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[172314_x_at]

Description F54D8.5 /REP_DB=WormBase Gene ID /WP=CE01311 /TR=Q20782 /GB=AAA20617.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 52      4grp_total > 02      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 235
1 2 3 4 range
A 3.9
(-2.9)
A 		33.8
(-1.8)
A 		2.2
(-3)
A 		154
(3)
P 		152
B 19
(-1.4)
A 		2.8
(-2.9)
A 		1.6
(-3)
A 		65.2
(3)
A 		64
C 7
(-2.9)
A 		2.6
(-3)
A 		2.2
(-3)
A 		236.3
(3)
P 		234
avr 10
(-2.7) 		13.1
(-2.6) 		2
(-3) 		151.8
(3) 		150

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 29.1
(-1.4)
A 		2.3
(-3)
A 		105.9
(3)
M 		10
(-2.6)
A 		7.7
(-2.7)
A 		6.6
(-2.8)
A 		104
B 10
(-1.9)
A 		27.3
(0.9)
A 		18.7
(-0.5)
A 		40.2
(3)
A 		4.7
(-2.8)
A 		3.4
(-3)
A 		37
C 1.3
(-3)
A 		44.9
(3)
A 		10.9
(-1.7)
A 		3.6
(-2.7)
A 		1.3
(-3)
A 		10.9
(-1.7)
A 		44
avr 13.5
(-1.7) 		24.8
(-0) 		45.2
(3) 		17.9
(-1) 		4.6
(-3) 		7
(-2.6) 		41
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 39
1 2 3 4 range
A 1.4
(-2.8)
A 		7.3
(-1.2)
A 		0.6
(-3)
A 		22.5
(3)
P 		22
B 6.1
(-0.5)
A 		0.7
(-2.9)
A 		0.4
(-3)
A 		13.9
(3)
A 		14
C 2.3
(-2.8)
A 		0.8
(-3)
A 		0.8
(-3)
A 		39.8
(3)
P 		39
avr 3.3
(-2.3) 		2.9
(-2.4) 		0.6
(-3) 		25.4
(3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 23
1 2 3 4 5 6 range
A 5.4
(-1.8)
A 		0.8
(-3)
A 		23.1
(3)
M 		2.5
(-2.5)
A 		2.3
(-2.6)
A 		1.6
(-2.8)
A 		22
B 3.5
(-1.6)
A 		9.1
(2)
A 		4.5
(-0.9)
A 		10.6
(3)
A 		1.9
(-2.6)
A 		1.3
(-3)
A 		9
C 0.5
(-3)
A 		13.7
(3)
A 		2.8
(-1.9)
A 		0.7
(-2.9)
A 		0.4
(-3)
A 		3.6
(-1.6)
A 		13
avr 3.1
(-1.9) 		7.9
(1.5) 		10.1
(3) 		4.6
(-0.8) 		1.5
(-3) 		2.2
(-2.5) 		9
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172314_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7963
Sequence Type Exemplar sequence
Representative Public ID F54D8.5 NCBI
Target Description F54D8.5 /REP_DB=WormBase Gene ID /WP=CE01311 /TR=Q20782 /GB=AAA20617.1 /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_065683(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065683 NCBI Caenorhabditis elegans F54D8.5 (F54D8.5) mRNA, complete cds. 11/11 None
F54D8.5 ENSEMBL cdna:known chromosome:CEL140:III:5090934:5091563:-1 gene:F54D8.5 11/11 None
B0513.8 ENSEMBL cdna:pseudogene chromosome:CEL140:IV:13857429:13858365:-1 gene:B0513.8 10/11 A 
R13D7.5 ENSEMBL cdna:pseudogene chromosome:CEL140:V:7394977:7395565:1 gene:R13D7.5 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_074340 8/11 Cross Hyb Matching Probes A 
NM_068042 4/11 Cross Hyb Matching Probes A 
SNAP00000001611 1/11 Cross Hyb Matching Probes None
GENEFINDER00000001626 2/11 Cross Hyb Matching Probes None
GENEFINDER00000030685 1/11 Cross Hyb Matching Probes None
Y45F3A.6 8/11 Cross Hyb Matching Probes None
Y75B8A.41 5/11 Cross Hyb Matching Probes None
Y46C8AL.6 4/11 Cross Hyb Matching Probes A 
F47D2.2 6/11 Cross Hyb Matching Probes A 
T09F5.7 8/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:15159605-15160171(+) 97.3 97.3
chrV:9763615-9764188(+) 98.2 98.2
chrV:7394984-7395538(+) 94.77 94.77
chrIII:10586894-10587470(+) 98.92 98.92
chrIV:17438873-17439449(+) 98.56 98.56
chrIV:3950423-3950999(+) 96.58 96.58
chrV:9496213-9496789(-) 98.92 98.92
chrIII:5091007-5091562(-) 100.0 100.0
chrIII:12315861-12316903(-) 97.3 97.3
chrIV:13857549-13858124(-) 98.74 98.74
Public Domain and Genome References
Gene Title
Ensembl F54D8.5
B0513.8
R13D7.5
Entrez Gene 186232 Entrez gene
SwissProt Q20782 EMBL-EBI
WormBase CE01311 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6278 RNA-dependent DNA replication inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3964 RNA-directed DNA polymerase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA20617 Hypothetical protein F54D8.5 [Caenorhabditis elegans] ref|NP_498084.1| F54D8.5 [Caenorhabditis elegans] 1.0E-102
blast CAB05805 Hypothetical protein T09F5.7 [Caenorhabditis elegans] ref|NP_506741.1| T09F5.7 [Caenorhabditis elegans] 6.0E-82
blast AAF60603 Hypothetical protein Y46C8AL.6 [Caenorhabditis elegans] ref|NP_500443.2| Y46C8AL.6 [Caenorhabditis elegans] 3.0E-69
Sequence
Target Sequence 
>C. ELEGANS:172314_X_AT
cacaaggctccatacattactttacaaaacctttgtgagacccatacttgaatatggtac
cgaagtaagtagtccgttgaaaaaacaagatattaaagcaattgaatccgtacaaaactc
gttcactaggaaactatacagcaggcaaaagggaaaatacatcagaacagatgaccccga
ctataagagcgctattcaacgtaatgaactatttaacttatcaactttagaggctcggcg
taaagctattgataaagttttcttgtcgaaaatgctagtgaacaaagttgatattgacac
tgaccaatttttcaaaatagataaaaatagtaaaactcgtaccaaaaccaagttcatctg
ggggaaatgcaaaaccaaactacgaaggcactttttcacaaatagagtattaagttctat
aaaaattagcgcaatgaatcttattttggcacctcatgtcctatgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACAAGGCTCCATACATTACTTTAC 546 193 66 Antisense
AAACCTTTGTGAGACCCATACTTGA 685 125 92 Antisense
GAATCCGTACAAAACTCGTTCACTA 429 329 169 Antisense
ATCAGAACAGATGACCCCGACTATA 265 27 226 Antisense
GACCCCGACTATAAGAGCGCTATTC 435 381 238 Antisense
AACTTATCAACTTTAGAGGCTCGGC 299 1 280 Antisense
GAGGCTCGGCGTAAAGCTATTGATA 231 405 295 Antisense
ACTCGTACCAAAACCAAGTTCATCT 322 97 400 Antisense
CAAACTACGAAGGCACTTTTTCACA 503 191 441 Antisense
TAGCGCAATGAATCTTATTTTGGCA 601 651 492 Antisense
TATTTTGGCACCTCATGTCCTATGC 691 661 507 Antisense
Sequence Source Affymetrix Proprietary Database