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[189379_at] glycine receptor

Description F58G6.4 /REP_DB=WormBase Gene ID /WP=CE28039 /TR=Q21005 /GB=CAA92466.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=glycine receptor
Cluster 6grp_total > 14      4grp_total > 23      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 301
1 2 3 4 range
A 317.8
(3)
P 		63.8
(-3)
A 		104.3
(-2)
A 		278.5
(2.1)
A 		254
B 306.3
(3)
P 		85.8
(-3)
A 		144.8
(-1.4)
A 		195.7
(-0)
A 		221
C 364.5
(3)
P 		69.5
(-3)
A 		86.7
(-2.7)
A 		258.9
(0.9)
P 		295
avr 329.5
(3) 		73
(-3) 		111.9
(-2.1) 		244.4
(1) 		257

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 180
1 2 3 4 5 6 range
A 214.1
(3)
A 		165.6
(1.4)
A 		147.4
(0.8)
P 		116.4
(-0.3)
A 		129.3
(0.2)
A 		34.3
(-3)
A 		180
B 210.4
(3)
P 		190
(2)
P 		150.3
(-0.1)
M 		118.1
(-1.7)
A 		93.6
(-3)
A 		102.4
(-2.5)
A 		117
C 174.2
(1.7)
A 		202.8
(3)
A 		82.8
(-2.2)
A 		127.7
(-0.3)
A 		88
(-2)
A 		65.6
(-3)
A 		137
avr 199.6
(3) 		186.1
(2.4) 		126.8
(-0.3) 		120.7
(-0.6) 		103.6
(-1.4) 		67.4
(-3) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 115.7
(3)
P 		13.9
(-3)
A 		27.3
(-2.2)
A 		40.8
(-1.4)
A 		102
B 97.7
(3)
P 		21.2
(-3)
A 		33.6
(-2)
A 		41.7
(-1.4)
A 		77
C 120.6
(3)
P 		20
(-3)
A 		30.2
(-2.4)
A 		43.7
(-1.6)
P 		101
avr 111.3
(3) 		18.4
(-3) 		30.4
(-2.2) 		42.1
(-1.5) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 65
1 2 3 4 5 6 range
A 39.5
(0.7)
A 		58.9
(3)
A 		32.1
(-0.2)
P 		29.5
(-0.5)
A 		39
(0.6)
A 		8.3
(-3)
A 		51
B 73.2
(3)
P 		63.2
(1.6)
P 		36.5
(-2.3)
M 		31.3
(-3)
A 		38
(-2)
A 		38.2
(-2)
A 		42
C 64.6
(3)
A 		61.9
(2.6)
A 		21.1
(-3)
A 		25.7
(-2.4)
A 		28.5
(-2)
A 		22
(-2.9)
A 		44
avr 59.1
(2.7) 		61.3
(3) 		29.9
(-1.9) 		28.8
(-2.1) 		35.2
(-1.1) 		22.8
(-3) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189379_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9902
Sequence Type Exemplar sequence
Representative Public ID F58G6.4 NCBI
Target Description F58G6.4 /REP_DB=WormBase Gene ID /WP=CE28039 /TR=Q21005 /GB=CAA92466.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=glycine 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_069314(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069314 NCBI Caenorhabditis elegans F58G6.4 (F58G6.4) mRNA, complete cds. 11/11 None
GENEFINDER00000020772 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9660941:9663830:1 11/11 None
F58G6.4 ENSEMBL cdna:known chromosome:CEL140:IV:9658030:9663918:1 gene:F58G6.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000020769 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:9661058-9663836(+) 100.0 100.0
Public Domain and Genome References
Gene Title glycine receptor
Ensembl F58G6.4
Entrez Gene 177799 Entrez gene
SwissProt Q21005 EMBL-EBI
WormBase CE28039 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 CAA92466 Hypothetical protein F58G6.4 [Caenorhabditis elegans] ref|NP_501715.1| F58G6.4 [Caenorhabditis elegans] 0.0
blast CAE56060 Hypothetical protein CBG23634 [Caenorhabditis briggsae] 0.0
blast CAD44128 Hypothetical protein F47A4.1b [Caenorhabditis elegans] emb|CAD44131.1| Hypothetical protein F47A4.1b [Caenorhabditis elegans] ref|NP_741878.1| F47A4.1b [Caenorhabditis elegans] 1.0E-120
blast CAD44128 Hypothetical protein F47A4.1b [Caenorhabditis elegans] emb|CAD44131.1| Hypothetical protein F47A4.1b [Caenorhabditis elegans] ref|NP_741878.1| F47A4.1b [Caenorhabditis elegans] 4.0E-96
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-13
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.5E-72
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-13
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.6E-28
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 6.5E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501715.1 4 239-261,273-290,305-327,428-450
F58G6.4 4 239-261,273-290,305-327,428-450
GENEFINDER00000020772 4 195-217,229-246,261-283,384-406
Sequence
Target Sequence 
>C. ELEGANS:189379_AT
agagcaatcccagctaggactatgcttggtgtcaactctcttctagcaatgacttttcag
tttggaaatatcattcgaaatttgccacgtgtatcttatgtaaaagcaattgatgtttgg
atgttatctggaatgctttttatatttttatcacttcttgaattggcagtagttggattt
atgtcaaggaatgaaggtctaccgcctaaagtcaaaaaacggaaacgacaagaagatgat
gatgaaggattttcatggaaaagtatgcaaactagtccgcacttggaattaagacagttt
tgggtagacaaacgggtgaattcattacggaatgacagcgcagtgccgcctgttgaagat
tatgcgccaatggaactcgaacaaccgtatcaaaatattacaaaacgaagagaaaaacgg
aaatggatgagtgggttgaggaaaaaatggagggcgatgagggaattacggcctgaaaca
gtagatttttatagcgcaatcttcttcccaacagcgtatatgcttttcaacatttcatat
tggagtttctacctgacaagtctttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAGCAATCCCAGCTAGGACTATGC 572 69 742 Antisense
GACTATGCTTGGTGTCAACTCTCTT 404 373 759 Antisense
AACTCTCTTCTAGCAATGACTTTTC 478 141 775 Antisense
AATTTGCCACGTGTATCTTATGTAA 250 175 820 Antisense
GAATGAAGGTCTACCGCCTAAAGTC 184 329 930 Antisense
GTATGCAAACTAGTCCGCACTTGGA 28 455 1004 Antisense
TACGGAATGACAGCGCAGTGCCGCC 380 647 1067 Antisense
CGCAGTGCCGCCTGTTGAAGATTAT 345 253 1080 Antisense
TTTTATAGCGCAATCTTCTTCCCAA 516 675 1228 Antisense
TCTTCTTCCCAACAGCGTATATGCT 333 617 1241 Antisense
GGAGTTTCTACCTGACAAGTCTTTC 220 513 1283 Antisense
Sequence Source Affymetrix Proprietary Database