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[192279_at] gamma-aminobutyric-acid receptor

Description T24D8.1 /REP_DB=WormBase Gene ID /WP=CE05005 /TR=Q22741 /GB=AAA81448.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor
Cluster 6grp_high1_10_10 > 03      4grp_high_8_8 > 26      6grp_total > 25      4grp_total > 38      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 222
1 2 3 4 range
A 278.3
(3)
P 		131.8
(-1.2)
A 		70.1
(-3)
P 		121.7
(-1.5)
P 		208
B 211.7
(3)
P 		158.9
(0.1)
P 		104.1
(-3)
P 		109.8
(-2.7)
M 		108
C 214
(3)
P 		166.9
(1.2)
P 		56.1
(-3)
A 		156.8
(0.8)
P 		158
avr 234.7
(3) 		152.5
(-0.1) 		76.8
(-3) 		129.4
(-1) 		158

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 179
1 2 3 4 5 6 range
A 186.3
(3)
P 		164.2
(2.1)
P 		128.8
(0.7)
P 		37.8
(-3)
A 		85.1
(-1.1)
A 		85.7
(-1.1)
A 		149
B 146.5
(3)
P 		133.4
(2)
P 		122.8
(1.3)
P 		92.2
(-1)
A 		70.5
(-2.5)
M 		64.3
(-3)
P 		82
C 217.1
(3)
P 		153.2
(0.7)
P 		69.8
(-2.3)
A 		65.4
(-2.5)
P 		50.8
(-3)
P 		80.5
(-1.9)
P 		166
avr 183.3
(3) 		150.3
(1.3) 		107.1
(-0.9) 		65.1
(-3) 		68.8
(-2.8) 		76.8
(-2.4) 		118
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 84
1 2 3 4 range
A 101.3
(3)
P 		28.6
(-2.2)
A 		18.3
(-3)
P 		17.8
(-3)
P 		84
B 67.5
(3)
P 		39.2
(-0.9)
P 		24.1
(-2.9)
P 		23.4
(-3)
M 		44
C 70.8
(3)
P 		48
(0.3)
P 		19.6
(-3)
A 		26.4
(-2.2)
P 		51
avr 79.9
(3) 		38.6
(-1.2) 		20.7
(-3) 		22.5
(-2.8) 		59

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 71
1 2 3 4 5 6 range
A 34.3
(0)
P 		58.4
(3)
P 		28
(-0.7)
P 		9.6
(-3)
A 		25.7
(-1)
A 		20.9
(-1.6)
A 		49
B 51
(3)
P 		44.4
(1.5)
P 		29.8
(-1.7)
P 		24.4
(-2.9)
A 		28.6
(-2)
M 		24
(-3)
P 		27
C 80.5
(3)
P 		46.8
(-0)
P 		17.8
(-2.6)
A 		13.1
(-3)
P 		16.5
(-2.7)
P 		27
(-1.8)
P 		67
avr 55.3
(3) 		49.9
(2.2) 		25.2
(-1.6) 		15.7
(-3) 		23.6
(-1.8) 		24
(-1.7) 		40
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192279_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18210
Sequence Type Exemplar sequence
Representative Public ID T24D8.1 NCBI
Target Description T24D8.1 /REP_DB=WormBase Gene ID /WP=CE05005 /TR=Q22741 /GB=AAA81448.1 /SUBMIT=ST.LOUIS /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 Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_076027
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000017742 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:2359643:2362512:1 None
SNAP00000017736 ENSEMBL cdna:SNAP chromosome:CEL140:X:2361139:2362400:1 None
T24D8.1 ENSEMBL cdna:known chromosome:CEL140:X:2360090:2364648:1 gene:T24D8.1 None
NM_076027 NCBI Caenorhabditis elegans T24D8.1 (T24D8.1) mRNA, complete cds. 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:2361138-2362974(+) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-aminobutyric-acid receptor
Ensembl T24D8.1
Entrez Gene 188854 Entrez gene
SwissProt Q22741 EMBL-EBI
WormBase CE31248 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 AAA81448 Hypothetical protein T24D8.1 [Caenorhabditis elegans] ref|NP_508428.2| T24D8.1 [Caenorhabditis elegans] 0.0
blast CAE58888 Hypothetical protein CBG02128 [Caenorhabditis briggsae] 0.0
blast AAA81448 Hypothetical protein T24D8.1 [Caenorhabditis elegans] ref|NP_508428.2| T24D8.1 [Caenorhabditis elegans] 1.0E-166
blast CAE58888 Hypothetical protein CBG02128 [Caenorhabditis briggsae] 1.0E-153
blast CAA86760 Hypothetical protein C09G5.1 [Caenorhabditis elegans] ref|NP_496306.2| GABA/Glycine Receptor family (see gbr) family member (ggr-1) [Caenorhabditis elegans] sp|Q09453|GLRB4_CAEEL Glycine receptor beta-type chain 4 precursor 6.0E-96
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.1E-23
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.7E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.0E-49
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.1E-23
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.0E-49
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.1E-23
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.4E-39
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508428.2 4 246-268,275-292,307-329,471-493
T24D8.1 4 246-268,275-292,307-329,471-493
GENEFINDER00000017742 3 291-313,320-337,352-374
SNAP00000017736 3 170-192,199-216,231-253
Sequence
Target Sequence 
>C. ELEGANS:192279_AT
tgcagacttatgtgcctacagctctaatagttgtgatttcctggtttaatttctggctgg
aaattgactcagctccagcaagagtatcgttgagcattaccactctcctaacaatttcaa
cacaagctaatgcagtgaaacttgcattgccagaagtgagctacatgaaagctatcgacg
tatggatgggatcttgcatggcattcgtattcggtgtcatgatagagtttacaatttgtc
actacgctaagaatttggagatgcttcgtggcgacggacaaccgtcgctgatcgtcgaca
ctgctctctcaacattgttcggagcggcccgagatatagacgatctggtgcgaaaagtgg
ccacgcttgcgacacctacaataggccttccacgaaggcgccactctcgcccgcccgccc
cacaccacgccccacactcccgtcaccctcataccatcgccctactaaagttttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCAGACTTATGTGCCTACAGCTCT 45 577 524 Antisense
GATTTCCTGGTTTAATTTCTGGCTG 454 425 558 Antisense
GTATCGTTGAGCATTACCACTCTCC 181 453 607 Antisense
TTACCACTCTCCTAACAATTTCAAC 19 683 620 Antisense
GCATGGCATTCGTATTCGGTGTCAT 224 311 719 Antisense
TGGAGATGCTTCGTGGCGACGGACA 236 547 779 Antisense
ACTGCTCTCTCAACATTGTTCGGAG 77 99 823 Antisense
GGAGCGGCCCGAGATATAGACGATC 377 517 844 Antisense
TGCGAAAAGTGGCCACGCTTGCGAC 464 583 872 Antisense
CGACACCTACAATAGGCCTTCCACG 405 225 893 Antisense
ATACCATCGCCCTACTAAAGTTTTG 119 21 974 Antisense
Sequence Source Affymetrix Proprietary Database