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[172886_x_at] neurotransmitter-gated ion-channel /// ---

Description Y57G11C.2 /REP_DB=WormBase Gene ID /WP=CE14928 /TR=O18228 /GB=CAB16504.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=neurotransmitter-gated ion-channel
Cluster 6grp_total > 20      4grp_total > 10      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 144
1 2 3 4 range
A 9.7
(-3)
A 		38
(0)
A 		16.5
(-2.3)
A 		65.9
(3)
A 		56
B 54.9
(-0.1)
A 		23.4
(-3)
A 		50.5
(-0.5)
A 		88.4
(3)
M 		65
C 31.4
(-2.1)
A 		52.6
(-1.2)
A 		9.6
(-3)
A 		153.1
(3)
P 		144
avr 32
(-2.5) 		38
(-2) 		25.5
(-3) 		102.5
(3) 		77

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 100
1 2 3 4 5 6 range
A 56.5
(-0.3)
A 		59.9
(0.1)
A 		75.6
(1.9)
M 		33.6
(-3)
A 		85.2
(3)
A 		40.5
(-2.2)
A 		52
B 37.4
(-2.5)
A 		44.2
(-1.4)
A 		33.9
(-3)
A 		73.7
(3)
A 		38.7
(-2.3)
A 		45
(-1.3)
A 		40
C 8.3
(-2.7)
A 		102.8
(3)
P 		57.1
(0.2)
A 		27.1
(-1.6)
A 		3.1
(-3)
A 		5.6
(-2.8)
A 		100
avr 34.1
(-2.4) 		69
(3) 		55.5
(0.9) 		44.8
(-0.8) 		42.3
(-1.2) 		30.4
(-3) 		39
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 3.5
(-3)
A 		8.3
(1.7)
A 		4.3
(-2.2)
A 		9.6
(3)
A 		6
B 17.5
(2.4)
A 		5.8
(-3)
A 		11.7
(-0.3)
A 		18.8
(3)
M 		13
C 10.4
(-1.1)
A 		15.1
(0.1)
A 		3.3
(-3)
A 		25.8
(3)
P 		23
avr 10.5
(-0.9) 		9.7
(-1.3) 		6.4
(-3) 		18.1
(3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 10.4
(-2.3)
A 		21.3
(1.5)
A 		16.5
(-0.2)
M 		8.5
(-3)
A 		25.7
(3)
A 		9.9
(-2.5)
A 		17
B 13
(-0.5)
A 		14.7
(0.5)
A 		8.2
(-3)
A 		19.5
(3)
A 		15.7
(1)
A 		16.8
(1.6)
A 		11
C 3.1
(-2.6)
A 		31.4
(3)
P 		14.5
(-0.3)
A 		5.5
(-2.1)
A 		1
(-3)
A 		1.9
(-2.8)
A 		30
avr 8.8
(-3) 		22.5
(3) 		13.1
(-1.1) 		11.2
(-1.9) 		14.1
(-0.7) 		9.5
(-2.7) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172886_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9756
Sequence Type Exemplar sequence
Representative Public ID Y57G11C.2 NCBI
Target Description Y57G11C.2 /REP_DB=WormBase Gene ID /WP=CE14928 /TR=O18228 /GB=CAB16504.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=neurotransmitter-gated ion-channel
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_001028362(11), NM_070376(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028362 NCBI Caenorhabditis elegans Y57G11C.49 (Y57G11C.49) mRNA, complete cds. 11/11 None
NM_070376 NCBI Caenorhabditis elegans Y57G11C.2 (Y57G11C.2) mRNA, complete cds. 9/11 None
SNAP00000003460 ENSEMBL cdna:SNAP chromosome:CEL140:IV:14716324:14720402:1 11/11 None
GENEFINDER00000003584 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:14709557:14720613:1 10/11 None
Y57G11C.2 ENSEMBL cdna:known chromosome:CEL140:IV:14709557:14714700:1 gene:Y57G11C.2 9/11 None
Y57G11C.49 ENSEMBL cdna:known chromosome:CEL140:IV:14715762:14720402:1 gene:Y57G11C.49 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000003459 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:14709562-14720408(+) 100.0 100.0
Public Domain and Genome References
Gene Title neurotransmitter-gated ion-channel

Ensembl Y57G11C.2
Y57G11C.49
Entrez Gene 190370 Entrez gene
3564870 Entrez gene
SwissProt O18228 EMBL-EBI
Q6BEQ0 EMBL-EBI
WormBase CE36675 Wormbase
CE36676 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
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 CAH04731 Hypothetical protein Y57G11C.49 [Caenorhabditis elegans] ref|NP_001023533.1| Y57G11C.49 [Caenorhabditis elegans] 0.0
blast CAB16504 Hypothetical protein Y57G11C.2 [Caenorhabditis elegans] ref|NP_502777.2| Y57G11C.2 [Caenorhabditis elegans] 0.0
blast CAE73922 Hypothetical protein CBG21535 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.7E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.5E-57
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.7E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-49
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.7E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.2E-37
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.7E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.6E-45
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001023533.1 4 260-282,295-313,328-350,440-458
NP_502777.2 4 239-261,274-292,307-329,419-437
Y57G11C.2 4 239-261,274-292,307-329,419-437
Y57G11C.49 4 260-282,295-313,328-350,440-458
SNAP00000003460 4 177-199,212-230,245-267,357-375
GENEFINDER00000003584 7 239-261,274-292,307-329,413-432,641-663,676-694,709-731
Sequence
Target Sequence 
>C. ELEGANS:172886_X_AT
aaacggcgacctcaattctacgtgtgggtactgcttattccaacatatattatcacagtt
gtttgcatttttggattatttaccccaactgccaatcatggattacgagaagaaagggtc
aatttgggaattacaacacttttatcatctgctgttatcttacaaattgttgctaatgca
atgccaaaaacttcagaacttccacttttgggaaacttcatattggctgaaatcttcgta
gtcgcgattggtgtactatttgcagttctcgtattaacccttcatcaacgtgctcatact
cgagaatggagaccccctgcatggatgttatggatacttcgaatgactggatcatcaaag
ttcttgtcaagaaatattacgaagattcgacataaaagtagtacggctgaacggattcat
tatactggagaaggagcgtatctattcaaaaacctcgacgaatctcttcaatcagtgcgt
gaatatattcaggaagaagatcgagactatttcagagaactcacttatgtcaaatttttc
gatcgattggactttcttcttcttctcatttttcaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAACGGCGACCTCAATTCTACGTGT 545 125 2017 Antisense
GTGTGGGTACTGCTTATTCCAACAT 482 485 2038 Antisense
ATTTACCCCAACTGCCAATCATGGA 228 13 2094 Antisense
CACTTTTATCATCTGCTGTTATCTT 470 197 2153 Antisense
TGCAGTTCTCGTATTAACCCTTCAT 309 575 2277 Antisense
CCTTCATCAACGTGCTCATACTCGA 532 269 2295 Antisense
TACTCGAGAATGGAGACCCCCTGCA 508 645 2313 Antisense
GACCCCCTGCATGGATGTTATGGAT 64 383 2327 Antisense
AAACCTCGACGAATCTCTTCAATCA 77 127 2466 Antisense
TCGATCGATTGGACTTTCTTCTTCT 204 603 2555 Antisense
TTCTTCTTCTTCTCATTTTTCAAGT 486 689 2570 Antisense
Sequence Source Affymetrix Proprietary Database