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[193732_at] glutamate-gated chloride channel protein

Description F25F8.2 /REP_DB=WormBase Gene ID /WP=CE09636 /GEN=glc-2 /TR=Q17328 /GB=AAB42252.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=glutamate-gated chloride channel protein
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 07      4grp_highest_8_8 > 51      4grp_high_8_8 > 32      6grp_highest_nonorm > 60      6grp_total > 06      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 11      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 915
1 2 3 4 range
A 1101.5
(3)
P 		451
(-1.9)
P 		311.1
(-3)
P 		424
(-2.1)
P 		790
B 1226.2
(3)
P 		375.4
(-2.7)
P 		322.8
(-3)
P 		442.9
(-2.2)
P 		903
C 1087.4
(3)
P 		452.8
(-2.1)
P 		340.8
(-3)
P 		368
(-2.8)
P 		747
avr 1138.4
(3) 		426.4
(-2.3) 		324.9
(-3) 		411.6
(-2.4) 		814

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 682
1 2 3 4 5 6 range
A 772.9
(3)
P 		403
(-0.3)
P 		205.2
(-2)
P 		205.9
(-2)
P 		248.6
(-1.6)
P 		91.1
(-3)
P 		682
B 493.3
(3)
P 		298.6
(-0.6)
P 		292.1
(-0.7)
P 		244.8
(-1.6)
P 		221.2
(-2)
P 		168.5
(-3)
P 		325
C 661.7
(3)
P 		301.2
(-1.5)
P 		269.2
(-1.9)
P 		211.1
(-2.6)
P 		217.7
(-2.6)
P 		181.8
(-3)
P 		480
avr 642.6
(3) 		334.3
(-0.7) 		255.5
(-1.7) 		220.6
(-2.1) 		229.2
(-2) 		147.1
(-3) 		496
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 339
1 2 3 4 range
A 401.1
(3)
P 		97.9
(-2.4)
P 		81.3
(-2.7)
P 		62.1
(-3)
P 		339
B 391
(3)
P 		92.7
(-2.7)
P 		74.8
(-3)
P 		94.4
(-2.6)
P 		316
C 360
(3)
P 		130.2
(-1.6)
P 		118.8
(-1.9)
P 		62.1
(-3)
P 		298
avr 384
(3) 		106.9
(-2.3) 		91.6
(-2.6) 		72.9
(-3) 		311

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 223
1 2 3 4 5 6 range
A 142.5
(3)
P 		143.3
(3)
P 		44.7
(-1.9)
P 		52.2
(-1.5)
P 		75
(-0.4)
P 		22.2
(-3)
P 		121
B 171.6
(3)
P 		99.4
(-1)
P 		70.9
(-2.6)
P 		64.8
(-2.9)
P 		89.9
(-1.5)
P 		62.9
(-3)
P 		109
C 245.2
(3)
P 		91.9
(-1.5)
P 		68.5
(-2.2)
P 		42.5
(-3)
P 		70.4
(-2.2)
P 		60.9
(-2.5)
P 		203
avr 186.4
(3) 		111.5
(-0.3) 		61.4
(-2.4) 		53.2
(-2.8) 		78.4
(-1.7) 		48.7
(-3) 		138
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193732_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1879
Sequence Type Exemplar sequence
Representative Public ID F25F8.2 NCBI
Target Description F25F8.2 /REP_DB=WormBase Gene ID /WP=CE09636 /GEN=glc-2 /TR=Q17328 /GB=AAB42252.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=glutamate-gated chloride channel protein
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_059069(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059069 NCBI Caenorhabditis elegans Glutamate-gated ChLoride channel family member (glc-2) (glc-2) mRNA, complete cds. 11/11 None
SNAP00000002866 ENSEMBL cdna:SNAP chromosome:CEL140:I:4885188:4887897:-1 11/11 None
GENEFINDER00000002870 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4885188:4887942:-1 11/11 None
F25F8.2 ENSEMBL cdna:known chromosome:CEL140:I:4885047:4887955:-1 gene:F25F8.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:4885187-4887942(-) 100.0 100.0
Public Domain and Genome References
Gene Title glutamate-gated chloride channel protein
Gene Symbol glc-2
Ensembl F25F8.2
Entrez Gene 172103 Entrez gene
SwissProt Q17328 EMBL-EBI
WormBase CE09636 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 AAB42252 Glutamate-gated chloride channel protein 2 [Caenorhabditis elegans] ref|NP_491470.1| Glutamate-gated ChLoride channel family member (glc-2) [Caenorhabditis elegans] gb|AAA50786.1| avermectin-sensitive glutamate-gated chloride channel GluCl beta prf||2021414B Glu-gated Cl channel:ISOTYPE=beta 0.0
blast AAO34107 avermectin-sensitive glutamate-gated chloride channel GluCl beta [synthetic construct] 0.0
blast CAE73122 Hypothetical protein CBG20504 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.1E-27
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.2E-71
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.1E-27
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.2E-71
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491470.1 4 247-269,276-295,310-332,403-425
F25F8.2 4 247-269,276-295,310-332,403-425
SNAP00000002866 4 232-254,261-280,295-317,388-410
GENEFINDER00000002870 4 247-269,276-295,310-332,403-425
Sequence
Target Sequence 
>C. ELEGANS:193732_AT
ggatgtctccgaatgcaacttttgttcaaacggcaattcagttattacttggtacaactg
tatgctccaaccactatgattgtgattgtctcatgggtttcattttggattgatcttcat
tcaactgctggacgtgtcgctttaggagtcactacgcttcttacaatgactacaatgcaa
tctgcaatcaacgccaagcttccaccagttagctacgtaaaagttgtggatgtctggctt
ggagcgtgccaaacatttgtattcggagcacttctggaatacgcatttgtcagttatcaa
gatagtgtccggcaaaatgacaggtcaagagagaaagctgcaaggaaggcgcagagaagg
agagaaaagttggaaatggtggatgcagaagtctatcagccaccgtgcacctgtcatact
ttcgaagcccgcgagacattccgtgacaaagtccgccgttacttcacaaaaccagattat
ctaccggcaaaaattgatttctatgccagatttgtcgtcccacttgcctttctcgctttc
aatgttatcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATGTCTCCGAATGCAACTTTTGT 185 515 709 Antisense
CATTCAACTGCTGGACGTGTCGCTT 186 215 826 Antisense
GTCGCTTTAGGAGTCACTACGCTTC 422 473 844 Antisense
GCAATCTGCAATCAACGCCAAGCTT 254 319 885 Antisense
GTGGATGTCTGGCTTGGAGCGTGCC 600 489 934 Antisense
TGCAGAAGTCTATCAGCCACCGTGC 342 577 1092 Antisense
ATACTTTCGAAGCCCGCGAGACATT 178 25 1124 Antisense
ACATTCCGTGACAAAGTCCGCCGTT 9 105 1144 Antisense
TCCGCCGTTACTTCACAAAACCAGA 299 597 1160 Antisense
TTTCTATGCCAGATTTGTCGTCCCA 8 673 1206 Antisense
CCTTTCTCGCTTTCAATGTTATCTA 690 267 1235 Antisense
Sequence Source Affymetrix Proprietary Database