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[191334_at] ligand-gated ionic channel

Description F12B6.3 /REP_DB=WormBase Gene ID /WP=CE09358 /TR=O01792 /GB=AAK21371.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster 6grp_total > 15      4grp_total > 50      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 60
1 2 3 4 range
A 2.2
(-3)
A 		42.5
(3)
A 		6.2
(-2.4)
A 		4
(-2.7)
A 		40
B 8.3
(-3)
A 		62.5
(3)
A 		34.3
(-0.1)
A 		13.7
(-2.4)
A 		54
C 20.2
(1.3)
A 		2.7
(-3)
A 		27.4
(3)
A 		2.6
(-3)
A 		25
avr 10.2
(-2.3) 		35.9
(3) 		22.6
(0.3) 		6.8
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 37.2
(2.6)
A 		39.6
(3)
A 		24.2
(0.5)
A 		17.5
(-0.5)
A 		12.7
(-1.3)
A 		2.1
(-3)
A 		38
B 31.7
(3)
A 		19.3
(0.4)
A 		21
(0.8)
A 		2.7
(-3)
A 		2.6
(-3)
A 		4.5
(-2.6)
A 		29
C 20.6
(2)
A 		18.1
(1.2)
A 		14.4
(0)
A 		4.9
(-3)
A 		23.9
(3)
A 		17.4
(0.9)
A 		19
avr 29.8
(3) 		25.7
(1.9) 		19.9
(0.3) 		8.4
(-2.9) 		13.1
(-1.6) 		8
(-3) 		22
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 0.8
(-2.9)
A 		9.2
(3)
A 		1.6
(-2.3)
A 		0.6
(-3)
A 		9
B 2.6
(-3)
A 		15.4
(3)
A 		8
(-0.5)
A 		2.9
(-2.9)
A 		13
C 6.7
(1.2)
A 		0.8
(-2.7)
A 		9.5
(3)
A 		0.4
(-3)
A 		9
avr 3.4
(-1.3) 		8.5
(3) 		6.4
(1.3) 		1.3
(-3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 6.9
(-0.2)
A 		14.1
(3)
A 		5.3
(-0.9)
A 		4.4
(-1.3)
A 		3.8
(-1.5)
A 		0.5
(-3)
A 		14
B 11
(3)
A 		6.4
(0.3)
A 		5.1
(-0.4)
A 		0.7
(-3)
A 		1
(-2.8)
A 		1.7
(-2.4)
A 		10
C 7.6
(2.9)
A 		5.5
(1)
A 		3.7
(-0.6)
A 		1
(-3)
A 		7.7
(3)
A 		5.8
(1.3)
A 		7
avr 8.5
(2.8) 		8.7
(3) 		4.7
(-0.6) 		2
(-3) 		4.2
(-1) 		2.7
(-2.4) 		7
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191334_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.59
Sequence Type Exemplar sequence
Representative Public ID F12B6.3 NCBI
Target Description F12B6.3 /REP_DB=WormBase Gene ID /WP=CE09358 /TR=O01792 /GB=AAK21371.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058545(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058545 NCBI Caenorhabditis elegans F12B6.3 (F12B6.3) mRNA, complete cds. 11/11 None
GENEFINDER00000032180 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:2243227:2249109:1 10/11 None
F12B6.3 ENSEMBL cdna:known chromosome:CEL140:I:2242231:2247282:1 gene:F12B6.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000032175 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:2242230-2247282(+) 91.99 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel
Ensembl F12B6.3
Entrez Gene 184377 Entrez gene
WormBase CE39013 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK21371 Hypothetical protein F12B6.3 [Caenorhabditis elegans] ref|NP_490946.2| F12B6.3 [Caenorhabditis elegans] 0.0
blast T15202 hypothetical protein F12B6.3 - Caenorhabditis elegans 0.0
blast CAE60301 Hypothetical protein CBG03886 [Caenorhabditis briggsae] 0.0
blast T15202 hypothetical protein F12B6.3 - Caenorhabditis elegans 1.0E-165
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.9E-11
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.0E-45
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.9E-11
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.8E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-43
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_490946.2 3 275-297,304-323,338-360
F12B6.3 3 275-297,304-323,338-360
GENEFINDER00000032180 6 200-219,224-246,253-272,287-309,408-430,440-459
Sequence
Target Sequence 
>C. ELEGANS:191334_AT
ccggctcgcatagtgttgggtgtgaactcgttgatgtcactcacttttcagttcggaaac
atcatccgatccctgccaccagtctcctatgtaaaagccatcgatctctggatgtgcacc
tgcgtcggcttcatcttcgcctccctcctcgaactcgccttcgtcgcctatcaggacaaa
aagctcatcttaaaatccggaaaatcaaatgcagcaatcagcactttggtcagctatctg
aaacactttgagccataccatgacgtgtcgtctccgccaccaccggctccgcttgatgag
aaaaaatcgatgagccgaacgacatcgactggtacgaatcgatcgagaagtgaacttgat
ggtttggatacgaaggatttggaggaggaaattgcggagtatcggaagttggcgtatgcc
aggaagaaatggagattgttggattttggagcaaatgttgataggatctcgtttattgtt
tttccactttcgcagcgttcaatgtggtttactggacatattaccttcaagacgtgcgga
tatccacttggacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCGGCTCGCATAGTGTTGGGTGTGA 83 265 1183 Antisense
AACTCGTTGATGTCACTCACTTTTC 654 141 1207 Antisense
TCGGAAACATCATCCGATCCCTGCC 560 605 1235 Antisense
GCCATCGATCTCTGGATGTGCACCT 523 281 1279 Antisense
CCTTCGTCGCCTATCAGGACAAAAA 666 267 1340 Antisense
GCAGCAATCAGCACTTTGGTCAGCT 709 311 1393 Antisense
TTGAGCCATACCATGACGTGTCGTC 467 705 1430 Antisense
GAGCCGAACGACATCGACTGGTACG 174 383 1494 Antisense
GATCTCGTTTATTGTTTTTCCACTT 333 417 1647 Antisense
TTTTCCACTTTCGCAGCGTTCAATG 342 677 1662 Antisense
AGACGTGCGGATATCCACTTGGACC 500 69 1712 Antisense
Sequence Source Affymetrix Proprietary Database