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[172897_x_at]

Description F38E1.2 /REP_DB=WormBase Gene ID /WP=CE04521 /TR=Q20162 /GB=AAA83479.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=transposon reverse transcriptase
Cluster 6grp_total > 73      4grp_total > 02      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 20
(-1.7)
A 		5.7
(-3)
A 		12
(-2.4)
A 		74.2
(3)
A 		69
B 25.4
(-0.9)
A 		18.8
(-3)
A 		37.7
(3)
A 		21.8
(-2)
A 		19
C 17
(-3)
A 		40.5
(-1.6)
A 		27.1
(-2.4)
A 		120.4
(3)
P 		103
avr 20.8
(-3) 		21.7
(-2.9) 		25.6
(-2.4) 		72.1
(3) 		51

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 40
1 2 3 4 5 6 range
A 4.5
(-2.6)
A 		5.5
(-2.4)
A 		2.4
(-3)
A 		4.4
(-2.6)
A 		31.7
(3)
A 		8.2
(-1.8)
A 		29
B 20.9
(-2.3)
A 		42.3
(3)
A 		38.1
(2)
A 		37.3
(1.8)
A 		21.4
(-2.2)
A 		18
(-3)
A 		24
C 3.5
(-2.6)
A 		11.6
(-0.4)
A 		22.6
(2.6)
A 		16
(0.8)
A 		2.2
(-3)
A 		24.1
(3)
A 		22
avr 9.6
(-3) 		19.8
(2.4) 		21
(3) 		19.2
(2.1) 		18.4
(1.6) 		16.8
(0.8) 		11
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 7.3
(0.8)
A 		1.2
(-3)
A 		3.1
(-1.8)
A 		10.9
(3)
A 		10
B 8.1
(2.1)
A 		4.6
(-3)
A 		8.7
(3)
A 		4.6
(-3)
A 		4
C 5.6
(-3)
A 		11.6
(-0.6)
A 		9.5
(-1.4)
A 		20.3
(3)
P 		15
avr 7
(-1.8) 		5.8
(-3) 		7.1
(-1.7) 		11.9
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 0.8
(-2.8)
A 		1.9
(-2.1)
A 		0.5
(-3)
A 		1.1
(-2.6)
A 		9.6
(3)
A 		2
(-2)
A 		9
B 7.3
(-2.5)
A 		14.1
(3)
A 		9.3
(-0.9)
A 		9.9
(-0.4)
A 		8.7
(-1.4)
A 		6.7
(-3)
A 		7
C 1.3
(-2.5)
A 		3.5
(-0.7)
A 		5.7
(1.1)
A 		3.2
(-1)
A 		0.7
(-3)
A 		8.1
(3)
A 		7
avr 3.1
(-3) 		6.5
(3) 		5.2
(0.7) 		4.7
(-0.2) 		6.3
(2.6) 		5.6
(1.4) 		3
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172897_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12399
Sequence Type Exemplar sequence
Representative Public ID F38E1.2 NCBI
Target Description F38E1.2 /REP_DB=WormBase Gene ID /WP=CE04521 /TR=Q20162 /GB=AAA83479.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=transposon 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_072760(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072760 NCBI Caenorhabditis elegans F38E1.2 (F38E1.2) mRNA, complete cds. 11/11 None
F38E1.2 ENSEMBL cdna:known chromosome:CEL140:V:8383372:8385513:1 gene:F38E1.2 11/11 A 
Y113G7A.2 ENSEMBL cdna:pseudogene chromosome:CEL140:V:20039690:20042402:1 gene:Y113G7A.2 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_058536 4/11 Cross Hyb Matching Probes A 
NM_062489 5/11 Cross Hyb Matching Probes A 
NM_067826 6/11 Cross Hyb Matching Probes A 
SNAP00000001197 4/11 Cross Hyb Matching Probes None
SNAP00000018816 5/11 Cross Hyb Matching Probes None
GENEFINDER00000018837 6/11 Cross Hyb Matching Probes None
Y37E3.18 4/11 Cross Hyb Matching Probes A 
R05F9.4 5/11 Cross Hyb Matching Probes A 
Y69A2AR.10 6/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4896162-4897195(+) 98.64 98.64
chrIV:2589045-2590079(+) 98.15 98.15
chrV:8383372-8384401(+) 100.0 100.0
chrV:20040226-20041262(+) 98.83 98.83
chrI:2131618-2132653(-) 98.74 98.74
Public Domain and Genome References
Ensembl F38E1.2
Y113G7A.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_505161 F38E1.2 [Caenorhabditis elegans] 0.0
blast NP_500227 Y69A2AR.10 [Caenorhabditis elegans] 1.0E-147
blast NP_490937 Y37E3.18 [Caenorhabditis elegans] gb|AAK27868.1| Hypothetical protein Y37E3.18 [Caenorhabditis elegans] 5.0E-38
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 5.2E-6
Sequence
Target Sequence 
>C. ELEGANS:172897_X_AT
gaaaccgcgaaactgtagtgttccaaccctgatagataatgacgaaaatgaaattgtctc
tgaactagacaaagcaaatcttctagcatcctactttgaggctcagtatacaaatcaaaa
taacaagaattttgctctagctgatgattttgtatcagatcaaccaattccctgggttac
tgatgcagaagttctaaaagtgatcatggcctcgaaaaagtcttgctctgtaacaagcga
ccaggtcccatttacgtttataaaaatactatcgcctctcatcagtagcattctggccca
gattttcaacttgagcatgatgagagggcaagtcccgcacgcttggaccgaatccattgt
aatacctcttggaaaaatcactaacgctaacaatccaaccgacttcagaccaattagctt
gacctcgcacttgtgcagagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAACCGCGAAACTGTAGTGTTCCA 663 357 558 Antisense
TAGTGTTCCAACCCTGATAGATAAT 650 653 573 Antisense
AAAGCAAATCTTCTAGCATCCTACT 9 125 628 Antisense
CATGGCCTCGAAAAAGTCTTGCTCT 365 209 762 Antisense
CAAGCGACCAGGTCCCATTTACGTT 430 181 791 Antisense
TAAAAATACTATCGCCTCTCATCAG 194 641 818 Antisense
CTCTCATCAGTAGCATTCTGGCCCA 378 231 833 Antisense
TCTGGCCCAGATTTTCAACTTGAGC 360 607 849 Antisense
GACCGAATCCATTGTAATACCTCTT 139 383 903 Antisense
GCTAACAATCCAACCGACTTCAGAC 454 301 943 Antisense
GCTTGACCTCGCACTTGTGCAGAGT 454 307 974 Antisense
Sequence Source Affymetrix Proprietary Database