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[180485_s_at]

Description C45B2.7 /REP_DB=WormBase Gene ID /WP=CE02557 /GEN=ptr-4 /GB=AAK68251.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 06      6grp_high1_10_10 > 60      6grp_highest_nonorm > 53      6grp_total > 60      4grp_total > 49      6grp_highest_sub > 04      6grp_cgc > 84      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1282
1 2 3 4 range
A 34.5
(-3)
A 		1312.3
(3)
P 		1249
(2.7)
P 		87.4
(-2.8)
A 		1278
B 41.1
(-2.9)
A 		1074.5
(2.8)
P 		1107.5
(3)
P 		30.6
(-3)
A 		1077
C 42
(-3)
A 		1093.6
(2.8)
P 		1121.6
(3)
P 		107.9
(-2.6)
P 		1080
avr 39.2
(-3) 		1160.1
(3) 		1159.4
(3) 		75.3
(-2.8) 		1121

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1276
1 2 3 4 5 6 range
A 856.1
(1.3)
P 		695.3
(0.1)
P 		772.4
(0.7)
P 		1109
(3)
P 		867.9
(1.3)
P 		238.2
(-3)
P 		871
B 682.4
(-0.6)
P 		750.1
(-0.2)
P 		805
(0.1)
P 		1338.2
(3)
P 		664.2
(-0.7)
P 		231.3
(-3)
P 		1107
C 765
(-0.4)
P 		666.8
(-0.9)
P 		920.5
(0.3)
P 		1487
(3)
P 		553.3
(-1.4)
P 		211
(-3)
P 		1276
avr 767.8
(-0) 		704.1
(-0.4) 		832.6
(0.4) 		1311.4
(3) 		695.1
(-0.4) 		226.8
(-3) 		1085
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 384
1 2 3 4 range
A 12.6
(-3)
A 		284.9
(2.2)
P 		326.5
(3)
P 		12.8
(-3)
A 		314
B 13.1
(-2.8)
A 		265.4
(3)
P 		256.6
(2.8)
P 		6.5
(-3)
A 		259
C 13.9
(-3)
A 		314.4
(1.8)
P 		390.9
(3)
P 		18.2
(-2.9)
P 		377
avr 13.2
(-3) 		288.2
(2.3) 		324.7
(3) 		12.5
(-3) 		312

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 297
1 2 3 4 5 6 range
A 157.8
(-0.3)
P 		247.3
(2.1)
P 		168.2
(-0)
P 		281.3
(3)
P 		261.9
(2.5)
P 		58
(-3)
P 		223
B 237.4
(0.4)
P 		249.7
(0.7)
P 		195.5
(-0.6)
P 		354.5
(3)
P 		269.9
(1.1)
P 		86.3
(-3)
P 		268
C 283.6
(2.6)
P 		203.5
(0.5)
P 		234.3
(1.3)
P 		299
(3)
P 		179
(-0.2)
P 		70.6
(-3)
P 		228
avr 226.3
(0.9) 		233.5
(1) 		199.3
(0.2) 		311.6
(3) 		236.9
(1.1) 		71.6
(-3) 		240
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 180485_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16578
Sequence Type Exemplar sequence
Representative Public ID C45B2.7 NCBI
Target Description C45B2.7 /REP_DB=WormBase Gene ID /WP=CE02557 /GEN=ptr-4 /GB=AAK68251.1 /SUBMIT=ST.LOUIS /CHR=X /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_076612(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076612 NCBI Caenorhabditis elegans PaTched Related family member (ptr-4) (ptr-4) mRNA, complete cds. 11/11 None
SNAP00000012818 ENSEMBL cdna:SNAP chromosome:CEL140:X:6060934:6064120:-1 11/11 None
GENEFINDER00000012832 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6060934:6066284:-1 11/11 None
C45B2.7 ENSEMBL cdna:known chromosome:CEL140:X:6060721:6065945:-1 gene:C45B2.7 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
chrX:6060933-6066688(-) 100.0 100.0
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:180485_S_AT
tcaacggcacacaattgctccttcatctatgcaaacaattggctcagcgcttgccatgat
ggctctcatttctttcttcttcctaccagacgcgcaatccgtattcttgatgaccttttc
cttactctccatctcaatgggtgtgtgcggaggacttgctcttcttggctcagatttgga
ctccgtcagtatgggttgcattgttatggctatcggattggctgttgactactcggtaca
catttgctatagatatcacagatctgaatataaaacagcacaagaaaaagtggctgacac
acttgcatccgtcggatggcccgtcactcaagccgtgtgctcaacattggtcggactagc
aatcactgtttttgttccagcatatttagtacgagtattcttccaaactgtttatcttgt
gaacatcattggacttttccacgcgctcgtctggctaccacagctcatttctgcattgga
tccatgcgaacgtgttcctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAACGGCACACAATTGCTCCTTCA 442 631 2574 Antisense
TTGGCTCAGCGCTTGCCATGATGGC 526 707 2612 Antisense
CCATGATGGCTCTCATTTCTTTCTT 596 269 2627 Antisense
TACCAGACGCGCAATCCGTATTCTT 133 651 2657 Antisense
TATTCTTGATGACCTTTTCCTTACT 383 663 2675 Antisense
GGACTCCGTCAGTATGGGTTGCATT 158 525 2751 Antisense
ATCGGATTGGCTGTTGACTACTCGG 501 33 2785 Antisense
GACTACTCGGTACACATTTGCTATA 233 373 2800 Antisense
CAAGCCGTGTGCTCAACATTGGTCG 241 187 2902 Antisense
TACCACAGCTCATTTCTGCATTGGA 100 651 3029 Antisense
TTGGATCCATGCGAACGTGTTCCTC 263 709 3049 Antisense
Sequence Source Affymetrix Proprietary Database