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[189599_at] channel protein

Description W10G11.16 /REP_DB=WormBase Gene ID /WP=CE14830 /TR=O44917 /GB=AAG24222.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=channel protein
Cluster 6grp_high1_10_10 > 14      4grp_high_8_8 > 51      6grp_total > 03      4grp_total > 52      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 164
1 2 3 4 range
A 194.8
(3)
P 		170.1
(1.8)
P 		169.5
(1.7)
P 		74.7
(-3)
A 		120
B 145.8
(2.8)
P 		149.9
(3)
P 		115.8
(1.3)
P 		31.2
(-3)
A 		119
C 146.9
(2)
P 		161.1
(3)
P 		156
(2.6)
P 		78.5
(-3)
P 		83
avr 162.5
(3) 		160.4
(2.9) 		147.1
(2.1) 		61.5
(-3) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 121
1 2 3 4 5 6 range
A 177.6
(3)
P 		156.8
(2)
P 		110.5
(-0.3)
A 		139.3
(1.1)
P 		145.2
(1.4)
P 		56.2
(-3)
A 		121
B 158.5
(2.9)
P 		161
(3)
P 		117.3
(0.5)
P 		155
(2.7)
P 		86
(-1.3)
P 		56.6
(-3)
A 		104
C 132.9
(2.5)
P 		138.3
(3)
P 		111.6
(0.3)
A 		87.5
(-2.1)
P 		108.4
(0)
P 		78.1
(-3)
P 		60
avr 156.3
(3) 		152
(2.7) 		113.1
(0.2) 		127.3
(1.1) 		113.2
(0.2) 		63.6
(-3) 		93
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 70.9
(3)
P 		36.9
(-0.4)
P 		44.3
(0.3)
P 		10.9
(-3)
A 		60
B 46.5
(3)
P 		37
(1.6)
P 		26.8
(0)
P 		6.7
(-3)
A 		40
C 48.6
(2.2)
P 		46.3
(1.8)
P 		54.4
(3)
P 		13.2
(-3)
P 		41
avr 55.3
(3) 		40.1
(1) 		41.8
(1.2) 		10.3
(-3) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 32.7
(-0.3)
P 		55.8
(3)
P 		24.1
(-1.5)
A 		35.3
(0.1)
P 		43.8
(1.3)
P 		13.7
(-3)
A 		42
B 55.1
(3)
P 		53.6
(2.7)
P 		28.5
(-1.7)
P 		41
(0.5)
P 		34.9
(-0.6)
P 		21.1
(-3)
A 		34
C 49.2
(3)
P 		42.2
(1.7)
P 		28.4
(-0.9)
A 		17.6
(-3)
P 		35.1
(0.3)
P 		26.1
(-1.4)
P 		32
avr 45.7
(2) 		50.5
(3) 		27
(-1.7) 		31.3
(-0.8) 		37.9
(0.5) 		20.3
(-3) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189599_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5466
Sequence Type Exemplar sequence
Representative Public ID W10G11.16 NCBI
Target Description W10G11.16 /REP_DB=WormBase Gene ID /WP=CE14830 /TR=O44917 /GB=AAG24222.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=channel protein
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_062178(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062178 NCBI Caenorhabditis elegans W10G11.16 (W10G11.16) mRNA, complete cds. 11/11 None
SNAP00000013260 ENSEMBL cdna:SNAP chromosome:CEL140:II:3563723:3567340:1 9/11 None
GENEFINDER00000013274 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3562870:3567340:1 11/11 None
W10G11.16 ENSEMBL cdna:known chromosome:CEL140:II:3566022:3567340:1 gene:W10G11.16 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:3566065-3567339(+) 99.8 99.8
Public Domain and Genome References
Gene Title channel protein
Ensembl W10G11.16
Entrez Gene 189344 Entrez gene
SwissProt O44917 EMBL-EBI
WormBase CE14830 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 AAG24222 Hypothetical protein W10G11.16 [Caenorhabditis elegans] ref|NP_494579.1| W10G11.16 [Caenorhabditis elegans] 0.0
blast CAE73804 Hypothetical protein CBG21354 [Caenorhabditis briggsae] 0.0
blast AAG24222 Hypothetical protein W10G11.16 [Caenorhabditis elegans] ref|NP_494579.1| W10G11.16 [Caenorhabditis elegans] 1.0E-177
blast CAE73804 Hypothetical protein CBG21354 [Caenorhabditis briggsae] 1.0E-175
blast AAZ42341 GABA-A receptor [Caenorhabditis remanei] 1.0E-108
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.2E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.7E-42
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-9
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.7E-42
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-9
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.6E-34
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494579.1 3 165-187,230-252,294-316
W10G11.16 3 165-187,230-252,294-316
SNAP00000013260 1 857-874
GENEFINDER00000013274 4 878-900,907-926,941-963,1005-1027
Sequence
Target Sequence 
>C. ELEGANS:189599_AT
gctccccgagctatacattgatcgctatgagaccacgacatgcccgaatgaacgaaaatc
tggcgcattttcttgtcttcgagcagttttccgtctgaaacgagatgtcggattccatat
tgctcagacctacatcccgacgagtcttgcgctgatgttctcgtgggttggtgtatggct
tcccgaagagtttatggaaggtcgtattggagtggctattaccgtacttttgacgctttc
gaccgaatctgctggagctcgagagcatctgccaagtgtgtcgtatttaaaggcaatcga
cttatggttcggttttatcactggattcgtcttttttacactgcttcagaccctttttgt
cattggttttgataaaagagcaaatcagctcaaaaaatgggctggtcgaaagacagcaga
catcactgaagaaattcgagaagctcttctacaaaaagctacacgataccataaaactgg
acgataccttgataatttctgccgtgtctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTCCCCGAGCTATACATTGATCGC 469 299 399 Antisense
GCATTTTCTTGTCTTCGAGCAGTTT 447 307 463 Antisense
GATTCCATATTGCTCAGACCTACAT 387 433 509 Antisense
GTGGGTTGGTGTATGGCTTCCCGAA 356 485 561 Antisense
GAGTGGCTATTACCGTACTTTTGAC 679 399 608 Antisense
TACTTTTGACGCTTTCGACCGAATC 514 643 623 Antisense
GACCGAATCTGCTGGAGCTCGAGAG 240 383 639 Antisense
GAGCATCTGCCAAGTGTGTCGTATT 225 389 661 Antisense
TGGATTCGTCTTTTTTACACTGCTT 526 549 720 Antisense
GCTTCAGACCCTTTTTGTCATTGGT 162 305 741 Antisense
ACCTTGATAATTTCTGCCGTGTCTT 534 87 884 Antisense
Sequence Source Affymetrix Proprietary Database