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[192324_at] gamma-aminobutyric-acid receptor

Description C39B10.2 /REP_DB=WormBase Gene ID /WP=CE02158 /TR=Q18518 /GB=CAA90332.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor
Cluster 6grp_total > 04      4grp_total > 54      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 86
1 2 3 4 range
A 68.1
(1.5)
M 		40.8
(-3)
A 		77.6
(3)
P 		70.7
(1.9)
A 		37
B 109.4
(3)
P 		61.5
(-1.2)
P 		41.4
(-3)
P 		55.6
(-1.7)
A 		68
C 99.3
(3)
P 		81.7
(1.6)
P 		71
(0.8)
P 		23.8
(-3)
A 		76
avr 92.3
(3) 		61.3
(-1.4) 		63.3
(-1.1) 		50
(-3) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 112
1 2 3 4 5 6 range
A 139.8
(3)
P 		69.1
(-1.2)
P 		73.6
(-0.9)
P 		68
(-1.3)
P 		77.7
(-0.7)
P 		38.5
(-3)
A 		101
B 56.7
(-0.5)
P 		69.9
(1.6)
P 		64.6
(0.7)
P 		79
(3)
A 		69.9
(1.6)
P 		41.2
(-3)
A 		38
C 93.9
(2.3)
P 		102.4
(3)
P 		55.9
(-0.7)
M 		97.4
(2.6)
P 		47.2
(-1.4)
P 		27.8
(-3)
M 		75
avr 96.8
(3) 		80.5
(1.4) 		64.7
(-0.2) 		81.5
(1.5) 		64.9
(-0.1) 		35.8
(-3) 		61
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31
1 2 3 4 range
A 24.8
(3)
M 		8.8
(-3)
A 		20.3
(1.3)
P 		10.3
(-2.4)
A 		16
B 34.9
(3)
P 		15.2
(-1.7)
P 		9.6
(-3)
P 		11.8
(-2.5)
A 		25
C 32.9
(3)
P 		23.5
(1)
P 		24.7
(1.3)
P 		4
(-3)
A 		29
avr 30.9
(3) 		15.8
(-1.1) 		18.2
(-0.4) 		8.7
(-3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26
1 2 3 4 5 6 range
A 25.8
(3)
P 		24.6
(2.6)
P 		16
(-0.6)
P 		17.3
(-0.1)
P 		23.5
(2.2)
P 		9.4
(-3)
A 		16
B 19.7
(-1)
P 		23.3
(0.6)
P 		15.7
(-2.9)
P 		20.9
(-0.5)
A 		28.4
(3)
P 		15.4
(-3)
A 		13
C 34.8
(3)
P 		31.2
(2.2)
P 		14.2
(-1.8)
M 		19.6
(-0.6)
P 		15.3
(-1.6)
P 		9.3
(-3)
M 		26
avr 26.8
(3) 		26.4
(2.8) 		15.3
(-1.5) 		19.3
(0.1) 		22.4
(1.3) 		11.4
(-3) 		15
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192324_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16465
Sequence Type Exemplar sequence
Representative Public ID C39B10.2 NCBI
Target Description C39B10.2 /REP_DB=WormBase Gene ID /WP=CE02158 /TR=Q18518 /GB=CAA90332.1 /SUBMIT=HINXTON /CHR=X /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_077352(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077352 NCBI Caenorhabditis elegans C39B10.2 (C39B10.2) mRNA, complete cds. 10/11 None
GENEFINDER00000006459 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:10454237:10458370:1 9/11 None
SNAP00000006450 ENSEMBL cdna:SNAP chromosome:CEL140:X:10454599:10457246:1 11/11 None
C39B10.2 ENSEMBL cdna:known chromosome:CEL140:X:10454237:10460269:1 gene:C39B10.2 10/11 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
chrX:10454236-10457246(+) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-aminobutyric-acid receptor
Ensembl C39B10.2
Entrez Gene 183331 Entrez gene
SwissProt Q18518 EMBL-EBI
WormBase CE36632 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 CAA90332 Hypothetical protein C39B10.2 [Caenorhabditis elegans] ref|NP_509753.2| C39B10.2 [Caenorhabditis elegans] 0.0
blast CAE70589 Hypothetical protein CBG17253 [Caenorhabditis briggsae] 0.0
blast CAE70589 Hypothetical protein CBG17253 [Caenorhabditis briggsae] 1.0E-175
blast CAE70589 Hypothetical protein CBG17253 [Caenorhabditis briggsae] 1.0E-164
blast NP_497489 Y39A3B.2 [Caenorhabditis elegans] gb|AAF60513.2| Hypothetical protein Y39A3B.2 [Caenorhabditis elegans] 1.0E-109
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.2E-31
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.5E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 6.0E-58
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.2E-24
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.2E-31
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.9E-51
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509753.2 4 243-265,274-296,306-328,430-452
C39B10.2 4 243-265,274-296,306-328,430-452
SNAP00000006450 3 187-209,218-240,250-272
Sequence
Target Sequence 
>C. ELEGANS:192324_AT
acagaagagcggttcctgctcgcgtcacattaagtttcaccacactggtctctcttacca
ctctgggaaacggacttcgatttggacttccacaagtgagctatgcaaaagccatcgact
tgtggtacggagcgtgtatgttcttcgtcttttgtgcacttttggaatttgcaactataa
atagctacatgcgaaagtcggaaaaatttgatagtatggcaaagaaaatgcaaagtgtgg
tactcactggaagaacaagggactatttggttcgcggcatcaaagagagcatgcggattg
caggaggagcagccggaaacgttgtggacgcactcaacgacgattggtgtacctactcca
cagagaacggacgtaagagcttctccgcaatggtcggagacatttttgaaagagccggca
atgcgatttctcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACAGAAGAGCGGTTCCTGCTCGCGT 328 109 809 Antisense
GCTCGCGTCACATTAAGTTTCACCA 533 299 826 Antisense
TCTCTCTTACCACTCTGGGAAACGG 263 611 857 Antisense
ACGGAGCGTGTATGTTCTTCGTCTT 24 95 935 Antisense
TCTTCGTCTTTTGTGCACTTTTGGA 406 617 950 Antisense
CAAGGGACTATTTGGTTCGCGGCAT 196 183 1064 Antisense
GAGCAGCCGGAAACGTTGTGGACGC 657 389 1115 Antisense
TGGACGCACTCAACGACGATTGGTG 318 547 1133 Antisense
ACGATTGGTGTACCTACTCCACAGA 33 95 1148 Antisense
GTAAGAGCTTCTCCGCAATGGTCGG 688 461 1181 Antisense
AAAGAGCCGGCAATGCGATTTCTCC 492 121 1217 Antisense
Sequence Source Affymetrix Proprietary Database