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[192154_s_at] gamma-aminobutyric-acid receptor

Description F46F3.2 /REP_DB=WormBase Gene ID /WP=CE19873 /TR=P90876 /GB=CAB03114.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 50      4grp_highest_8_8 > 53      4grp_high_8_8 > 09      6grp_highest_nonorm > 61      6grp_total > 41      4grp_total > 23      6grp_highest_sub > 03_04      6grp_high1_sub > 03_04      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 181
1 2 3 4 range
A 361.2
(-0.6)
P 		297.9
(-3)
P 		334.7
(-1.6)
P 		455.2
(3)
P 		157
B 447
(3)
P 		339.1
(-3)
P 		343.8
(-2.7)
P 		408.7
(0.9)
P 		108
C 419.9
(3)
P 		311.1
(-1.5)
P 		274
(-3)
P 		287.7
(-2.4)
P 		146
avr 409.4
(3) 		316
(-3) 		317.5
(-2.9) 		383.9
(1.4) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 264
1 2 3 4 5 6 range
A 420.8
(1)
P 		393.9
(0.4)
P 		507.5
(3)
P 		412.9
(0.9)
P 		373.8
(-0)
P 		243.5
(-3)
P 		264
B 357.5
(-0.8)
P 		451.9
(2.1)
P 		480.4
(3)
P 		464.1
(2.5)
P 		317.8
(-2)
P 		287
(-3)
P 		193
C 371.4
(0.4)
P 		399.5
(1.6)
P 		428.8
(2.9)
P 		432
(3)
P 		341
(-1)
P 		294.1
(-3)
P 		138
avr 383.2
(0.3) 		415.1
(1.3) 		472.2
(3) 		436.3
(1.9) 		344.2
(-0.9) 		274.9
(-3) 		197
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 94
1 2 3 4 range
A 131.5
(3)
P 		64.7
(-3)
P 		87.5
(-1)
P 		66.6
(-2.8)
P 		67
B 142.5
(3)
P 		83.7
(-2.6)
P 		79.7
(-3)
P 		87.1
(-2.3)
P 		63
C 139
(3)
P 		89.4
(-0.3)
P 		95.5
(0.1)
P 		48.5
(-3)
P 		91
avr 137.7
(3) 		79.3
(-2) 		87.6
(-1.3) 		67.4
(-3) 		70

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 91
1 2 3 4 5 6 range
A 77.6
(-1.6)
P 		140.1
(3)
P 		110.5
(0.8)
P 		104.7
(0.4)
P 		112.8
(1)
P 		59.3
(-3)
P 		81
B 124.4
(-0.6)
P 		150.4
(3)
P 		116.7
(-1.7)
P 		122.9
(-0.8)
P 		129.1
(0.1)
P 		107
(-3)
P 		43
C 137.7
(3)
P 		121.9
(1.1)
P 		109.1
(-0.4)
P 		86.9
(-3)
P 		110.3
(-0.2)
P 		98.5
(-1.6)
P 		51
avr 113.2
(0) 		137.5
(3) 		112.1
(-0.1) 		104.8
(-1) 		117.4
(0.5) 		88.3
(-3) 		49
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192154_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13088
Sequence Type Exemplar sequence
Representative Public ID F46F3.2 NCBI
Target Description F46F3.2 /REP_DB=WormBase Gene ID /WP=CE19873 /TR=P90876 /GB=CAB03114.1 /SUBMIT=HINXTON /CHR=5 /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_073553(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073553 NCBI Caenorhabditis elegans F46F3.2 (F46F3.2) mRNA, complete cds. 11/11 None
SNAP00000004391 ENSEMBL cdna:SNAP chromosome:CEL140:V:11671953:11675145:-1 11/11 None
GENEFINDER00000004394 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11671953:11674584:-1 11/11 None
F46F3.2 ENSEMBL cdna:known chromosome:CEL140:V:11671953:11675165:-1 gene:F46F3.2 11/11 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:11671952-11675145(-) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-aminobutyric-acid receptor
Ensembl F46F3.2
Entrez Gene 179600 Entrez gene
SwissProt P90876 EMBL-EBI
WormBase CE31948 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 CAB03114 Hypothetical protein F46F3.2 [Caenorhabditis elegans] ref|NP_505954.2| F46F3.2 [Caenorhabditis elegans] 0.0
blast CAE75317 Hypothetical protein CBG23289 [Caenorhabditis briggsae] 0.0
blast AAG24222 Hypothetical protein W10G11.16 [Caenorhabditis elegans] ref|NP_494579.1| W10G11.16 [Caenorhabditis elegans] 5.0E-86
blast AAG24222 Hypothetical protein W10G11.16 [Caenorhabditis elegans] ref|NP_494579.1| W10G11.16 [Caenorhabditis elegans] 6.0E-86
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 5.2E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-26
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 5.2E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-26
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 5.2E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-26
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505954.2 4 458-480,485-502,522-544,586-608
F46F3.2 4 458-480,485-502,522-544,586-608
SNAP00000004391 4 472-494,499-516,536-558,600-622
GENEFINDER00000004394 5 7-29,390-412,417-434,454-476,518-540
Sequence
Target Sequence 
>C. ELEGANS:192154_S_AT
cattcgacatttgcatccagacacatgcaacggtgtaagaaaatctggagtttattcatg
tctagaagcaaaattctacatgcatcgagaagttggttatcacattgcaaatacttatat
tcctacagcaatttgtgtggtcttctcatggatttcagtatggttacccgaagaatttgt
tgaaggtcgaatatttgtttctctcaccgtatttctgacactttccgctgaaaataactc
agcaaaagaagaacttccaaaagtttcttacgtgaaagctattgatatctggttcgggtt
tacttccacttttgtattcctgacaatgcttcaagctctcgttgtgatttcattggagca
taacagtaaacgactgagactaaagtttgaaaacaatcttgacggatacagtaaatatca
aatgacaaaatcaatgcttctaagtcggtattatcatcgaatggctcgtcagattgacac
attttgcaaagtaatgtatccagttatttttcttcttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATTCGACATTTGCATCCAGACACA 350 217 1173 Antisense
ATTCCTACAGCAATTTGTGTGGTCT 256 9 1291 Antisense
GTGTGGTCTTCTCATGGATTTCAGT 81 489 1307 Antisense
GTCGAATATTTGTTTCTCTCACCGT 263 475 1358 Antisense
GTATTTCTGACACTTTCCGCTGAAA 270 453 1381 Antisense
TATCTGGTTCGGGTTTACTTCCACT 335 653 1458 Antisense
ACTTCCACTTTTGTATTCCTGACAA 463 103 1474 Antisense
GTATTCCTGACAATGCTTCAAGCTC 124 453 1486 Antisense
GCTTCAAGCTCTCGTTGTGATTTCA 123 305 1500 Antisense
GTCGGTATTATCATCGAATGGCTCG 38 471 1616 Antisense
ATGTATCCAGTTATTTTTCTTCTTT 691 47 1666 Antisense
Sequence Source Affymetrix Proprietary Database