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[188291_at]

Description F54G8.5 /REP_DB=WormBase Gene ID /WP=CE00207 /GEN=ptr-9 /TR=SW:Q03602 /GB=CAA79560.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 91      4grp_total > 35      6grp_cgc > 97      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 29
(-3)
A 		50.5
(2)
A 		54.8
(3)
A 		51.4
(2.2)
A 		26
B 52.3
(0.4)
A 		73.6
(3)
A 		24.3
(-3)
A 		25.4
(-2.9)
A 		49
C 39.9
(-1.7)
A 		61.1
(1.9)
A 		32.6
(-3)
A 		67.6
(3)
A 		35
avr 40.4
(-2.2) 		61.7
(3) 		37.2
(-3) 		48.1
(-0.3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 69
1 2 3 4 5 6 range
A 45.3
(1.3)
A 		28.1
(-0.5)
A 		48.4
(1.6)
A 		3.8
(-3)
A 		61.7
(3)
A 		43
(1.1)
A 		58
B 8.8
(-3)
A 		59.1
(3)
A 		30.5
(-0.4)
A 		59.3
(3)
A 		42.4
(1)
A 		35.1
(0.1)
A 		51
C 49.5
(0.7)
A 		58.5
(1.6)
A 		10.8
(-3)
A 		73
(3)
A 		34.1
(-0.8)
A 		34
(-0.8)
A 		62
avr 34.5
(-1.5) 		48.6
(3) 		29.9
(-3) 		45.4
(2) 		46.1
(2.2) 		37.4
(-0.6) 		19
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 10.6
(-0.3)
A 		11
(0.1)
A 		14.3
(3)
A 		7.5
(-3)
A 		7
B 16.7
(2.3)
A 		18.2
(3)
A 		5.6
(-2.9)
A 		5.4
(-3)
A 		13
C 13.2
(-1.3)
A 		17.6
(3)
A 		11.4
(-3)
A 		11.4
(-3)
A 		6
avr 13.5
(1.3) 		15.6
(3) 		10.4
(-1.2) 		8.1
(-3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19
1 2 3 4 5 6 range
A 8.3
(-0.5)
A 		10
(0.1)
A 		10.5
(0.2)
A 		1
(-3)
A 		18.6
(3)
A 		10.5
(0.2)
A 		18
B 3.1
(-3)
A 		19.7
(3)
A 		7.4
(-1.4)
A 		15.7
(1.6)
A 		17.2
(2.1)
A 		13.1
(0.6)
A 		17
C 18.3
(3)
A 		17.8
(2.8)
A 		2.7
(-3)
A 		14.7
(1.6)
A 		11
(0.2)
A 		11.4
(0.3)
A 		16
avr 9.9
(-1) 		15.8
(3) 		6.9
(-3) 		10.5
(-0.6) 		15.6
(2.9) 		11.7
(0.2) 		9
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188291_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6406
Sequence Type Exemplar sequence
Representative Public ID F54G8.5 NCBI
Target Description F54G8.5 /REP_DB=WormBase Gene ID /WP=CE00207 /GEN=ptr-9 /TR=SW:Q03602 /GB=CAA79560.1 /SUBMIT=HINXTON /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_066629(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066629 NCBI Caenorhabditis elegans PaTched Related family member (ptr-9) (ptr-9) mRNA, complete cds. 11/11 None
SNAP00000023861 ENSEMBL cdna:SNAP chromosome:CEL140:III:9157148:9161538:-1 11/11 None
GENEFINDER00000023868 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9157148:9161409:-1 11/11 None
F54G8.5 ENSEMBL cdna:known chromosome:CEL140:III:9157148:9161538:-1 gene:F54G8.5 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:9157440-9159346(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-9
Ensembl F54G8.5
Entrez Gene 191747 Entrez gene
SwissProt Q03602 EMBL-EBI
WormBase CE37974 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8158 hedgehog receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA79560 Hypothetical protein F54G8.5 [Caenorhabditis elegans] ref|NP_499030.2| PaTched Related family member (ptr-9) [Caenorhabditis elegans] sp|Q03602|PTR9_CAEEL Patched related family protein 0.0
blast CAE62665 Hypothetical protein CBG06803 [Caenorhabditis briggsae] 0.0
blast CAA16339 Hypothetical protein Y39A1B.2 [Caenorhabditis elegans] ref|NP_499380.1| PaTched Related family member (ptr-19) [Caenorhabditis elegans] 3.0E-71
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 1.7E-49
Pfam IPR003392 EMBL-EBI Patched family 8.2E-43
Pfam IPR003392 EMBL-EBI Patched family 9.5E-43
Pfam IPR003392 EMBL-EBI Patched family 8.2E-43
Pfam IPR003392 EMBL-EBI Patched family 1.7E-49
Pfam IPR003392 EMBL-EBI Patched family 8.2E-43
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499030.2 11 20-42,267-289,294-316,321-343,393-415,475-497,666-688,692-714,721-743,763-785,790-812
F54G8.5 11 20-42,267-289,294-316,321-343,393-415,475-497,666-688,692-714,721-743,763-785,790-812
SNAP00000023861 11 20-42,267-289,294-316,321-343,382-404,467-489,658-680,684-706,713-735,755-777,782-804
GENEFINDER00000023868 10 371-393,398-420,425-447,497-519,579-601,770-792,796-818,825-847,867-889,894-916
Sequence
Target Sequence 
>C. ELEGANS:188291_AT
gaagtgaatatagttctccatccgagttctggctggatccatttgagaagaaaaatcgtg
ggaaaaaatattcagaatccgatttttccgacgaacttcacacatttctcgcgaaagagc
ctcatttaaaatttcgaaatgatattagattcacaatgatggggaagattgaagcaatga
aaatgatgtttcgagtaaggaaattagggaaggataatgatgctccacgagcagaatata
tgagaaaagtgatggaaaatagtcaattcaatggatttgtatatgataccagttttttat
tggttgatcagcaaatgactacggtttataatgtaattgttgatgtggtttcagcaattt
taacaatgttatctatttgtgtattgatggttcctcgcccggtatctgcaatgtgtattg
cttttgccatattatcagtgaatattggagtaatcggagccctggcagctacaaatacac
gacttgatattatctcaatgataacaattgtgatgagtgtgggattttcagttgattatg
tcacgcataccacttttcattt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGTGAATATAGTTCTCCATCCGA 615 333 641 Antisense
CTCCATCCGAGTTCTGGCTGGATCC 87 235 656 Antisense
GATTTTTCCGACGAACTTCACACAT 372 427 721 Antisense
CACACATTTCTCGCGAAAGAGCCTC 376 193 739 Antisense
GAAGGATAATGATGCTCCACGAGCA 278 335 849 Antisense
TTTGTGTATTGATGGTTCCTCGCCC 211 667 1016 Antisense
CTCGCCCGGTATCTGCAATGTGTAT 425 233 1034 Antisense
GTGTATTGCTTTTGCCATATTATCA 124 487 1053 Antisense
ATTGGAGTAATCGGAGCCCTGGCAG 323 3 1084 Antisense
GCCCTGGCAGCTACAAATACACGAC 134 287 1099 Antisense
ATGTCACGCATACCACTTTTCATTT 590 47 1178 Antisense
Sequence Source Affymetrix Proprietary Database