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[192628_at] ligand-gated ion channel

Description F11A5.10 /REP_DB=WormBase Gene ID /WP=CE24896 /GEN=glc-1 /TR=O17793 /GB=CAB07361.2 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ion channel
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 83      4grp_highest_8_8 > 54      4grp_high_8_8 > 09      6grp_highest_nonorm > 63      6grp_total > 74      4grp_total > 23      6grp_cgc > 76      6grp_high1_sub > 04      6grp_cgc_sub > 03_04      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 514
1 2 3 4 range
A 858.4
(3)
P 		472.3
(-1.7)
P 		367.9
(-3)
P 		766.8
(1.9)
P 		491
B 846.8
(2.8)
P 		445
(-2.1)
P 		373.6
(-3)
P 		865.8
(3)
P 		492
C 882.1
(3)
P 		511.3
(-1.5)
P 		392.7
(-3)
P 		741.7
(1.3)
P 		489
avr 862.4
(3) 		476.2
(-1.8) 		378.1
(-3) 		791.4
(2.1) 		484

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 690
1 2 3 4 5 6 range
A 267.5
(-2.9)
P 		257.7
(-3)
P 		574.9
(1.8)
P 		624.7
(2.6)
P 		652.2
(3)
P 		561.6
(1.6)
P 		395
B 261.6
(-3)
P 		322.7
(-2.5)
P 		947.6
(3)
P 		778
(1.5)
P 		656
(0.4)
P 		667.7
(0.6)
P 		686
C 278.2
(-3)
P 		387.8
(-1.4)
P 		523.6
(0.5)
P 		700.6
(3)
P 		576.3
(1.2)
P 		686.1
(2.8)
P 		422
avr 269.1
(-3) 		322.7
(-2.3) 		682
(2.7) 		701.1
(3) 		628.2
(2) 		638.5
(2.1) 		432
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 226
1 2 3 4 range
A 312.5
(3)
P 		102.5
(-2.8)
P 		96.2
(-3)
P 		112.2
(-2.6)
P 		216
B 270
(3)
P 		109.9
(-2.2)
P 		86.6
(-3)
P 		184.5
(0.2)
P 		183
C 292
(3)
P 		147
(-2.2)
P 		136.9
(-2.6)
P 		125.1
(-3)
P 		167
avr 291.5
(3) 		119.8
(-2.6) 		106.6
(-3) 		140.6
(-1.9) 		185

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 217
1 2 3 4 5 6 range
A 49.3
(-3)
P 		91.6
(-1.3)
P 		125.2
(0.1)
P 		158.4
(1.4)
P 		196.8
(3)
P 		136.7
(0.6)
P 		148
B 91
(-3)
P 		107.4
(-2.4)
P 		230.1
(1.8)
P 		206.1
(0.9)
P 		266.5
(3)
P 		249
(2.4)
P 		176
C 103.1
(-3)
P 		118.3
(-2.3)
P 		133.3
(-1.6)
P 		140.9
(-1.2)
P 		186.5
(1)
P 		229.7
(3)
P 		127
avr 81.1
(-3) 		105.8
(-1.9) 		162.9
(0.6) 		168.5
(0.9) 		216.6
(3) 		205.1
(2.5) 		136
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192628_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14690
Sequence Type Exemplar sequence
Representative Public ID F11A5.10 NCBI
Target Description F11A5.10 /REP_DB=WormBase Gene ID /WP=CE24896 /GEN=glc-1 /TR=O17793 /GB=CAB07361.2 /SUBMIT=HINXTON /CHR=5 /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_074689(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074689 NCBI Caenorhabditis elegans Glutamate-gated ChLoride channel family member (glc-1) (glc-1) mRNA, complete cds. 11/11 None
SNAP00000027003 ENSEMBL cdna:SNAP chromosome:CEL140:V:16222293:16224413:1 11/11 None
GENEFINDER00000027015 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16222293:16224413:1 11/11 None
F11A5.10 ENSEMBL cdna:known chromosome:CEL140:V:16222192:16224501:1 gene:F11A5.10 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
chrV:16222292-16224413(+) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ion channel
Gene Symbol glc-1
Ensembl F11A5.10
Entrez Gene 180086 Entrez gene
SwissProt O17793 EMBL-EBI
WormBase CE24896 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 CAB07361 Hypothetical protein F11A5.10 [Caenorhabditis elegans] ref|NP_507090.1| Glutamate-gated ChLoride channel family member (glc-1) [Caenorhabditis elegans] gb|AAO34106.1| avermectin-sensitive glutamate-gated chloride channel GluCl alpha [synthetic construct] gb|AAA50785.1| avermectin-sensitive glutamate-gated chloride channel GluCl alpha prf||2021414A Glu-gated Cl channel:ISOTYPE=alpha 0.0
blast AAP13536 avermectin-sensitive chloride channel GluCl alpha/yellow fluorescent protein fusion [synthetic construct] 0.0
blast CAB03329 Hypothetical protein R11G10.1b [Caenorhabditis elegans] ref|NP_001024077.1| altered AVeRmectin sensitivity family member (avr-15) [Caenorhabditis elegans] 1.0E-177
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.4E-26
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.6E-76
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_507090.1 4 276-298,305-324,339-361,433-455
F11A5.10 4 276-298,305-324,339-361,433-455
SNAP00000027003 4 276-298,305-324,339-361,433-455
GENEFINDER00000027015 4 276-298,305-324,339-361,433-455
Sequence
Target Sequence 
>C. ELEGANS:192628_AT
cactggcatttattcctgtttgcgaactactattcagttaaagagagagttcagttttta
ccttctccaactctacatcccgtcatgcatgctagtcatcgtatcctgggtttcattttg
gtttgatcgaactgcaatcccggctcgtgtcaccctcggagtcaccacgctgcttacaat
gacagctcaatcagccggtatcaattcacaactacctccagtttcctatatcaaggcgat
tgatgtctggattggtgcatgtatgacattcattttctgcgcgttgttggagtttgcatt
ggtaaatcatatagctaacaagcagggtgttgagagaaaagctcgaactgaaagagagaa
agctgaaattccacttcttcaaaatttgcacaatgatgttcccacaaaggttttcaatca
agaggaaaaagtaaggacagttccactgaatcgccggcaaatgaatagcttcttgaattt
gctcgagacaaaaaccgaatggaatgacatatcaaaacgagtcgatcttatttctcgagc
cc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACTGGCATTTATTCCTGTTTGCGA 296 199 783 Antisense
TGGTTTGATCGAACTGCAATCCCGG 503 551 901 Antisense
GAGTCACCACGCTGCTTACAATGAC 120 401 941 Antisense
ATGACAGCTCAATCAGCCGGTATCA 390 45 961 Antisense
GGTATCAATTCACAACTACCTCCAG 254 503 979 Antisense
CTACCTCCAGTTTCCTATATCAAGG 285 225 994 Antisense
GGCGATTGATGTCTGGATTGGTGCA 636 541 1017 Antisense
GATGTTCCCACAAAGGTTTTCAATC 295 401 1177 Antisense
AAGGACAGTTCCACTGAATCGCCGG 301 161 1215 Antisense
ATAGCTTCTTGAATTTGCTCGAGAC 673 21 1247 Antisense
CGAGTCGATCTTATTTCTCGAGCCC 661 249 1300 Antisense
Sequence Source Affymetrix Proprietary Database