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[172991_at]

Description C52621_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C52621 /DEF=C.elegans cDNA clone yk270c5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 07      6grp_high1_10_10 > 70      6grp_highest_nonorm > 71      6grp_total > 40      4grp_total > 49      6grp_highest_sub > 04      6grp_cgc > 50      6grp_high1_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 694
1 2 3 4 range
A 58.7
(-2.5)
A 		531.8
(2.6)
P 		573.2
(3)
P 		7.1
(-3)
A 		566
B 19.4
(-3)
A 		517.8
(2.9)
P 		523.1
(3)
P 		50.1
(-2.6)
A 		504
C 6.9
(-3)
A 		700.6
(3)
P 		612.4
(2.2)
P 		23.5
(-2.9)
A 		694
avr 28.3
(-3) 		583.4
(3) 		569.6
(2.9) 		26.9
(-3) 		557

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 443
1 2 3 4 5 6 range
A 329
(3)
P 		297.2
(2.2)
P 		294.1
(2.1)
P 		295.3
(2.1)
P 		260.2
(1.2)
P 		96.8
(-3)
P 		232
B 328.1
(0.2)
P 		346.7
(0.5)
P 		328.4
(0.2)
P 		477.2
(3)
P 		280.1
(-0.8)
P 		162.4
(-3)
P 		315
C 279.9
(-1.7)
P 		399.3
(0.4)
P 		264.7
(-2)
P 		539.5
(3)
P 		292.9
(-1.5)
P 		211
(-3)
P 		329
avr 312.3
(0.3) 		347.7
(1.1) 		295.7
(-0) 		437.3
(3) 		277.7
(-0.4) 		156.7
(-3) 		281
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 212
1 2 3 4 range
A 21.4
(-2.2)
A 		115.4
(1.6)
P 		149.9
(3)
P 		1
(-3)
A 		149
B 6.2
(-3)
A 		127.9
(3)
P 		121.2
(2.7)
P 		10.7
(-2.8)
A 		122
C 2.3
(-3)
A 		201.4
(2.7)
P 		213.4
(3)
P 		4
(-3)
A 		211
avr 10
(-2.8) 		148.2
(2.5) 		161.5
(3) 		5.2
(-3) 		156

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 103
1 2 3 4 5 6 range
A 60.7
(-0.3)
P 		105.7
(3)
P 		64
(-0)
P 		74.9
(0.7)
P 		78.5
(1)
P 		23.6
(-3)
P 		82
B 114.2
(1.9)
P 		115.4
(2)
P 		79.8
(-1.2)
P 		126.4
(3)
P 		113.8
(1.9)
P 		60.6
(-3)
P 		66
C 103.8
(1)
P 		121.8
(3)
P 		67.4
(-3)
P 		108.5
(1.5)
P 		94.8
(0)
P 		70.6
(-2.6)
P 		54
avr 92.9
(1) 		114.3
(3) 		70.4
(-1.2) 		103.3
(1.9) 		95.7
(1.2) 		51.6
(-3) 		63
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 172991_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26464
Sequence Type Exemplar sequence
Representative Public ID C52621 NCBI
Target Description C52621_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C52621 /DEF=C.elegans cDNA clone yk270c5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_076612
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000012818 ENSEMBL cdna:SNAP chromosome:CEL140:X:6060934:6064120:-1 None
GENEFINDER00000012832 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6060934:6066284:-1 None
NM_076612 NCBI Caenorhabditis elegans PaTched Related family member (ptr-4) (ptr-4) mRNA, complete cds. A 
C45B2.7 ENSEMBL cdna:known chromosome:CEL140:X:6060721:6065945:-1 gene:C45B2.7 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
chrX:6060782-6060972(-) 76.31 76.31
Public Domain and Genome References
Gene Title
Gene Symbol ptr-4
Ensembl C45B2.7
Entrez Gene 180876 Entrez gene
SwissProt Q95YD0 EMBL-EBI
WormBase CE30905 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 AAK68251 Patched related family protein 4 [Caenorhabditis elegans] ref|NP_509013.2| PaTched Related family member (ptr-4) [Caenorhabditis elegans] 0.0
blast CAE68859 Hypothetical protein CBG14821 [Caenorhabditis briggsae] 0.0
blast CAA21636 Hypothetical protein Y38F1A.3 [Caenorhabditis elegans] ref|NP_496761.2| PaTched Related family member (ptr-18) [Caenorhabditis elegans] 1.0E-81
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
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509013.2 11 30-52,341-363,375-397,446-468,475-497,575-597,789-806,811-833,838-860,885-907,914-936
C45B2.7 11 30-52,341-363,375-397,446-468,475-497,575-597,789-806,811-833,838-860,885-907,914-936
SNAP00000012818 10 150-172,184-206,255-277,284-306,384-406,598-615,620-642,647-669,694-716,723-745
GENEFINDER00000012832 11 121-143,439-461,473-495,544-566,573-595,673-695,887-904,909-931,936-958,983-1005,1012-1034
Sequence
Target Sequence 
>C. ELEGANS:172991_AT
gtcacgttctcgaagaggaacacgttcgcatggatccaatgcagaaatgagctgtggtag
cctcatctcaaaacatattccactttcactccattaaatcaattatctgaacagtctcaa
tcattcagtgccttttcaccccgactctagaaacaattttatgtttcacgtgtgcaagtt
catttaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCACGTTCTCGAAGAGGAACACGT 403 465 13 Antisense
GAGGAACACGTTCGCATGGATCCAA 374 405 27 Antisense
ACGTTCGCATGGATCCAATGCAGAA 314 93 34 Antisense
TGAGCTGTGGTAGCCTCATCTCAAA 638 569 60 Antisense
CTTTCACTCCATTAAATCAATTATC 694 221 95 Antisense
ATCAATTATCTGAACAGTCTCAATC 45 27 110 Antisense
AACAGTCTCAATCATTCAGTGCCTT 403 137 122 Antisense
TCAATCATTCAGTGCCTTTTCACCC 428 633 129 Antisense
TTTTCACCCCGACTCTAGAAACAAT 573 675 145 Antisense
CAATTTTATGTTTCACGTGTGCAAG 93 181 166 Antisense
GTTTCACGTGTGCAAGTTCATTTAA 464 449 175 Antisense
Sequence Source Affymetrix Proprietary Database