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[175079_s_at]

Description C53223_rc /REP_DB=TREMBL Accession /GB=C53223 /CHR=1 /FEA=Genomic Cluster /REVCOMP /DEF=C.elegans cDNA clone yk295d4 : 3prime end, single read.
Cluster 6grp_total > 93      4grp_total > 49      6grp_cgc > 89      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 141
1 2 3 4 range
A 3
(-3)
A 		136.7
(3)
A 		104.5
(1.6)
A 		22.2
(-2.1)
A 		134
B 4.9
(-2.9)
A 		102.6
(2.9)
A 		103.7
(3)
A 		2.6
(-3)
A 		101
C 16.4
(-2.8)
A 		105.8
(1.3)
A 		143.1
(3)
P 		12.8
(-3)
A 		130
avr 8.1
(-3) 		115
(2.9) 		117.1
(3) 		12.5
(-2.8) 		109

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 164
1 2 3 4 5 6 range
A 5.7
(-3)
A 		107.4
(1.4)
A 		54.5
(-0.9)
A 		88.4
(0.6)
A 		143.3
(3)
A 		58
(-0.7)
A 		138
B 18.5
(-3)
A 		78.9
(-0.3)
A 		61.9
(-1.1)
A 		89.9
(0.1)
A 		154.8
(3)
M 		107.4
(0.9)
P 		136
C 19.4
(-3)
A 		65.2
(-1.2)
A 		83.2
(-0.4)
A 		43.6
(-2)
A 		169.4
(3)
M 		100.7
(0.3)
A 		150
avr 14.5
(-3) 		83.8
(-0.1) 		66.5
(-0.8) 		74
(-0.5) 		155.8
(3) 		88.7
(0.2) 		141
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 1.1
(-3)
A 		29.7
(3)
A 		27.3
(2.5)
A 		3.3
(-2.5)
A 		29
B 1.5
(-2.8)
A 		25.3
(3)
A 		24
(2.7)
A 		0.6
(-3)
A 		25
C 5.4
(-2.6)
A 		30.4
(0.5)
A 		49.9
(3)
P 		2.2
(-3)
A 		48
avr 2.7
(-2.9) 		28.5
(2) 		33.7
(3) 		2
(-3) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 62
1 2 3 4 5 6 range
A 1
(-3)
A 		38.2
(2.3)
A 		11.9
(-1.5)
A 		22.4
(0)
A 		43.2
(3)
A 		14.1
(-1.1)
A 		42
B 6.4
(-3)
A 		26.3
(-0.9)
A 		15
(-2.1)
A 		23.8
(-1.2)
A 		62.9
(3)
M 		40.1
(0.6)
P 		57
C 7.2
(-3)
A 		19.9
(-1.4)
A 		21.2
(-1.2)
A 		8.8
(-2.8)
A 		54.8
(3)
M 		33.7
(0.3)
A 		48
avr 4.9
(-3) 		28.1
(-0.1) 		16
(-1.6) 		18.3
(-1.3) 		53.6
(3) 		29.3
(0) 		49
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175079_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28208
Sequence Type Exemplar sequence
Representative Public ID C53223 NCBI
Target Description C53223_rc /REP_DB=TREMBL Accession /GB=C53223 /CHR=1 /FEA=Genomic Cluster /REVCOMP /DEF=C.elegans cDNA clone yk295d4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_058820(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058820 NCBI Caenorhabditis elegans PaTched Related family member (ptr-2) (ptr-2) mRNA, complete cds. 11/11 A 
SNAP00000040653 ENSEMBL cdna:SNAP chromosome:CEL140:I:3789416:3792797:-1 11/11 None
GENEFINDER00000040662 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3789416:3792797:-1 11/11 None
C32E8.8 ENSEMBL cdna:known chromosome:CEL140:I:3789321:3792799:-1 gene:C32E8.8 11/11 A 
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
chrI:3791863-3792143(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-2
Ensembl C32E8.8
Entrez Gene 171950 Entrez gene
SwissProt P91129 EMBL-EBI
WormBase CE08532 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1636728_AT Ptc-related dm
DROSGENOME1:146674_AT Ptc-related dm
CHICKEN:GGAAFFX.4657.1.S1_S_AT similar to CG11212-PA gga
MOE430B:1431518_AT patched domain containing 3 mm
MOUSE430_2:1431518_AT patched domain containing 3 mm
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 AAB42325 Patched related family protein 2 [Caenorhabditis elegans] ref|NP_491221.1| PaTched Related family member (ptr-2) [Caenorhabditis elegans] 0.0
blast CAE66666 Hypothetical protein CBG12004 [Caenorhabditis briggsae] 0.0
blast CAE68940 Hypothetical protein CBG14920 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491221.1 12 17-39,265-287,300-322,332-354,375-397,407-429,490-512,701-723,730-752,762-784,797-819,834-856
C32E8.8 12 17-39,265-287,300-322,332-354,375-397,407-429,490-512,701-723,730-752,762-784,797-819,834-856
SNAP00000040653 12 17-39,265-287,300-322,332-354,375-397,407-429,490-512,701-723,730-752,762-784,797-819,834-856
GENEFINDER00000040662 12 17-39,265-287,300-322,332-354,375-397,407-429,490-512,701-723,730-752,762-784,797-819,834-856
Sequence
Target Sequence 
>C. ELEGANS:175079_S_AT
gcagtctcggaggcgtcactgtaatgaaaggagaaaatgagacagatatccttgcatcag
cgaaagcctggttcatgatctatcatctgaagtttcacccagaagaaatgagctatattt
cgggagaatgggagctagaactcggcagaatgctcacccagtatccagaagatccataca
tctctatcacctacttccactctcaaactctagcagatgagcttaagagaaatgcggata
cactgattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAGTCTCGGAGGCGTCACTGTAAT 573 311 14 Antisense
GAGACAGATATCCTTGCATCAGCGA 368 393 52 Antisense
ATCCTTGCATCAGCGAAAGCCTGGT 28 41 61 Antisense
AAAGCCTGGTTCATGATCTATCATC 470 125 76 Antisense
GATCTATCATCTGAAGTTTCACCCA 44 421 90 Antisense
GGGAGAATGGGAGCTAGAACTCGGC 189 375 135 Antisense
TAGAACTCGGCAGAATGCTCACCCA 112 653 149 Antisense
ATGCTCACCCAGTATCCAGAAGATC 642 41 163 Antisense
AGATCCATACATCTCTATCACCTAC 533 65 183 Antisense
CTTCCACTCTCAAACTCTAGCAGAT 315 219 207 Antisense
AAGAGAAATGCGGATACACTGATTC 400 151 238 Antisense
Sequence Source Affymetrix Proprietary Database