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[188188_s_at]

Description Y38F1A.3 /REP_DB=WormBase Gene ID /WP=CE21608 /GEN=ptr-18 /TR=Q9XWL9 /GB=CAA21636.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 80      6grp_total > 82      4grp_total > 57      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 713
1 2 3 4 range
A 92.3
(-2.2)
P 		448.8
(1.3)
P 		623.8
(3)
P 		11.2
(-3)
A 		613
B 58.5
(-2.9)
P 		451.9
(1.3)
P 		610.5
(3)
P 		53.1
(-3)
A 		557
C 48.2
(-3)
M 		645.9
(2.3)
P 		724.3
(3)
P 		70.6
(-2.8)
A 		676
avr 66.3
(-2.8) 		515.5
(1.6) 		652.9
(3) 		45
(-3) 		608

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 424
1 2 3 4 5 6 range
A 66.7
(-3)
A 		419.8
(2.2)
P 		262.5
(-0.1)
P 		298.4
(0.4)
P 		473.9
(3)
P 		147.5
(-1.8)
P 		407
B 87.7
(-3)
M 		469.6
(2.7)
P 		281
(-0.1)
P 		489.7
(3)
P 		412.9
(1.9)
P 		124.2
(-2.5)
P 		402
C 108.9
(-3)
P 		418.6
(1.9)
P 		267.5
(-0.5)
P 		490.5
(3)
P 		484.9
(2.9)
P 		125.2
(-2.7)
P 		382
avr 87.8
(-3) 		436
(2.7) 		270.3
(-0) 		426.2
(2.5) 		457.2
(3) 		132.3
(-2.3) 		369
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 251
1 2 3 4 range
A 33.6
(-1.8)
P 		97.4
(0.6)
P 		163.1
(3)
P 		1.6
(-3)
A 		162
B 18.7
(-2.7)
P 		111.6
(1.6)
P 		141.5
(3)
P 		11.3
(-3)
A 		130
C 16
(-2.9)
M 		185.7
(1.3)
P 		252.4
(3)
P 		11.9
(-3)
A 		241
avr 22.8
(-2.5) 		131.6
(1.2) 		185.7
(3) 		8.3
(-3) 		177

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 156
1 2 3 4 5 6 range
A 12.3
(-3)
A 		149.3
(3)
P 		57.2
(-1)
P 		75.7
(-0.2)
P 		143
(2.7)
P 		35.9
(-2)
P 		137
B 30.5
(-3)
M 		156.3
(2.5)
P 		68.2
(-1.4)
P 		129.7
(1.3)
P 		167.8
(3)
P 		46.3
(-2.3)
P 		137
C 40.4
(-3)
P 		127.7
(1.5)
P 		68.1
(-1.6)
P 		98.6
(-0)
P 		156.9
(3)
P 		41.9
(-2.9)
P 		117
avr 27.7
(-3) 		144.4
(2.5) 		64.5
(-1.3) 		101.3
(0.4) 		155.9
(3) 		41.4
(-2.4) 		128
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188188_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2994
Sequence Type Exemplar sequence
Representative Public ID Y38F1A.3 NCBI
Target Description Y38F1A.3 /REP_DB=WormBase Gene ID /WP=CE21608 /GEN=ptr-18 /TR=Q9XWL9 /GB=CAA21636.1 /SUBMIT=HINXTON /CHR=2 /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_064360(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064360 NCBI Caenorhabditis elegans PaTched Related family member (ptr-18) (ptr-18) mRNA, complete cds. 11/11 None
SNAP00000020278 ENSEMBL cdna:SNAP chromosome:CEL140:II:12965465:12977790:1 11/11 None
GENEFINDER00000020297 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12969348:12977790:1 10/11 None
Y38F1A.3 ENSEMBL cdna:known chromosome:CEL140:II:12966443:12978053:1 gene:Y38F1A.3 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
chrII:12966663-12977787(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-18
Ensembl Y38F1A.3
Entrez Gene 174940 Entrez gene
SwissProt Q9XWL9 EMBL-EBI
WormBase CE36233 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 CAA21636 Hypothetical protein Y38F1A.3 [Caenorhabditis elegans] ref|NP_496761.2| PaTched Related family member (ptr-18) [Caenorhabditis elegans] 0.0
blast CAE59402 Hypothetical protein CBG02766 [Caenorhabditis briggsae] 0.0
blast CAE58022 Hypothetical protein CBG01094 [Caenorhabditis briggsae] 1.0E-108
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
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Pfam IPR003392 EMBL-EBI Patched family 2.3E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496761.2 11 224-246,259-281,286-308,329-351,361-383,439-461,643-665,672-694,699-718,739-761,776-798
Y38F1A.3 11 224-246,259-281,286-308,329-351,361-383,439-461,643-665,672-694,699-718,739-761,776-798
SNAP00000020278 11 261-283,296-318,323-345,366-388,398-420,476-498,680-702,709-731,736-755,776-798,813-835
GENEFINDER00000020297 10 246-268,281-303,308-330,351-373,383-405,664-686,691-713,720-742,762-784,903-925
Sequence
Target Sequence 
>C. ELEGANS:188188_S_AT
gttttttgtgctctcatctgtatgatcatgattttaaccttgttcacaccttctccagtg
acaattgtcacttcaacagccgcagttttgtcgatcaacttgggagtttttggatgtctg
gtctatatgaacattgatctggatccgatttcgatgaccacacttctcatggccatcggt
ttctctgtagactttgtagcacatattacgtggcactactataagggagacttccactca
aagcgagcaagaatccggcatgcacttgccggaatcgcctggccaatgttccaagcggga
acttctactatgttagcaattaccgtgcttgccctggttcatgcctacatggttcaggtc
ttcgtgaaagtcgtcgtgttggtaatcttcctaggaatgttccatggtcttgtcgtgctc
ccgatcgtcttctcagccctcccattcacaaaaacatcaggtccgcaaaagaaaaaggta
gctccgttgcaaatgcacgaagctggtccgattcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTTTTTGTGCTCTCATCTGTATGA 451 449 1786 Antisense
GATTTTAACCTTGTTCACACCTTCT 672 427 1815 Antisense
CACACCTTCTCCAGTGACAATTGTC 410 195 1830 Antisense
TCAACAGCCGCAGTTTTGTCGATCA 598 629 1858 Antisense
CCATCGGTTTCTCTGTAGACTTTGT 609 267 1958 Antisense
GGAGACTTCCACTCAAAGCGAGCAA 611 513 2011 Antisense
GCCTACATGGTTCAGGTCTTCGTGA 79 283 2128 Antisense
GTCGTCGTGTTGGTAATCTTCCTAG 683 471 2155 Antisense
GGAATGTTCCATGGTCTTGTCGTGC 331 533 2179 Antisense
AGGTAGCTCCGTTGCAAATGCACGA 423 57 2261 Antisense
AATGCACGAAGCTGGTCCGATTCCA 475 165 2277 Antisense
Sequence Source Affymetrix Proprietary Database