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[188307_at]

Description Y53F4B.28 /REP_DB=WormBase Gene ID /WP=CE24422 /GEN=ptr-20 /TR=Q9NAB5 /GB=CAB61102.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      4grp_highest_8_8 > 13      4grp_high_8_8 > 30      6grp_highest_nonorm > 72      6grp_total > 83      4grp_total > 24      6grp_highest_sub > 05      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 876
1 2 3 4 range
A 133.3
(-3)
P 		417.1
(-0.3)
P 		505.3
(0.5)
P 		774.9
(3)
P 		642
B 113.5
(-3)
P 		482.6
(-0.5)
P 		558.7
(0.1)
P 		989.1
(3)
P 		876
C 133.5
(-3)
P 		578.5
(0.9)
P 		567.8
(0.8)
P 		810.7
(3)
P 		677
avr 126.8
(-3) 		492.7
(0) 		543.9
(0.4) 		858.2
(3) 		731

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 587
1 2 3 4 5 6 range
A 292.4
(-3)
P 		454.9
(-0.7)
P 		381.3
(-1.8)
P 		385.7
(-1.7)
P 		722.6
(3)
P 		363.2
(-2)
P 		430
B 174.5
(-3)
P 		448.1
(0.1)
P 		332.5
(-1.2)
P 		608.2
(1.9)
P 		705.6
(3)
P 		416
(-0.3)
P 		531
C 192.7
(-3)
P 		438.8
(-0.4)
P 		493.4
(0.2)
P 		565
(0.9)
P 		761.1
(3)
P 		386.9
(-1)
P 		568
avr 219.9
(-3) 		447.3
(-0.3) 		402.4
(-0.9) 		519.6
(0.5) 		729.8
(3) 		388.7
(-1) 		510
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 175
1 2 3 4 range
A 48.5
(-3)
P 		90.5
(0)
P 		132.1
(3)
P 		113.4
(1.7)
P 		84
B 36.2
(-3)
P 		119.2
(-0.1)
P 		129.5
(0.2)
P 		210.8
(3)
P 		175
C 44.2
(-3)
P 		166.3
(1.8)
P 		197.9
(3)
P 		136.7
(0.6)
P 		154
avr 43
(-3) 		125.3
(1.5) 		153.2
(3) 		153.6
(3) 		111

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 233
1 2 3 4 5 6 range
A 53.9
(-3)
P 		161.8
(0.9)
P 		83
(-1.9)
P 		97.8
(-1.4)
P 		218
(3)
P 		88.4
(-1.7)
P 		164
B 60.7
(-3)
P 		149.1
(-0.7)
P 		80.7
(-2.5)
P 		161.1
(-0.3)
P 		286.7
(3)
P 		155.1
(-0.5)
P 		226
C 71.4
(-3)
P 		133.9
(-0.9)
P 		125.6
(-1.1)
P 		113.6
(-1.6)
P 		246.3
(3)
P 		129.5
(-1)
P 		175
avr 62
(-3) 		148.3
(-0.3) 		96.4
(-1.9) 		124.2
(-1) 		250.3
(3) 		124.3
(-1) 		188
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188307_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2623
Sequence Type Exemplar sequence
Representative Public ID Y53F4B.28 NCBI
Target Description Y53F4B.28 /REP_DB=WormBase Gene ID /WP=CE24422 /GEN=ptr-20 /TR=Q9NAB5 /GB=CAB61102.1 /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_064713(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064713 NCBI Caenorhabditis elegans PaTched Related family member (ptr-20) (ptr-20) mRNA, complete cds. 11/11 None
SNAP00000043066 ENSEMBL cdna:SNAP chromosome:CEL140:II:15158073:15163362:1 11/11 None
GENEFINDER00000043116 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:15158073:15163362:1 11/11 None
Y53F4B.28 ENSEMBL cdna:known chromosome:CEL140:II:15158073:15163493:1 gene:Y53F4B.28 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:15158069-15163359(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-20
Ensembl Y53F4B.28
Entrez Gene 175165 Entrez gene
SwissProt Q9NAB5 EMBL-EBI
WormBase CE24422 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 CAB61102 Hypothetical protein Y53F4B.28 [Caenorhabditis elegans] ref|NP_497114.1| PaTched Related family member (ptr-20) [Caenorhabditis elegans] 0.0
blast CAE59727 Hypothetical protein CBG03163 [Caenorhabditis briggsae] 0.0
blast CAE58022 Hypothetical protein CBG01094 [Caenorhabditis briggsae] 7.0E-75
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 7.3E-70
Pfam IPR003392 EMBL-EBI Patched family 3.3E-55
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497114.1 11 20-42,245-267,280-302,306-328,347-369,384-406,471-493,672-694,699-721,785-807,814-836
Y53F4B.28 11 20-42,245-267,280-302,306-328,347-369,384-406,471-493,672-694,699-721,785-807,814-836
SNAP00000043066 11 20-42,245-267,280-302,306-328,347-369,384-406,471-493,672-694,699-721,785-807,814-836
GENEFINDER00000043116 11 20-42,245-267,280-302,306-328,347-369,384-406,471-493,672-694,699-721,785-807,814-836
Sequence
Target Sequence 
>C. ELEGANS:188307_AT
cttcagccccattcaactttatatccacgtcagtatccgccgtcgtactaatgtcccttc
tagtgttggtatttatcatgaatttcgaggcaattatttctgtagcagtgtcaattgtat
caatatgtctcggaatagttgtgtacctccatttatggaatgtgaatctcgatgcagttt
cactgatatctatgctaatgtcaattggattttccgtggactattcggctcatgtttgct
atcactactttgctcatgtgcatgaggatgagcaactctggagatcacataactacgccg
agactcgtgaccgtcttctaagcaccttccgcggagtcgcctggccagtaatgcagtccg
ggctctccacgattcttggcatgttcccattgatgtttgtacgtgcgtatgttgtagcag
tattctggaagactgtgatcctggtcggtatacttggaatgcttcatgctctcattctgt
tgccagtaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTCAGCCCCATTCAACTTTATATC 221 221 2018 Antisense
ACTTTATATCCACGTCAGTATCCGC 403 103 2033 Antisense
GTCGTACTAATGTCCCTTCTAGTGT 668 471 2059 Antisense
GGAATAGTTGTGTACCTCCATTTAT 357 533 2149 Antisense
GGACTATTCGGCTCATGTTTGCTAT 461 523 2235 Antisense
TGTTTGCTATCACTACTTTGCTCAT 432 561 2250 Antisense
AGATCACATAACTACGCCGAGACTC 631 65 2299 Antisense
GCCTGGCCAGTAATGCAGTCCGGGC 552 281 2356 Antisense
GCTCTCCACGATTCTTGGCATGTTC 9 301 2379 Antisense
ACTGTGATCCTGGTCGGTATACTTG 48 97 2449 Antisense
CATGCTCTCATTCTGTTGCCAGTAA 344 211 2482 Antisense
Sequence Source Affymetrix Proprietary Database