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[193954_at] gamma-aminobutyric-acid receptor (beta-1 subunit)

Description C09G5.1 /REP_DB=WormBase Gene ID /WP=CE01481 /GEN=gbr-4 /TR=SW:Q09453 /GB=CAA86760.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor (beta-1 subunit)
Cluster 6grp_total > 44      4grp_total > 22      6grp_cgc > 44      6grp_cgc_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 156
1 2 3 4 range
A 156.2
(2.9)
A 		15.2
(-3)
A 		16.8
(-2.9)
A 		159.3
(3)
A 		144
B 154.7
(2.5)
A 		18.4
(-2.8)
A 		12.1
(-3)
A 		168
(3)
P 		156
C 144.5
(3)
A 		37.8
(-2)
A 		15.7
(-3)
A 		136.4
(2.6)
P 		129
avr 151.8
(2.9) 		23.8
(-2.6) 		14.9
(-3) 		154.6
(3) 		140

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 143
1 2 3 4 5 6 range
A 63
(-1.9)
A 		153.7
(3)
A 		124.9
(1.4)
M 		43.4
(-3)
A 		79.9
(-1)
A 		73
(-1.4)
A 		110
B 75.1
(-1.2)
M 		104.6
(1.6)
A 		119.4
(3)
P 		63.2
(-2.3)
A 		88.4
(0.1)
A 		56.3
(-3)
A 		63
C 121.2
(2.4)
P 		118.6
(2.3)
A 		132.8
(3)
A 		11.1
(-3)
A 		14.3
(-2.8)
A 		75.5
(0.2)
A 		122
avr 86.4
(0.3) 		125.6
(3) 		125.7
(3) 		39.2
(-3) 		60.9
(-1.5) 		68.3
(-1) 		87
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 54
1 2 3 4 range
A 56.9
(3)
A 		3.3
(-3)
A 		4.4
(-2.9)
A 		23.3
(-0.8)
A 		54
B 49.3
(3)
A 		4.5
(-2.8)
A 		2.8
(-3)
A 		35.8
(1.3)
P 		47
C 47.8
(3)
A 		10.9
(-2.2)
A 		5.5
(-3)
A 		23
(-0.5)
P 		42
avr 51.3
(3) 		6.2
(-2.7) 		4.2
(-3) 		27.4
(-0) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 53
1 2 3 4 5 6 range
A 11.6
(-2.9)
A 		54.7
(3)
A 		27.2
(-0.8)
M 		11
(-3)
A 		24.1
(-1.2)
A 		17.8
(-2.1)
A 		44
B 26.1
(-0.1)
M 		34.8
(2.7)
A 		29
(0.8)
P 		16.7
(-3)
A 		35.9
(3)
A 		21
(-1.7)
A 		19
C 44.9
(3)
P 		36.2
(1.8)
A 		33.8
(1.4)
A 		2.2
(-3)
A 		4.6
(-2.7)
A 		25.3
(0.2)
A 		43
avr 27.5
(0.3) 		41.9
(3) 		30
(0.8) 		10
(-3) 		21.5
(-0.8) 		21.4
(-0.9) 		32
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193954_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3736
Sequence Type Exemplar sequence
Representative Public ID C09G5.1 NCBI
Target Description C09G5.1 /REP_DB=WormBase Gene ID /WP=CE01481 /GEN=gbr-4 /TR=SW:Q09453 /GB=CAA86760.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor (beta-1 subunit)
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_063905(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063905 NCBI Caenorhabditis elegans GABA/Glycine Receptor family (see gbr) family member (ggr-1) (ggr-1) mRNA, complete cds. 11/11 None
SNAP00000014218 ENSEMBL cdna:SNAP chromosome:CEL140:II:10699981:10704435:1 10/11 None
GENEFINDER00000014233 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10696352:10702300:1 11/11 None
C09G5.1 ENSEMBL cdna:known chromosome:CEL140:II:10694965:10702435:1 gene:C09G5.1 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
chrII:10699938-10702297(+) 100.0 100.0
Public Domain and Genome References
Gene Title gamma-aminobutyric-acid receptor (beta-1 subunit)
Gene Symbol ggr-1
Ensembl C09G5.1
Entrez Gene 191636 Entrez gene
SwissProt Q09453 EMBL-EBI
WormBase CE36915 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
15276 ligand-gated ion channel activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
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 0.0
blast CAE59621 Hypothetical protein CBG03030 [Caenorhabditis briggsae] 0.0
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 1.0E-167
blast CAE59621 Hypothetical protein CBG03030 [Caenorhabditis briggsae] 1.0E-158
blast CAE58888 Hypothetical protein CBG02128 [Caenorhabditis briggsae] 2.0E-91
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.2E-30
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.7E-20
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.2E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0019
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-10
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.2E-30
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.9E-11
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.7E-43
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.2E-30
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.9E-11
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-45
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496306.2 4 251-273,280-302,312-334,440-459
C09G5.1 4 251-273,280-302,312-334,440-459
SNAP00000014218 3 159-178,220-242,341-363
GENEFINDER00000014233 4 312-334,341-363,373-395,501-520
Sequence
Target Sequence 
>C. ELEGANS:193954_AT
tggaagggtttcactctcgattacaacacttttgacgttagctacacagtcgagtgcagc
taggatggctcttccacaggcatcggatgtgaaagcaattgacgtttggatgggtacctg
catggcattcgttttctcagcaatgatagagttcaccgttgtcaactattgtgtgcgacg
aaaagttcgcacgaagataaaaccacgtgggctctcggagcaagtacatgacatggtggc
gcagtacagggagaaaaaggataagttcaacaatggaaactgtgagatcagctacgaaat
ggctctgcaaccgaacgaggacaacgcgacagttcaacgaaatttcgagaaaaaagaagt
gcgtgagatgaatcaggcgtcactttttgtccggcgatcactacttccgacttcgaaacg
gaagaccattgaagacagaataaaccgagtcgaggagaaccgaaagaatgcacaaaaaat
cgatcgttacagccgggcactattcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAAGGGTTTCACTCTCGATTACA 296 545 693 Antisense
CGAGTGCAGCTAGGATGGCTCTTCC 555 249 743 Antisense
GCTCTTCCACAGGCATCGGATGTGA 614 299 760 Antisense
GTACCTGCATGGCATTCGTTTTCTC 165 457 806 Antisense
AGATAAAACCACGTGGGCTCTCGGA 137 63 887 Antisense
GACATGGTGGCGCAGTACAGGGAGA 467 369 922 Antisense
ACGAAATGGCTCTGCAACCGAACGA 205 91 986 Antisense
CGAGGACAACGCGACAGTTCAACGA 21 251 1008 Antisense
ATGAATCAGGCGTCACTTTTTGTCC 551 43 1060 Antisense
ATCACTACTTCCGACTTCGAAACGG 254 23 1089 Antisense
GATCGTTACAGCCGGGCACTATTCC 225 417 1174 Antisense
Sequence Source Affymetrix Proprietary Database