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[192360_at] gamma-aminobutyric acid receptor

Description F11H8.2 /REP_DB=WormBase Gene ID /WP=CE04375 /TR=Q19358 /GB=AAA81158.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=gamma-aminobutyric acid receptor
Cluster 6grp_high1_10_10 > 15      6grp_total > 05      4grp_total > 21      6grp_high1_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 250
1 2 3 4 range
A 206.9
(-0.7)
A 		263.8
(0.8)
A 		117.1
(-3)
A 		351.4
(3)
P 		234
B 356.5
(3)
P 		232.8
(-0.9)
A 		166.7
(-3)
A 		323
(1.9)
P 		190
C 344.2
(2.4)
P 		200
(-1.2)
A 		128.6
(-3)
A 		367.4
(3)
P 		239
avr 302.5
(1.7) 		232.2
(-0.3) 		137.5
(-3) 		347.3
(3) 		210

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 317
1 2 3 4 5 6 range
A 368.8
(3)
P 		277.6
(0.7)
P 		168.6
(-2.1)
P 		131.4
(-3)
A 		250.2
(0)
P 		170.8
(-2)
A 		237
B 448
(3)
P 		428.8
(2.6)
P 		226
(-1.7)
A 		273.6
(-0.7)
P 		230
(-1.6)
P 		165.2
(-3)
P 		283
C 303.1
(0.8)
M 		390.8
(3)
P 		202.7
(-1.8)
P 		153.6
(-3)
P 		246.4
(-0.7)
P 		199
(-1.9)
P 		237
avr 373.3
(3) 		365.7
(2.8) 		199.1
(-2.4) 		186.2
(-2.8) 		242.2
(-1) 		178.3
(-3) 		195
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 75.3
(3)
A 		57.3
(0.6)
A 		30.6
(-3)
A 		51.4
(-0.2)
P 		45
B 113.7
(3)
P 		57.5
(-1.5)
A 		38.6
(-3)
A 		68.8
(-0.6)
P 		75
C 114
(3)
P 		57.5
(-1.9)
A 		44.8
(-3)
A 		61.9
(-1.5)
P 		69
avr 101
(3) 		57.4
(-1.2) 		38
(-3) 		60.7
(-0.8) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 125
1 2 3 4 5 6 range
A 68
(0.2)
P 		98.7
(3)
P 		36.7
(-2.7)
P 		33.3
(-3)
A 		75.5
(0.9)
P 		41.6
(-2.2)
A 		65
B 155.9
(3)
P 		142.7
(2.2)
P 		54.9
(-3)
A 		72.5
(-2)
P 		93.4
(-0.7)
P 		61.6
(-2.6)
P 		101
C 112.3
(2.5)
M 		119.3
(3)
P 		51.6
(-1.6)
P 		30.9
(-3)
P 		79.7
(0.3)
P 		66.6
(-0.6)
P 		88
avr 112.1
(2.3) 		120.2
(3) 		47.7
(-2.8) 		45.6
(-3) 		82.9
(0) 		56.6
(-2.1) 		75
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192360_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7533
Sequence Type Exemplar sequence
Representative Public ID F11H8.2 NCBI
Target Description F11H8.2 /REP_DB=WormBase Gene ID /WP=CE04375 /TR=Q19358 /GB=AAA81158.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=gamma-aminobutyric acid receptor
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_066131(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066131 NCBI Caenorhabditis elegans F11H8.2 (F11H8.2) mRNA, complete cds. 11/11 None
GENEFINDER00000017881 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7009518:7019333:1 11/11 None
F11H8.2 ENSEMBL cdna:known chromosome:CEL140:III:7009174:7019504:1 gene:F11H8.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000017875 6/11 Cross Hyb Matching Probes None
SNAP00000017876 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:7014024-7019330(+) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-aminobutyric acid receptor
Ensembl F11H8.2
Entrez Gene 3565717 Entrez gene
SwissProt Q19358 EMBL-EBI
WormBase CE36534 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.18420.1.S1_AT similar to Glycine receptor alpha-2 chain precursor cfa
HG-U133_PLUS_2:207462_AT glycine receptor, alpha 2 hs
HG-U133A:207462_AT glycine receptor, alpha 2 hs
HG-FOCUS:207462_AT glycine receptor, alpha 2 hs
HG-U133A_2:207462_AT glycine receptor, alpha 2 hs
HG-U95AV2:34554_AT glycine receptor, alpha 2 hs
HUGENEFL:X52008_AT glycine receptor, alpha 2 hs
U133_X3P:G4504020_3P_AT glycine receptor, alpha 2 hs
HG-U95C:66488_AT glycine receptor, alpha 2 hs
MOE430B:1434098_AT glycine receptor, alpha 2 subunit mm
MOUSE430_2:1434098_AT glycine receptor, alpha 2 subunit mm
MOE430B:1443351_AT Glycine receptor, alpha 2 subunit, mRNA (cDNA clone MGC:67503 IMAGE:5708257) mm
MOUSE430_2:1443351_AT Glycine receptor, alpha 2 subunit, mRNA (cDNA clone MGC:67503 IMAGE:5708257) mm
RN-U34:X57281_AT glycine receptor, alpha 2 subunit rn
RG-U34A:X57281_AT glycine receptor, alpha 2 subunit rn
RAE230A:1371153_A_AT glycine receptor, alpha 2 subunit rn
RAT230_2:1371153_A_AT glycine receptor, alpha 2 subunit rn
RAE230A:1387696_A_AT glycine receptor, alpha 2 subunit rn
RAT230_2:1387696_A_AT glycine receptor, alpha 2 subunit rn
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
5216 ion channel 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 AAA81158 Hypothetical protein F11H8.2 [Caenorhabditis elegans] ref|NP_498532.3| F11H8.2 [Caenorhabditis elegans] 0.0
blast CAE70064 Hypothetical protein CBG16500 [Caenorhabditis briggsae] 0.0
blast CAE70064 Hypothetical protein CBG16500 [Caenorhabditis briggsae] 1.0E-174
blast CAC42346 Hypothetical protein T21C12.1b [Caenorhabditis elegans] ref|NP_001022782.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42382.1| ionotropic GABA receptor subunit UNC-49A [Caenorhabditis elegans] 1.0E-102
blast CAC42346 Hypothetical protein T21C12.1b [Caenorhabditis elegans] ref|NP_001022782.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42382.1| ionotropic GABA receptor subunit UNC-49A [Caenorhabditis elegans] 1.0E-101
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.7E-36
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-74
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.7E-36
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-74
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498532.3 4 259-281,288-307,322-344,435-457
F11H8.2 4 259-281,288-307,322-344,435-457
GENEFINDER00000017881 4 239-261,268-287,302-324,434-456
Sequence
Target Sequence 
>C. ELEGANS:192360_AT
atttcccatcttcactgattgtcgtgatatcatgggtgtcattttggttgaatcgagaag
cagttcaagctagagttgctattggagtaacaactgtgttaaccatgacaactctgatga
caagtaccaatgcttcccttccaaaagtttcatacgtaaaatctcttgatgtttttcttg
gagtttgtttttttattgtatttgcctcacttttggagtacgcagcaattggatatttga
tgaagcggaatcgaagtgtacctgctgcatcaccggttcaatattatgaaacagaggaat
ttttcgaaattcaatgtcacccgaaatttgttagaggggctattaactactgtgatggtg
tgctgaaacgagaagccagcaggaaaaagagtaggaatcgacgtgatagctctatgaaaa
actatcaaaataataacattcatcatcgaccatcggatggtcacgtagatcaacggatac
ctcttctatcaatggttccgatgcctcctattccattcaaaccacagaatggagcatggg
gaaaagtcgatctattctctcgttttgcatttcccatcttctttgtaatat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTCCCATCTTCACTGATTGTCGT 68 17 713 Antisense
ATGACAAGTACCAATGCTTCCCTTC 520 43 829 Antisense
GCTTCCCTTCCAAAAGTTTCATACG 411 295 844 Antisense
TTGCCTCACTTTTGGAGTACGCAGC 75 701 914 Antisense
GGAATCGAAGTGTACCTGCTGCATC 385 533 959 Antisense
TGCTGCATCACCGGTTCAATATTAT 129 583 975 Antisense
ATAACATTCATCATCGACCATCGGA 478 25 1145 Antisense
GATCAACGGATACCTCTTCTATCAA 25 423 1180 Antisense
TTCTATCAATGGTTCCGATGCCTCC 600 689 1196 Antisense
GGAAAAGTCGATCTATTCTCTCGTT 184 529 1252 Antisense
GCATTTCCCATCTTCTTTGTAATAT 671 307 1279 Antisense
Sequence Source Affymetrix Proprietary Database