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[191567_at] Ligand-gated ionic channel

Description F55D10.5 /REP_DB=WormBase Gene ID /WP=CE04660 /TR=Q20828 /GB=AAA81730.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Ligand-gated ionic channel
Cluster 6grp_total > 23      4grp_total > 39      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 234
1 2 3 4 range
A 344.7
(3)
P 		110.9
(-3)
A 		121.2
(-2.7)
A 		273.2
(1.2)
A 		234
B 309.3
(3)
P 		150
(-2.1)
A 		121.6
(-3)
A 		120.2
(-3)
A 		189
C 266.5
(3)
P 		163.8
(-1)
A 		111.5
(-3)
A 		135.6
(-2.1)
A 		155
avr 306.8
(3) 		141.6
(-2.3) 		118.1
(-3) 		176.3
(-1.1) 		189

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 134
1 2 3 4 5 6 range
A 186.9
(3)
A 		151.6
(0.7)
A 		174.2
(2.2)
A 		153.8
(0.8)
A 		120
(-1.4)
A 		95
(-3)
A 		92
B 226.6
(3)
P 		150.6
(-0.5)
A 		127.6
(-1.6)
A 		104.5
(-2.7)
A 		170.7
(0.4)
M 		98.1
(-3)
A 		129
C 187.4
(3)
P 		186.1
(2.9)
P 		178.7
(2.4)
A 		148.3
(0.5)
A 		119.2
(-1.3)
A 		92.8
(-3)
A 		95
avr 200.3
(3) 		162.8
(0.9) 		160.2
(0.7) 		135.5
(-0.7) 		136.6
(-0.6) 		95.3
(-3) 		105
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 103
1 2 3 4 range
A 125.5
(3)
P 		24.1
(-3)
A 		31.7
(-2.6)
A 		40
(-2.1)
A 		101
B 98.6
(3)
P 		37
(-2.1)
A 		28.2
(-2.8)
A 		25.6
(-3)
A 		73
C 88.2
(3)
P 		47.1
(-0.8)
A 		38.9
(-1.5)
A 		22.9
(-3)
A 		65
avr 104.1
(3) 		36.1
(-2.5) 		32.9
(-2.7) 		29.5
(-3) 		75

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 56
1 2 3 4 5 6 range
A 34.5
(-0.8)
A 		53.9
(3)
A 		37.9
(-0.1)
A 		39
(0.1)
A 		36.2
(-0.4)
A 		23.1
(-3)
A 		31
B 78.8
(3)
P 		50.1
(-0.4)
A 		31
(-2.6)
A 		27.7
(-3)
A 		69.3
(1.9)
M 		36.6
(-2)
A 		51
C 69.4
(3)
P 		56.8
(1.1)
P 		45.5
(-0.6)
A 		29.8
(-3)
A 		38.6
(-1.7)
A 		31.1
(-2.8)
A 		40
avr 60.9
(3) 		53.6
(1.6) 		38.1
(-1.5) 		32.2
(-2.6) 		48
(0.5) 		30.3
(-3) 		31
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191567_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17054
Sequence Type Exemplar sequence
Representative Public ID F55D10.5 NCBI
Target Description F55D10.5 /REP_DB=WormBase Gene ID /WP=CE04660 /TR=Q20828 /GB=AAA81730.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Ligand-gated ionic 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_076409(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076409 NCBI Caenorhabditis elegans F55D10.5 (F55D10.5) mRNA, complete cds. 11/11 None
SNAP00000004379 ENSEMBL cdna:SNAP chromosome:CEL140:X:4722979:4724592:-1 11/11 None
GENEFINDER00000004385 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4722979:4726819:-1 11/11 None
F55D10.5 ENSEMBL cdna:known chromosome:CEL140:X:4722979:4728244:-1 gene:F55D10.5 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
chrX:4722979-4728245(-) 100.0 100.0
Public Domain and Genome References
Gene Title Ligand-gated ionic channel
Ensembl F55D10.5
Entrez Gene 186307 Entrez gene
SwissProt Q20828 EMBL-EBI
WormBase CE38372 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA81730 Hypothetical protein F55D10.5 [Caenorhabditis elegans] ref|NP_508810.2| F55D10.5 [Caenorhabditis elegans] gb|AAW34234.1| acetylcholine-gated chloride channel subunit ACC-3 [Caenorhabditis elegans] 0.0
blast CAE68641 Hypothetical protein CBG14531 [Caenorhabditis briggsae] 0.0
blast AAA81730 Hypothetical protein F55D10.5 [Caenorhabditis elegans] ref|NP_508810.2| F55D10.5 [Caenorhabditis elegans] gb|AAW34234.1| acetylcholine-gated chloride channel subunit ACC-3 [Caenorhabditis elegans] 1.0E-112
blast CAE75188 Hypothetical protein CBG23132 [Caenorhabditis briggsae] 1.0E-111
blast CAE74088 Hypothetical protein CBG21746 [Caenorhabditis briggsae] 1.0E-107
blast CAE68641 Hypothetical protein CBG14531 [Caenorhabditis briggsae] 1.0E-100
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 7.4E-12
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-75
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.2E-14
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-75
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.3E-10
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-6
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.2E-14
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-75
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508810.2 4 276-298,305-324,339-361,491-513
F55D10.5 4 276-298,311-328,338-360,510-532
SNAP00000004379 2 32-54,184-206
GENEFINDER00000004385 4 299-321,328-347,362-384,531-553
Sequence
Target Sequence 
>C. ELEGANS:191567_AT
ggaacctgccacgagtaagctatgtaaaagctttagacgtttggatgttagtctgtctaa
catttgtgttttgttccttattggaacttgcgatcattggctcaatgggtgctcgttctg
agaaccgacaagctcaacaacaaaaacaacaagatgaagaagcgacaaaacatcagaaag
gtcgggagaatagtacatgctctcatctaatgtctccatcatcgtgcccaaacagcccaa
ggatatgtagaaaccatattccgaatgatgttccgcagtcgttcaaaagttacggatcaa
caggtattaatgagggcaaaatggaaaatactttgattagcggtaacggttgttacccaa
gaatgcgaaaacggctcataattgcgtcgagcagcacaatttcccatgctccaaatgcca
accgatccgagaaagtattacttctagatggattagaagagacacaattttctcaagtgg
aaaccaagtttagttcaatggcatcgataaaaatgaagaagcattggaccacagaagaaa
tcgatcgattgtcgatgataatgtttcccggattgttcacactgttcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAACCTGCCACGAGTAAGCTATGT 150 531 995 Antisense
CATTTGTGTTTTGTTCCTTATTGGA 332 215 1055 Antisense
GGAACTTGCGATCATTGGCTCAATG 466 529 1077 Antisense
CAATGGGTGCTCGTTCTGAGAACCG 19 183 1097 Antisense
ACATGCTCTCATCTAATGTCTCCAT 162 107 1189 Antisense
GTGCCCAAACAGCCCAAGGATATGT 381 477 1218 Antisense
CCGAATGATGTTCCGCAGTCGTTCA 708 261 1255 Antisense
TGCGTCGAGCAGCACAATTTCCCAT 214 581 1377 Antisense
TCCAAATGCCAACCGATCCGAGAAA 707 585 1404 Antisense
TTGTCGATGATAATGTTTCCCGGAT 199 707 1543 Antisense
TTCCCGGATTGTTCACACTGTTCAA 392 697 1559 Antisense
Sequence Source Affymetrix Proprietary Database