[Home] | [Total List]

[188390_at]

Description F56C11.2 /REP_DB=WormBase Gene ID /WP=CE17902 /GEN=ptr-11 /TR=O44978 /GB=AAB97556.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 27      6grp_high1_10_10 > 62      4grp_highest_8_8 > 02      4grp_high_8_8 > 46      6grp_highest_nonorm > 62      6grp_total > 72      4grp_total > 49      6grp_highest_sub > 03_04      6grp_cgc > 75      6grp_high1_sub > 03      6grp_cgc_sub > 03_04      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 744
1 2 3 4 range
A 181.4
(-3)
P 		764.5
(2.4)
P 		825.7
(3)
P 		233.9
(-2.5)
P 		644
B 184.4
(-3)
P 		714.6
(2.5)
P 		759.3
(3)
P 		339.1
(-1.4)
P 		575
C 157.6
(-3)
P 		646.3
(0.9)
P 		901.8
(3)
P 		201.8
(-2.6)
P 		744
avr 174.5
(-3) 		708.5
(1.9) 		828.9
(3) 		258.3
(-2.2) 		654

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 491
1 2 3 4 5 6 range
A 276.8
(-3)
P 		496.3
(0.9)
P 		610.9
(3)
P 		543.3
(1.8)
P 		533.3
(1.6)
P 		410.1
(-0.6)
P 		334
B 393
(-3)
P 		597.6
(3)
P 		546
(1.5)
P 		590.5
(2.8)
P 		539.6
(1.3)
P 		399.5
(-2.8)
P 		205
C 339.4
(-3)
P 		452.3
(-1.4)
P 		768
(3)
P 		436.8
(-1.6)
P 		697.4
(2)
P 		429.7
(-1.7)
P 		429
avr 336.4
(-3) 		515.4
(0.5) 		641.6
(3) 		523.5
(0.7) 		590.1
(2) 		413.1
(-1.5) 		305
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 280
1 2 3 4 range
A 66.1
(-1.9)
P 		165.9
(1.3)
P 		215.9
(3)
P 		34.2
(-3)
P 		182
B 58.8
(-3)
P 		176.5
(3)
P 		176
(3)
P 		72.3
(-2.3)
P 		118
C 52.2
(-2.6)
P 		185.8
(0.2)
P 		314.3
(3)
P 		34
(-3)
P 		280
avr 59
(-2.6) 		176.1
(1.1) 		235.4
(3) 		46.8
(-3) 		189

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 175
1 2 3 4 5 6 range
A 51
(-3)
P 		176.5
(3)
P 		133
(0.9)
P 		137.8
(1.1)
P 		160.9
(2.3)
P 		99.8
(-0.7)
P 		126
B 136.7
(-2.7)
P 		198.9
(1.6)
P 		132.6
(-3)
P 		156.4
(-1.4)
P 		219.2
(3)
P 		149
(-1.9)
P 		87
C 125.8
(-1.3)
P 		138
(-0.8)
P 		195.5
(1.7)
P 		87.8
(-3)
P 		225.7
(3)
P 		143.8
(-0.6)
P 		138
avr 104.5
(-3) 		171.1
(1.1) 		153.7
(0) 		127.3
(-1.6) 		201.9
(3) 		130.9
(-1.4) 		97
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188390_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2551
Sequence Type Exemplar sequence
Representative Public ID F56C11.2 NCBI
Target Description F56C11.2 /REP_DB=WormBase Gene ID /WP=CE17902 /GEN=ptr-11 /TR=O44978 /GB=AAB97556.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058286(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058286 NCBI Caenorhabditis elegans PaTched Related family member (ptr-11) (ptr-11) mRNA, complete cds. 11/11 None
SNAP00000010368 ENSEMBL cdna:SNAP chromosome:CEL140:I:160404:166816:-1 11/11 None
GENEFINDER00000010377 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:160404:166816:-1 11/11 None
F56C11.2 ENSEMBL cdna:known chromosome:CEL140:I:160172:166819:-1 gene:F56C11.2 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
chrI:160403-166816(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-11
Ensembl F56C11.2
Entrez Gene 171609 Entrez gene
SwissProt O44978 EMBL-EBI
WormBase CE17902 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 AAB97556 Patched related family protein 11 [Caenorhabditis elegans] ref|NP_490687.1| PaTched Related family member (ptr-11) [Caenorhabditis elegans] 0.0
blast CAE61284 Hypothetical protein CBG05104 [Caenorhabditis briggsae] 0.0
blast CAA87375 Hypothetical protein K07C10.1 [Caenorhabditis elegans] ref|NP_496392.1| PaTched Related family member (ptr-13) [Caenorhabditis elegans] 1.0E-110
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_490687.1 11 15-37,236-258,268-290,339-361,376-398,433-455,640-659,666-688,698-717,741-763,767-789
F56C11.2 11 15-37,236-258,268-290,339-361,376-398,433-455,640-659,666-688,698-717,741-763,767-789
SNAP00000010368 11 15-37,236-258,268-290,339-361,376-398,433-455,640-659,666-688,698-717,741-763,767-789
GENEFINDER00000010377 11 15-37,236-258,268-290,339-361,376-398,433-455,640-659,666-688,698-717,741-763,767-789
Sequence
Target Sequence 
>C. ELEGANS:188390_AT
aagtcaattcaacgctacactctttgactgtgactctgcaattctcagtatcatcctgac
tgttggcactgacttaattggatcgattgcggttacggtagtctgtatggcaatcgtttg
ttttgtgtttattgcaaattttaatgcagttgctgtgattacatctgttattgcaagtat
ctgttatgttctcgtcggtggtctctccctttggggtgccgacctggacccggtaatcca
agtggacgtccttctcgccacgggattctcggtcgactacaccgctcacgtggcctacaa
cttttttcgtgcacgtggcactccacaagaacgtgtctacagtagtctggcagaaatggc
aatgccaatgtgtgaagccggactgtcgacattcctatgcatgcttccgttgatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGTCAATTCAACGCTACACTCTTT 425 155 1857 Antisense
TACACTCTTTGACTGTGACTCTGCA 124 643 1872 Antisense
GTATCATCCTGACTGTTGGCACTGA 691 453 1904 Antisense
AGTATCTGTTATGTTCTCGTCGGTG 394 63 2032 Antisense
CGACCTGGACCCGGTAATCCAAGTG 349 245 2076 Antisense
GTAATCCAAGTGGACGTCCTTCTCG 145 463 2089 Antisense
CTCACGTGGCCTACAACTTTTTTCG 134 229 2141 Antisense
ACAACTTTTTTCGTGCACGTGGCAC 337 113 2153 Antisense
GTGGCACTCCACAAGAACGTGTCTA 513 491 2171 Antisense
TGAAGCCGGACTGTCGACATTCCTA 145 575 2229 Antisense
ATTCCTATGCATGCTTCCGTTGATT 140 9 2247 Antisense
Sequence Source Affymetrix Proprietary Database