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[174995_s_at]

Description CEK010AYR_rc /REP_DB=TREMBL Accession /GB=D27452 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk10a11 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 33      4grp_high_8_8 > 55      6grp_highest_nonorm > 80      6grp_total > 20      4grp_total > 48      6grp_highest_sub > 02_03      6grp_cgc > 73      6grp_high1_sub > 02      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 206
1 2 3 4 range
A 144
(-2.7)
P 		139.9
(-3)
P 		217.6
(3)
P 		190.2
(0.9)
A 		78
B 124.5
(-0.9)
P 		194.4
(2.7)
P 		201.2
(3)
P 		81.7
(-3)
P 		120
C 146.9
(-3)
P 		243.7
(1.1)
P 		287.6
(3)
P 		179.8
(-1.6)
P 		141
avr 138.5
(-3) 		192.7
(0.4) 		235.5
(3) 		150.6
(-2.3) 		97

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 322
1 2 3 4 5 6 range
A 186.7
(-1)
P 		296.1
(2.4)
P 		314.4
(3)
P 		263.2
(1.4)
P 		244.8
(0.8)
P 		120.6
(-3)
P 		194
B 211
(0.5)
P 		306.7
(3)
P 		272.2
(2.1)
P 		301.4
(2.9)
P 		249.9
(1.5)
P 		79
(-3)
P 		228
C 192.8
(-1.7)
P 		400.8
(3)
P 		267
(-0)
P 		236.5
(-0.7)
P 		147.4
(-2.8)
P 		137.5
(-3)
P 		263
avr 196.8
(-0.7) 		334.5
(3) 		284.5
(1.6) 		267
(1.2) 		214
(-0.3) 		112.4
(-3) 		222
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 52.4
(2.1)
P 		30.4
(-2.5)
P 		56.9
(3)
P 		27.8
(-3)
A 		29
B 39.7
(1.4)
P 		48
(3)
P 		46.6
(2.7)
P 		17.4
(-3)
P 		31
C 48.6
(-1.4)
P 		70.1
(0.4)
P 		100.2
(3)
P 		30.3
(-3)
P 		70
avr 46.9
(0) 		49.5
(0.4) 		67.9
(3) 		25.2
(-3) 		43

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 93
1 2 3 4 5 6 range
A 34.4
(-2.6)
P 		105.3
(3)
P 		68.5
(0.1)
P 		66.7
(-0.1)
P 		73.9
(0.5)
P 		29.4
(-3)
P 		76
B 73.4
(0.6)
P 		102.1
(3)
P 		66.1
(0)
P 		79.8
(1.2)
P 		101.5
(3)
P 		29.4
(-3)
P 		73
C 71.5
(-1)
P 		122.3
(3)
P 		68
(-1.3)
P 		47.6
(-2.9)
P 		47.7
(-2.9)
P 		46
(-3)
P 		76
avr 59.8
(-1) 		109.9
(3) 		67.5
(-0.4) 		64.7
(-0.6) 		74.4
(0.2) 		34.9
(-3) 		75
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174995_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20782
Sequence Type Exemplar sequence
Representative Public ID CEK010AYR NCBI
Target Description CEK010AYR_rc /REP_DB=TREMBL Accession /GB=D27452 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk10a11 : 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_062585(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062585 NCBI Caenorhabditis elegans PaTched Related family member (ptr-6) (ptr-6) mRNA, complete cds. 11/11 A 
SNAP00000020500 ENSEMBL cdna:SNAP chromosome:CEL140:II:5242541:5246810:-1 11/11 None
GENEFINDER00000020506 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:5242541:5246810:-1 11/11 None
C54A12.1 ENSEMBL cdna:known chromosome:CEL140:II:5242440:5247544:-1 gene:C54A12.1 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
chrII:5242444-5242872(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-6
Ensembl C54A12.1
Entrez Gene 173898 Entrez gene
SwissProt Q09938 EMBL-EBI
WormBase CE01865 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 AAA68302 Hypothetical protein C54A12.1 [Caenorhabditis elegans] ref|NP_494986.1| PaTched Related family member (ptr-6) [Caenorhabditis elegans] 0.0
blast CAE59072 Hypothetical protein CBG02358 [Caenorhabditis briggsae] 0.0
blast CAE63242 Hypothetical protein CBG07607 [Caenorhabditis briggsae] 1.0E-124
blast CAE63242 Hypothetical protein CBG07607 [Caenorhabditis briggsae] 1.0E-123
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_494986.1 11 60-82,333-355,375-397,404-426,446-468,475-497,618-637,838-860,880-902,923-942,957-979
C54A12.1 11 60-82,333-355,375-397,404-426,446-468,475-497,618-637,838-860,880-902,923-942,957-979
SNAP00000020500 11 27-49,296-318,338-360,367-389,409-431,438-460,581-600,801-823,843-865,886-905,920-942
GENEFINDER00000020506 11 27-49,300-322,342-364,371-393,413-435,442-464,585-604,805-827,847-869,890-909,924-946
Sequence
Target Sequence 
>C. ELEGANS:174995_S_AT
gtggtccatggaagtttgtctacaattctcggagtttttgttctagcatttattgattcc
tacatggttcttgtcttctttaaaactatctctcttgttcttattattggtgcctggcat
gctctaatgcttctcccgatacttctctcaatgtgtattccagttatcgaacgactttca
gatgcatccaagaaagcatccgatcgtcggagaaagctgaaggaaaataaaaatagtgtt
tatgcaattaatttgccggtaaatgtatcctcgtga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGTCCATGGAAGTTTGTCTACAA 465 489 23 Antisense
GTTCTAGCATTTATTGATTCCTACA 636 443 62 Antisense
CCTACATGGTTCTTGTCTTCTTTAA 698 265 81 Antisense
GTCTTCTTTAAAACTATCTCTCTTG 349 469 95 Antisense
TATCTCTCTTGTTCTTATTATTGGT 359 659 109 Antisense
ATTGGTGCCTGGCATGCTCTAATGC 264 3 128 Antisense
TCCCGATACTTCTCTCAATGTGTAT 123 597 156 Antisense
GTGTATTCCAGTTATCGAACGACTT 464 485 175 Antisense
CGAACGACTTTCAGATGCATCCAAG 428 251 190 Antisense
GCATCCAAGAAAGCATCCGATCGTC 120 309 206 Antisense
TTTGCCGGTAAATGTATCCTCGTGA 170 669 274 Antisense
Sequence Source Affymetrix Proprietary Database