[Home] | [Total List]

[188240_at]

Description C54A12.1 /REP_DB=WormBase Gene ID /WP=CE01865 /GEN=ptr-6 /TR=Q09938 /GB=AAA68302.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 33      6grp_highest_nonorm > 80      6grp_total > 20      4grp_total > 57      6grp_highest_sub > 02_03      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 291
1 2 3 4 range
A 101.6
(-1.9)
P
168.2
(0.3)
P
248.2
(3)
P
67.9
(-3)
A
180
B 79.5
(-2.1)
P
192.5
(2.7)
P
198.4
(3)
P
59.8
(-3)
A
139
C 140.5
(-0.6)
P
233.6
(1.3)
P
315.8
(3)
P
24.6
(-3)
A
291
avr 107.2
(-1.3)
198.1
(1.3)
254.1
(3)
50.8
(-3)
203

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 290
1 2 3 4 5 6 range
A 145.8
(-1.1)
P
295.9
(3)
P
282.7
(2.6)
P
203.4
(0.5)
P
174.3
(-0.3)
P
74.2
(-3)
P
222
B 125.8
(-1.9)
P
352.7
(3)
P
290.9
(1.7)
P
174.1
(-0.8)
P
219.9
(0.1)
P
73.3
(-3)
P
279
C 153.8
(-0.9)
P
320.6
(3)
P
188.3
(-0.1)
P
229.6
(0.9)
P
145
(-1.1)
P
62.4
(-3)
P
258
avr 141.8
(-1.3)
323.1
(3)
254
(1.4)
202.4
(0.1)
179.7
(-0.4)
70
(-3)
253
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 37
(-0)
P
36.5
(-0.1)
P
64.9
(3)
P
9.9
(-3)
A
55
B 25.3
(-0.8)
P
47.6
(3)
P
46
(2.7)
P
12.7
(-3)
A
35
C 46.5
(-0.6)
P
67.2
(0.6)
P
110.1
(3)
P
4.1
(-3)
A
106
avr 36.3
(-0.5)
50.4
(0.8)
73.7
(3)
8.9
(-3)
65

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 99
1 2 3 4 5 6 range
A 26.9
(-2.4)
P
105.2
(3)
P
61.6
(-0)
P
51.6
(-0.7)
P
52.6
(-0.6)
P
18.1
(-3)
P
87
B 43.8
(-1.9)
P
117.4
(3)
P
70.6
(-0.1)
P
46.1
(-1.7)
P
89.4
(1.1)
P
27.3
(-3)
P
90
C 57
(-0.2)
P
97.8
(3)
P
47.9
(-0.9)
P
46.2
(-1)
P
46.9
(-1)
P
20.9
(-3)
P
77
avr 42.6
(-1.5)
106.8
(3)
60
(-0.3)
48
(-1.2)
63
(-0.1)
22.1
(-3)
85
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188240_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5119
Sequence Type Exemplar sequence
Representative Public ID C54A12.1 NCBI
Target Description C54A12.1 /REP_DB=WormBase Gene ID /WP=CE01865 /GEN=ptr-6 /TR=Q09938 /GB=AAA68302.1 /SUBMIT=ST.LOUIS /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_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:5242538-5247542(-) 97.97 100.0
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:188240_AT
cagagtcgagcaatcgccgatcagttgaatgtgatcttaagttcaacaatcacaaatgac
acgctggcaatgttttgtatgttctgtgtagctctcatcttcattccaaatccaatttgt
gcacttttcattacatttgcgatggttactattgatattggtgtaattggatttttatca
ttatggagtgttaagctggatccgatttcaatgattacaattattatgtccattggattt
tcaattgaattttccgctcatattactcatggatttgttagtaatgatagtaatctgtcg
gcttttgatcgatgcgtagatgctatggaaaagttggcttggccagtggtccatg


BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position
Strandedness
CAGAGTCGAGCAATCGCCGATCAGT 637 205 2440 Antisense
AATGACACGCTGGCAATGTTTTGTA 603 165 2494 Antisense
TGTATGTTCTGTGTAGCTCTCATCT 260 561 2515 Antisense
CTCTCATCTTCATTCCAAATCCAAT 74 231 2531 Antisense
AAATCCAATTTGTGCACTTTTCATT 666 117 2547 Antisense
GTGCACTTTTCATTACATTTGCGAT 396 481 2558 Antisense
GGAGTGTTAAGCTGGATCCGATTTC 495 515 2624 Antisense
TGAATTTTCCGCTCATATTACTCAT 23 571 2685 Antisense
GATAGTAATCTGTCGGCTTTTGATC 418 425 2725 Antisense
GGCTTTTGATCGATGCGTAGATGCT 126 513 2739 Antisense
AAGTTGGCTTGGCCAGTGGTCCATG 351 155 2770 Antisense
Sequence Source Affymetrix Proprietary Database