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[193505_at] ligand-gated ionic channel subunit

Description ZC317.3 /REP_DB=WormBase Gene ID /WP=CE28159 /GEN=glc-3 /TR=Q23074 /GB=AAB04959.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel subunit
Cluster 6grp_highest_10_10 > 50      6grp_high1_10_10 > 16      4grp_highest_8_8 > 60      4grp_high_8_8 > 25      6grp_highest_nonorm > 80      6grp_total > 06      4grp_total > 38      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 197
1 2 3 4 range
A 253.9
(3)
P 		113.7
(-2.1)
P 		88.5
(-3)
P 		150
(-0.8)
P 		165
B 258.1
(3)
P 		148.2
(-1.5)
P 		111.8
(-3)
P 		203.2
(0.7)
P 		146
C 282.6
(3)
P 		130.1
(-1.6)
P 		85.4
(-3)
P 		156.2
(-0.8)
P 		197
avr 264.9
(3) 		130.7
(-1.7) 		95.2
(-3) 		169.8
(-0.4) 		170

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 266
1 2 3 4 5 6 range
A 361.1
(3)
P 		195.6
(-0.8)
P 		142.2
(-2)
P 		117.8
(-2.5)
P 		97.1
(-3)
P 		103.2
(-2.9)
P 		264
B 258
(3)
P 		156.1
(-0.8)
P 		128.2
(-1.8)
P 		95.1
(-3)
P 		115.9
(-2.2)
P 		124.2
(-1.9)
P 		163
C 262.9
(2.8)
P 		269.2
(3)
P 		150.2
(-1.3)
P 		147.5
(-1.4)
P 		108.9
(-2.8)
P 		103.9
(-3)
P 		165
avr 294
(3) 		207
(0.2) 		140.2
(-1.9) 		120.1
(-2.6) 		107.3
(-3) 		110.4
(-2.9) 		187
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 92.4
(3)
P 		24.7
(-2.8)
P 		23.1
(-2.9)
P 		22
(-3)
P 		70
B 82.3
(3)
P 		36.6
(-1.9)
P 		25.9
(-3)
P 		43.3
(-1.1)
P 		56
C 93.6
(3)
P 		37.4
(-2)
P 		29.8
(-2.7)
P 		26.3
(-3)
P 		67
avr 89.4
(3) 		32.9
(-2.4) 		26.3
(-3) 		30.5
(-2.6) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 72
1 2 3 4 5 6 range
A 66.6
(2.6)
P 		69.6
(3)
P 		31
(-2.2)
P 		29.9
(-2.4)
P 		29.3
(-2.4)
P 		25.1
(-3)
P 		45
B 89.8
(3)
P 		52
(-0.5)
P 		31.1
(-2.5)
P 		25.2
(-3)
P 		47.1
(-1)
P 		46.3
(-1)
P 		65
C 97.5
(3)
P 		82.1
(1.6)
P 		38.2
(-2.2)
P 		29.7
(-3)
P 		35.2
(-2.5)
P 		34.8
(-2.5)
P 		68
avr 84.6
(3) 		67.9
(1.2) 		33.4
(-2.5) 		28.3
(-3) 		37.2
(-2.1) 		35.4
(-2.2) 		56
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193505_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11524
Sequence Type Exemplar sequence
Representative Public ID ZC317.3 NCBI
Target Description ZC317.3 /REP_DB=WormBase Gene ID /WP=CE28159 /GEN=glc-3 /TR=Q23074 /GB=AAB04959.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel subunit
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_072040(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072040 NCBI Caenorhabditis elegans Glutamate-gated ChLoride channel family member (glc-3) (glc-3) mRNA, complete cds. 9/11 None
SNAP00000026639 ENSEMBL cdna:SNAP chromosome:CEL140:V:5449241:5452498:-1 9/11 None
GENEFINDER00000026646 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5449241:5452836:-1 9/11 None
ZC317.3 ENSEMBL cdna:known chromosome:CEL140:V:5449099:5453527:-1 gene:ZC317.3 9/11 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:5449212-5453240(-) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel subunit
Gene Symbol glc-3
Ensembl ZC317.3
Entrez Gene 178930 Entrez gene
SwissProt Q9U990 EMBL-EBI
WormBase CE28159 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 AAB04959 Glutamate-gated chloride channel protein 3 [Caenorhabditis elegans] emb|CAB51708.1| Glutamate-gated chloride channel subunit [Caenorhabditis elegans] ref|NP_504441.1| Glutamate-gated ChLoride channel family member (glc-3) [Caenorhabditis elegans] 0.0
blast CAE64628 Hypothetical protein CBG09387 [Caenorhabditis briggsae] 0.0
blast AAU95605 glutamate gated chloride channel alpha subunit [Cylicocyclus nassatus] 1.0E-169
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-34
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.6E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 7.8E-70
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-34
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.6E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 7.8E-70
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-34
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.6E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 7.8E-70
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504441.1 4 246-268,275-294,309-331,454-473
ZC317.3 4 246-268,275-294,309-331,454-473
SNAP00000026639 4 229-251,258-277,292-314,437-456
GENEFINDER00000026646 4 239-261,268-287,302-324,447-466
Sequence
Target Sequence 
>C. ELEGANS:193505_AT
gatggttttgtcatgtccgatgcatttacaatactatccaatggatgttcaaacgtgtct
gattgatcttgcctcttacgcatatactgaaaatgatatcgagtatcgatggaagaagac
tgatccagttcaattgaagaaaggactgcattcttcacttccaagttttgaacttaataa
tgtaagcagttttaaaattagaaaaaggttatcttatgcctccggaatcaacgccaaact
tccaccggtctcatacacaaaagcgatcgatgtttggattggcgcctgccttacttttat
ttttggtgctttattagaatttgcatgggtaacttacatatcgtcgaggagtttttataa
acgaaataaaaactgctcaagtcgaaattcactattgatcgaaacaaaacaggcactgat
tattccgaacacagtggtagctcagtttccagagcatcccgaggagtcctatttcctact
ctcttcgtatgtttcaactttgtctactggaccaagtattcacaatatcacgcaccggaa
gcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGGTTTTGTCATGTCCGATGCAT 20 409 480 Antisense
AACGTGTCTGATTGATCTTGCCTCT 669 143 531 Antisense
GATCTTGCCTCTTACGCATATACTG 680 419 544 Antisense
GAAAGGACTGCATTCTTCACTTCCA 457 361 618 Antisense
TTATGCCTCCGGAATCAACGCCAAA 67 681 693 Antisense
TTCCACCGGTCTCATACACAAAAGC 706 695 719 Antisense
GATCGATGTTTGGATTGGCGCCTGC 312 417 744 Antisense
GTAGCTCAGTTTCCAGAGCATCCCG 493 457 916 Antisense
AGCATCCCGAGGAGTCCTATTTCCT 640 75 932 Antisense
TTCCTACTCTCTTCGTATGTTTCAA 595 699 952 Antisense
TCACAATATCACGCACCGGAAGCCA 305 629 999 Antisense
Sequence Source Affymetrix Proprietary Database