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[190663_s_at] ligand-gated ion channel

Description T27E9.9 /REP_DB=WormBase Gene ID /WP=CE24020 /TR=Q9U358 /GB=CAB04879.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=ligand-gated ion channel
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 15      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 70      6grp_total > 15      4grp_total > 46      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 250
1 2 3 4 range
A 434.6
(3)
P 		251.3
(-1.5)
P 		209.7
(-2.5)
P 		191.3
(-3)
P 		243
B 382.5
(3)
P 		243.9
(-1.2)
P 		185
(-3)
P 		231.4
(-1.6)
P 		198
C 357.5
(3)
P 		242.1
(-2)
P 		218.7
(-3)
P 		223.3
(-2.8)
P 		139
avr 391.5
(3) 		245.8
(-1.7) 		204.5
(-3) 		215.3
(-2.7) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 332
1 2 3 4 5 6 range
A 426.6
(3)
P 		389.4
(2.1)
P 		238.4
(-1.5)
P 		207.5
(-2.2)
P 		235.5
(-1.5)
P 		173.3
(-3)
P 		253
B 505.6
(3)
P 		439.8
(1.8)
P 		269.3
(-1.5)
P 		308.2
(-0.7)
P 		211.3
(-2.5)
P 		187.3
(-3)
P 		318
C 341.6
(1.1)
P 		411.6
(3)
P 		192.4
(-3)
P 		265.9
(-1)
P 		246.1
(-1.5)
P 		197.7
(-2.9)
P 		219
avr 424.6
(3) 		413.6
(2.7) 		233.4
(-1.8) 		260.5
(-1.1) 		231
(-1.9) 		186.1
(-3) 		239
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 158.2
(3)
P 		54.5
(-1.8)
P 		54.8
(-1.8)
P 		28
(-3)
P 		130
B 122
(3)
P 		60.2
(-1.7)
P 		42.9
(-3)
P 		49.3
(-2.5)
P 		79
C 118.3
(3)
P 		69.6
(-0.6)
P 		76.2
(-0.1)
P 		37.6
(-3)
P 		81
avr 132.8
(3) 		61.4
(-1.5) 		58
(-1.7) 		38.3
(-3) 		95

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 134
1 2 3 4 5 6 range
A 78.6
(-0.7)
P 		138.5
(3)
P 		51.9
(-2.4)
P 		52.6
(-2.4)
P 		71.1
(-1.2)
P 		42.2
(-3)
P 		96
B 175.9
(3)
P 		146.4
(1.4)
P 		65.4
(-3)
P 		81.6
(-2.1)
P 		85.8
(-1.9)
P 		69.8
(-2.8)
P 		111
C 126.6
(3)
P 		125.6
(2.9)
P 		49
(-3)
P 		53.5
(-2.7)
P 		79.6
(-0.6)
P 		66.2
(-1.7)
P 		78
avr 127
(2.3) 		136.8
(3) 		55.4
(-3) 		62.6
(-2.5) 		78.8
(-1.3) 		59.4
(-2.7) 		81
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190663_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7365
Sequence Type Exemplar sequence
Representative Public ID T27E9.9 NCBI
Target Description T27E9.9 /REP_DB=WormBase Gene ID /WP=CE24020 /TR=Q9U358 /GB=CAB04879.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=ligand-gated ion channel
Cluster Evidence This cluster is supported by a 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_067388(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067388 NCBI Caenorhabditis elegans T27E9.9 (T27E9.9) mRNA, complete cds. 11/11 None
GENEFINDER00000014276 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13480452:13483300:-1 10/11 None
T27E9.9 ENSEMBL cdna:known chromosome:CEL140:III:13480276:13483671:-1 gene:T27E9.9 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
chrIII:13480607-13483636(-) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ion channel
Ensembl T27E9.9
Entrez Gene 176778 Entrez gene
SwissProt Q9U358 EMBL-EBI
WormBase CE24020 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
6811 ion transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
45211 postsynaptic membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4890 GABA-A receptor activity inferred from electronic annotation QuickGO AmiGO
5230 extracellular ligand-gated ion channel activity inferred from electronic annotation QuickGO AmiGO
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04879 Hypothetical protein T27E9.9 [Caenorhabditis elegans] ref|NP_499789.1| T27E9.9 [Caenorhabditis elegans] 0.0
blast CAE69266 Hypothetical protein CBG15319 [Caenorhabditis briggsae] 0.0
blast AAA81730 Hypothetical protein F55D10.5 [Caenorhabditis elegans] ref|NP_508810.2| F55D10.5 [Caenorhabditis elegans] gb|AAW34234.1| acetylcholine-gated chloride channel subunit ACC-3 [Caenorhabditis elegans] 1.0E-96
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-12
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 5.7E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.5E-63
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-12
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.5E-63
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499789.1 4 261-283,295-312,327-349,379-401
T27E9.9 4 261-283,295-312,327-349,379-401
GENEFINDER00000014276 4 234-256,266-285,298-320,387-409
Sequence
Target Sequence 
>C. ELEGANS:190663_S_AT
acagtaccaccgattacgattctcaaagggaacattacactgcccgattatgttcttgtc
gatttctcgtcgagcagtgagcttaggctctaccctcccggaatcttcaacgaactaatc
gccacgttcactttccaacgtctctacgggttctatattctacaggtgtacgtacctgca
tacatttccgttttcatttcatgggtctcttttacacttggcgctgagcaaatcccctcg
aggactactgtcggcgtcaactccttgctggcactcacatttcaattcggagcggtcgtg
aataatctcccaaaaacttctgatgtcaaggcaattgatgtttggattttgagctcaatg
gctttcattttcgcgtcattaattgaactggcagttgttgggtatttgtcgagagatggg
cagcatggaagtattaaatgtcggtgctcctggctgtgcatgaactgcaaagactggacg
gctctgaaaatagatcagatgtcctcaatagtatttccggtcagttttctcgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACAGTACCACCGATTACGATTCTCA 670 91 649 Antisense
TACACTGCCCGATTATGTTCTTGTC 486 643 684 Antisense
GTTCTTGTCGATTTCTCGTCGAGCA 652 443 700 Antisense
AGCAGTGAGCTTAGGCTCTACCCTC 506 77 721 Antisense
CGAACTAATCGCCACGTTCACTTTC 561 249 759 Antisense
TACCTGCATACATTTCCGTTTTCAT 698 649 821 Antisense
ATTTCATGGGTCTCTTTTACACTTG 338 13 844 Antisense
TACACTTGGCGCTGAGCAAATCCCC 179 643 861 Antisense
CAATGGCTTTCATTTTCGCGTCATT 321 183 1004 Antisense
TGCTCCTGGCTGTGCATGAACTGCA 566 581 1093 Antisense
TAGTATTTCCGGTCAGTTTTCTCGC 483 651 1157 Antisense
Sequence Source Affymetrix Proprietary Database