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[193182_at] Glycine receptor alpha chain

Description F09C12.1 /REP_DB=WormBase Gene ID /WP=CE01901 /GEN=gbr-6 /TR=Q10052 /GB=AAA68348.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Glycine receptor alpha chain
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 24      6grp_highest_nonorm > 90      6grp_total > 02      4grp_total > 14      6grp_highest_sub > 01_02      6grp_cgc > 52      6grp_high1_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 135
1 2 3 4 range
A 103.8
(-1.4)
P 		69.6
(-3)
M 		89.2
(-2.1)
A 		195.5
(3)
P 		126
B 160.1
(3)
P 		99.9
(-1.2)
A 		73.1
(-3)
A 		143.5
(1.9)
P 		87
C 127.6
(2.2)
P 		60.5
(-3)
A 		71.6
(-2.1)
P 		137.2
(3)
P 		77
avr 130.5
(0.9) 		76.7
(-3) 		78
(-2.9) 		158.7
(3) 		82

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 120
1 2 3 4 5 6 range
A 161.7
(3)
P 		145.2
(1.5)
P 		115.1
(-1.2)
P 		135.3
(0.6)
P 		95.8
(-3)
P 		130.6
(0.2)
P 		66
B 144.7
(0.9)
P 		178.5
(3)
P 		80
(-3)
P 		140.4
(0.7)
P 		148.3
(1.2)
P 		99.8
(-1.8)
P 		99
C 113.8
(-0.4)
P 		180.9
(3)
P 		60.8
(-3)
P 		143.9
(1.2)
P 		100.8
(-1)
P 		89.8
(-1.6)
P 		120
avr 140.1
(1) 		168.2
(3) 		85.3
(-3) 		139.9
(1) 		115
(-0.9) 		106.7
(-1.5) 		83
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 37.8
(3)
P 		15.1
(-3)
M 		23.3
(-0.8)
A 		28.6
(0.6)
P 		23
B 51.1
(3)
P 		24.7
(-1.6)
A 		16.9
(-3)
A 		30.6
(-0.6)
P 		34
C 42.2
(3)
P 		17.4
(-3)
A 		24.9
(-1.2)
P 		23.1
(-1.6)
P 		25
avr 43.7
(3) 		19.1
(-3) 		21.7
(-2.4) 		27.4
(-1) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 45
1 2 3 4 5 6 range
A 29.8
(-1.9)
P 		51.6
(3)
P 		25.1
(-3)
P 		34.3
(-0.9)
P 		28.9
(-2.1)
P 		31.8
(-1.5)
P 		27
B 50.4
(1.6)
P 		59.4
(2.9)
P 		19.4
(-3)
P 		37.2
(-0.4)
P 		60.2
(3)
P 		37.2
(-0.4)
P 		41
C 42.2
(1)
P 		55.2
(3)
P 		15.5
(-3)
P 		28.9
(-1)
P 		32.6
(-0.4)
P 		30.1
(-0.8)
P 		40
avr 40.8
(0.5) 		55.4
(3) 		20
(-3) 		33.5
(-0.7) 		40.6
(0.5) 		33
(-0.8) 		35
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193182_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4114
Sequence Type Exemplar sequence
Representative Public ID F09C12.1 NCBI
Target Description F09C12.1 /REP_DB=WormBase Gene ID /WP=CE01901 /GEN=gbr-6 /TR=Q10052 /GB=AAA68348.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Glycine receptor alpha chain
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_062550(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062550 NCBI Caenorhabditis elegans GABA/Glycine Receptor family (see gbr) family member (ggr-3) (ggr-3) mRNA, complete cds. 11/11 None
F09C12.1 ENSEMBL cdna:known chromosome:CEL140:II:5130367:5133035:1 gene:F09C12.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000009141 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:5130364-5133033(+) 100.0 100.0
Public Domain and Genome References
Gene Title Glycine receptor alpha chain
Gene Symbol ggr-3
Ensembl F09C12.1
Entrez Gene 191638 Entrez gene
SwissProt Q10052 EMBL-EBI
WormBase CE01901 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 AAA68348 Gaba/glycine receptor family (see gbr) protein 3 [Caenorhabditis elegans] ref|NP_494951.1| GABA/Glycine Receptor family (see gbr) family member (ggr-3) [Caenorhabditis elegans] 0.0
blast CAE59048 Hypothetical protein CBG02331 [Caenorhabditis briggsae] 0.0
blast AAM69066 Hypothetical protein T21F2.1a [Caenorhabditis elegans] ref|NP_741945.2| T21F2.1a [Caenorhabditis elegans] 1.0E-106
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.1E-19
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.2E-61
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494951.1 3 282-304,311-333,348-370
F09C12.1 3 282-304,311-333,348-370
Sequence
Target Sequence 
>C. ELEGANS:193182_AT
aatgtacctaccaacatatctctccgtattcatttcatggattgctttctggattgatac
ccgggcgcttcctgctcgaatcactcttggtgtatcttctctaatggctctgacctttca
atttggtaatattgtcaaaaatctgccacgtgtttcatttgttaaagccattgatctctg
gtttttcgtttgtgtcgcatttatatttttctcgctcgttgagttggctgtcgttggatt
cgttgataaaataacagaaatcaagcggaggtcacggagaatcaaatttcagcgggcaat
tgccggaggcacaataaaaaatgatcggccagtaagtttcagaaagtactcctgcacatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGTACCTACCAACATATCTCTCC 610 163 879 Antisense
ATATCTCTCCGTATTCATTTCATGG 571 19 894 Antisense
TGCTTTCTGGATTGATACCCGGGCG 567 579 921 Antisense
TCCTGCTCGAATCACTCTTGGTGTA 28 595 948 Antisense
CACTCTTGGTGTATCTTCTCTAATG 30 199 960 Antisense
TTCTCTAATGGCTCTGACCTTTCAA 596 691 975 Antisense
AATCTGCCACGTGTTTCATTTGTTA 404 169 1018 Antisense
TGATCTCTGGTTTTTCGTTTGTGTC 485 565 1050 Antisense
TTTTCTCGCTCGTTGAGTTGGCTGT 247 677 1085 Antisense
GTTGGCTGTCGTTGGATTCGTTGAT 11 437 1101 Antisense
GTTTCAGAAAGTACTCCTGCACATC 694 449 1214 Antisense
Sequence Source Affymetrix Proprietary Database