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[193769_s_at] member of the ligand-gated ionic channels family

Description F18G5.4 /REP_DB=WormBase Gene ID /WP=CE04412 /TR=SW:P54245 /GB=AAA81080.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=member of the ligand-gated ionic channels family
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 25      4grp_high_8_8 > 02      6grp_highest_nonorm > 90      6grp_total > 04      4grp_total > 14      6grp_highest_sub > De      6grp_high1_sub > 01_02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 286
1 2 3 4 range
A 273
(3)
P 		77
(-3)
A 		90.5
(-2.6)
M 		248.3
(2.2)
P 		196
B 246.9
(0.5)
P 		91.4
(-2.9)
A 		85.4
(-3)
A 		359
(3)
P 		274
C 231.3
(0.5)
P 		72.6
(-3)
P 		86.6
(-2.7)
P 		343.7
(3)
P 		271
avr 250.4
(1.3) 		80.3
(-3) 		87.5
(-2.8) 		317
(3) 		237

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 177.8
(3)
P 		161.8
(1.7)
P 		143.9
(0.2)
P 		163.5
(1.8)
P 		115.2
(-2.2)
P 		106.1
(-3)
P 		72
B 195.1
(3)
P 		161.6
(1.1)
P 		90.1
(-3)
P 		117.7
(-1.4)
P 		127.2
(-0.9)
P 		116.8
(-1.5)
P 		105
C 170.3
(1.8)
P 		189
(3)
P 		108.8
(-2.3)
P 		158.4
(1)
P 		97.8
(-3)
P 		122.8
(-1.4)
P 		91
avr 181.1
(3) 		170.8
(2.1) 		114.3
(-2.9) 		146.5
(-0.1) 		113.4
(-3) 		115.2
(-2.8) 		68
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 99.4
(3)
P 		16.7
(-3)
A 		23.6
(-2.5)
M 		36.3
(-1.6)
P 		83
B 78.7
(3)
P 		22.6
(-2.7)
A 		19.8
(-3)
A 		76.5
(2.8)
P 		59
C 76.6
(3)
P 		20.9
(-3)
P 		30.2
(-2)
P 		58
(1)
P 		56
avr 84.9
(3) 		20.1
(-3) 		24.5
(-2.6) 		56.9
(0.4) 		65

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 46
1 2 3 4 5 6 range
A 32.8
(-1.7)
P 		57.5
(3)
P 		31.3
(-2)
P 		41.5
(-0)
P 		34.8
(-1.3)
P 		25.8
(-3)
P 		32
B 67.9
(3)
P 		53.8
(1.2)
P 		21.9
(-3)
P 		31.2
(-1.8)
P 		51.7
(0.9)
P 		43.5
(-0.2)
P 		46
C 63.1
(3)
P 		57.7
(2.1)
P 		27.7
(-3)
P 		31.9
(-2.3)
P 		31.7
(-2.3)
P 		41.1
(-0.7)
P 		35
avr 54.6
(2.7) 		56.3
(3) 		27
(-3) 		34.9
(-1.4) 		39.4
(-0.5) 		36.8
(-1) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193769_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17291
Sequence Type Exemplar sequence
Representative Public ID F18G5.4 NCBI
Target Description F18G5.4 /REP_DB=WormBase Gene ID /WP=CE04412 /TR=SW:P54245 /GB=AAA81080.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=member of the ligand-gated ionic channels family
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_077155(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077155 NCBI Caenorhabditis elegans F18G5.4 (F18G5.4) mRNA, complete cds. 11/11 None
GENEFINDER00000036143 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9235140:9242181:-1 11/11 None
F18G5.4 ENSEMBL cdna:known chromosome:CEL140:X:9235068:9242205:-1 gene:F18G5.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000036133 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:9235139-9242181(-) 100.0 100.0
Public Domain and Genome References
Gene Title member of the ligand-gated ionic channels family
Ensembl F18G5.4
Entrez Gene 181155 Entrez gene
SwissProt P54245 EMBL-EBI
WormBase CE35495 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
4889 nicotinic acetylcholine-activated cation-selective channel activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel 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 AAA81080 Hypothetical protein F18G5.4 [Caenorhabditis elegans] ref|NP_509556.3| F18G5.4 [Caenorhabditis elegans] sp|P54245|YZN4_CAEEL Hypothetical acetylcholine receptor-like protein F18G5.4 in chromosome X precursor 0.0
blast CAE69855 Hypothetical protein CBG16183 [Caenorhabditis briggsae] 0.0
blast AAF39790 Acetylcholine receptor protein 21 [Caenorhabditis elegans] ref|NP_498452.2| AcetylCholine Receptor family member (acr-21) [Caenorhabditis elegans] 9.0E-82
blast AAF39790 Acetylcholine receptor protein 21 [Caenorhabditis elegans] ref|NP_498452.2| AcetylCholine Receptor family member (acr-21) [Caenorhabditis elegans] 1.0E-81
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 7.2E-18
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.5E-79
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 7.2E-18
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.5E-79
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509556.3 2 323-345,384-406
F18G5.4 2 323-345,384-406
GENEFINDER00000036143 4 40-62,380-402,409-431,441-463
Sequence
Target Sequence 
>C. ELEGANS:193769_S_AT
gcacgtgcctgcgtggatgcagaagtggattctggggtacttggccactttcatgagaat
gtcaataagagaacccgatagtatagcattgctaaaagcgtcacagagcaaaaagtcaac
tattcggagaagctcaatacttcgagatttgaaaagggtgaaaaatatgtcaaacgttag
agcaaaatcaaaagagcaaaatgcaaatcgagagtgcgagtgcatggacccacttgtgca
tatctacgcagagtccatcatgagctgcctggcagcagacacaaaacctatgaacgggtc
aactattagagaagattttgcaagtgaaagcacatttcttggacgcgttgttagtgatgg
cataatgccaagaataagtgcttcatccaactctgtgctgacagaattcgaaacaagatt
tagacggatattaaaaagggtttaccgaagtcttcagcaacatgaaatacgagaagaaat
tcttgacgaaagatctcgaattcaatgcagtggcaacaacttgcatctgtcgttgatcga
cttttactatgtcttttttgcact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCACGTGCCTGCGTGGATGCAGAAG 509 315 1497 Antisense
GGTACTTGGCCACTTTCATGAGAAT 687 503 1532 Antisense
GAGAGTGCGAGTGCATGGACCCACT 255 395 1706 Antisense
TGGACCCACTTGTGCATATCTACGC 573 545 1721 Antisense
ATCTACGCAGAGTCCATCATGAGCT 147 31 1738 Antisense
GCCTGGCAGCAGACACAAAACCTAT 318 283 1763 Antisense
AAGCACATTTCTTGGACGCGTTGTT 428 151 1824 Antisense
AATAAGTGCTTCATCCAACTCTGTG 79 173 1869 Antisense
GGGTTTACCGAAGTCTTCAGCAACA 471 495 1934 Antisense
GTGGCAACAACTTGCATCTGTCGTT 511 491 2006 Antisense
ACTTTTACTATGTCTTTTTTGCACT 536 101 2036 Antisense
Sequence Source Affymetrix Proprietary Database