)
A 		6
C 4.1
(-2.7)
A 		40.3
(3)
A 		24.3
(0.5)
A 		15.6
(-0.9)
A 		2.1
(-3)
A 		16.4
(-0.8)
A 		38
avr 8.7
(-2.5) 		23.5
(3) 		22.3
(2.6) 		9.2
(-2.3) 		7.4
(-3) 		10.7
(-1.8) 		16
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 5.7
(-2.5)
A 		2.6
(-3)
A 		3.1
(-2.9)
A 		39.2
(3)
A 		37
B 3.1
(-2)
A 		1.1
(-3)
A 		3.9
(-1.6)
A 		12.7
(3)
A 		12
C 2.4
(-3)
A 		4.9
(-2.8)
A 		1.6
(-3)
A 		110.5
(3)
P 		109
avr 3.7
(-2.9) 		2.9
(-3) 		2.9
(-3) 		54.1
(3) 		51

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12
1 2 3 4 5 6 range
A 2.1
(-2.8)
A 		7.6
(2.3)
A 		8.4
(3)
A 		1.9
(-3)
A 		3.5
(-1.5)
A 		2.4
(-2.5)
A 		7
B 3.6
(3)
A 		3
(1.6)
A 		1
(-3)
A 		1.2
(-2.5)
A 		3.5
(2.8)
A 		2.1
(-0.5)
A 		3
C 1.5
(-2.6)
A 		12.3
(3)
A 		6.2
(-0.2)
A 		3.1
(-1.8)
A 		0.7
(-3)
A 		5.5
(-0.5)
A 		12
avr 2.4
(-2.7) 		7.6
(3) 		5.2
(0.4) 		2.1
(-3) 		2.6
(-2.5) 		3.3
(-1.7) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172727_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5527
Sequence Type Exemplar sequence
Representative Public ID R05F9.4 NCBI
Target Description R05F9.4 /REP_DB=WormBase Gene ID /WP=CE04806 /GB=AAA83167.1 /SUBMIT=ST.LOUIS /CHR=2 /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_058536(9), NM_062489(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058536 NCBI Caenorhabditis elegans Y37E3.18 (Y37E3.18) mRNA, complete cds. 9/11 A 
NM_062489 NCBI Caenorhabditis elegans R05F9.4 (R05F9.4) mRNA, complete cds. 11/11 A 
Y37E3.18 ENSEMBL cdna:known chromosome:CEL140:I:2130472:2131902:-1 gene:Y37E3.18 9/11 A 
R05F9.4 ENSEMBL cdna:known chromosome:CEL140:II:4896914:4898344:1 gene:R05F9.4 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_063332 1/11 Cross Hyb Matching Probes A 
NM_075927 4/11 Cross Hyb Matching Probes A 
NM_072761 5/11 Cross Hyb Matching Probes None
NM_058704 2/11 Cross Hyb Matching Probes A 
NM_067826 7/11 Cross Hyb Matching Probes A 
NM_062865 7/11 Cross Hyb Matching Probes A 
NM_069210 4/11 Cross Hyb Matching Probes A 
NM_072760 5/11 Cross Hyb Matching Probes None
SNAP00000001197 8/11 Cross Hyb Matching Probes None
GENEFINDER00000035332 2/11 Cross Hyb Matching Probes None
SNAP00000032522 7/11 Cross Hyb Matching Probes None
SNAP00000018816 6/11 Cross Hyb Matching Probes None
GENEFINDER00000018837 7/11 Cross Hyb Matching Probes None
K09H9.4 2/11 Cross Hyb Matching Probes A 
C29F5.6 7/11 Cross Hyb Matching Probes A 
M110.6 1/11 Cross Hyb Matching Probes A 
Y69A2AR.10 7/11 Cross Hyb Matching Probes A 
Y11D7A.6 4/11 Cross Hyb Matching Probes A 
F38E1.2 5/11 Cross Hyb Matching Probes A 
F38E1.1 3/11 Cross Hyb Matching Probes None
F52E1.12 5/11 Cross Hyb Matching Probes A 
Y60A3A.11 1/11 Cross Hyb Matching Probes A 
Y113G7A.2 7/11 Cross Hyb Matching Probes A 
F31A9.6 4/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4896911-4898342(+) 100.0 100.0
chrIV:2589795-2591226(+) 98.18 98.18
chrV:20040978-20042405(+) 98.11 98.11
chrV:8384122-8385541(+) 97.62 97.62
chrI:2130471-2131902(-) 99.23 99.23
chrII:6301810-6302725(-) 62.82 62.82
chrX:1789006-1790339(-) 90.15 90.15
Public Domain and Genome References
Ensembl Y37E3.18
R05F9.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_490937 Y37E3.18 [Caenorhabditis elegans] gb|AAK27868.1| Hypothetical protein Y37E3.18 [Caenorhabditis elegans] 0.0
blast NP_494890 R05F9.4 [Caenorhabditis elegans] gb|AAA83167.1| Hypothetical protein R05F9.4 [Caenorhabditis elegans] 0.0
blast NP_500227 Y69A2AR.10 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.2E-55
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.8E-55
Sequence
Target Sequence 
>C. ELEGANS:172727_X_AT
taccacctagacggttaccctattgagcgaaaagctattacccgagaccttggattttta
atctctgaaaagctggatttctctgagcattggaggaaatgtatcaatctagctaaattt
caactggccaacatgttcaaccagtacagtacctccaataagaaactaatgattctctta
ttcaaaactttcatccgccctcgtttagaatatggaacagtagtgtcttctccgacaaaa
aaatcggatgagaaagcaatagagtctgtacaaaacgcattcactaggcgcctttatagt
agaatcaaaaaaagatatattaatccaactgataaagattacaaaactgccatggaacgt
aacgaactattcgacttccaaaccttaagcacgagacgtaaaataattgacagaatccaa
ataatcagaatgaatactggtaaagtagacttaaaaacatctgagttttttgagcaacaa
gagacccacactcgttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACCACCTAGACGGTTACCCTATTG 360 585 856 Antisense
AGCTATTACCCGAGACCTTGGATTT 616 61 888 Antisense
AAGCTGGATTTCTCTGAGCATTGGA 91 151 925 Antisense
TTTCAACTGGCCAACATGTTCAACC 588 671 973 Antisense
CATGTTCAACCAGTACAGTACCTCC 65 211 987 Antisense
TCTTATTCAAAACTTTCATCCGCCC 57 615 1031 Antisense
TCATCCGCCCTCGTTTAGAATATGG 608 621 1046 Antisense
ATGGAACAGTAGTGTCTTCTCCGAC 561 51 1067 Antisense
AAACGCATTCACTAGGCGCCTTTAT 318 127 1128 Antisense
ATTCGACTTCCAAACCTTAAGCACG 223 9 1224 Antisense
AGCAACAAGAGACCCACACTCGTTC 608 75 1328 Antisense
Sequence Source Affymetrix Proprietary Database