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[191519_at] ligand-gated ionic channel

Description F11C7.1 /REP_DB=WormBase Gene ID /WP=CE23644 /TR=Q19351 /GB=AAC69013.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster 6grp_total > 14      4grp_total > 05      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 150
1 2 3 4 range
A 55.1
(-0.8)
A 		8
(-3)
A 		23.6
(-2.3)
A 		139.1
(3)
M 		131
B 69.1
(3)
M 		10.7
(-3)
A 		21.9
(-1.8)
A 		39
(-0.1)
A 		58
C 16.5
(-3)
A 		31.2
(-2.4)
A 		44
(-1.8)
A 		158.1
(3)
A 		142
avr 46.9
(-1.1) 		16.6
(-3) 		29.8
(-2.2) 		112.1
(3) 		96

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 56.1
(3)
A 		34.3
(0.2)
A 		43.1
(1.3)
A 		36.6
(0.5)
A 		19
(-1.8)
A 		9.5
(-3)
A 		47
B 48.4
(3)
A 		6.4
(-2.8)
A 		12.9
(-1.9)
A 		26.5
(-0)
A 		5.3
(-3)
A 		8.3
(-2.6)
A 		43
C 36
(0.8)
A 		52.9
(3)
A 		31.3
(0.2)
A 		24.6
(-0.7)
A 		13.2
(-2.1)
A 		6.6
(-3)
A 		46
avr 46.8
(3) 		31.2
(0.6) 		29.1
(0.3) 		29.2
(0.3) 		12.5
(-2.3) 		8.1
(-3) 		39
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 20.1
(2.9)
A 		1.7
(-3)
A 		6.2
(-1.6)
A 		20.4
(3)
M 		19
B 22
(3)
M 		2.6
(-3)
A 		5.1
(-2.2)
A 		8.3
(-1.2)
A 		19
C 5.5
(-3)
A 		9
(-2)
A 		15.3
(-0.2)
A 		26.7
(3)
A 		21
avr 15.9
(1.9) 		4.4
(-3) 		8.9
(-1.1) 		18.5
(3) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15
1 2 3 4 5 6 range
A 10.3
(1.8)
A 		12.2
(3)
A 		9.4
(1.3)
A 		9.3
(1.2)
A 		5.7
(-0.9)
A 		2.3
(-3)
A 		10
B 16.8
(3)
A 		2.1
(-3)
A 		3.1
(-2.6)
A 		7
(-1)
A 		2.2
(-3)
A 		3.1
(-2.6)
A 		15
C 13.4
(1.8)
A 		16.1
(3)
A 		8
(-0.5)
A 		4.9
(-1.8)
A 		4.3
(-2.1)
A 		2.2
(-3)
A 		14
avr 13.5
(3) 		10.1
(1.1) 		6.8
(-0.7) 		7.1
(-0.5) 		4.1
(-2.1) 		2.5
(-3) 		11
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191519_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17708
Sequence Type Exemplar sequence
Representative Public ID F11C7.1 NCBI
Target Description F11C7.1 /REP_DB=WormBase Gene ID /WP=CE23644 /TR=Q19351 /GB=AAC69013.2 /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_078423(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078423 NCBI Caenorhabditis elegans F11C7.1 (F11C7.1) mRNA, complete cds. 11/11 None
F11C7.1 ENSEMBL cdna:known chromosome:CEL140:X:17428906:17431926:1 gene:F11C7.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000036956 8/11 Cross Hyb Matching Probes None
SNAP00000036937 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:17428904-17431925(+) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel
Ensembl F11C7.1
Entrez Gene 184344 Entrez gene
SwissProt Q19351 EMBL-EBI
WormBase CE23644 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
Protein Similarities
Method ID Description E-Value
blast AAC69013 Hypothetical protein F11C7.1 [Caenorhabditis elegans] ref|NP_510824.1| F11C7.1 [Caenorhabditis elegans] 0.0
blast CAE69678 Hypothetical protein CBG15930 [Caenorhabditis briggsae] 1.0E-123
blast CAD54179 Hypothetical protein Y44A6E.1a [Caenorhabditis elegans] emb|CAA22072.2| Hypothetical protein Y44A6E.1a [Caenorhabditis elegans] emb|CAD54133.1| Hypothetical protein Y44A6E.1a [Caenorhabditis elegans] ref|NP_001024239.1| Y44A6E.1a [Caenorhabditis elegans] 8.0E-79
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.4E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 7.5E-56
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510824.1 3 36-58,286-308,321-338
F11C7.1 3 36-58,286-308,321-338
Sequence
Target Sequence 
>C. ELEGANS:191519_AT
gatgctcctagaagctgttcgatcaccgatcaaagtttcttataccggtgaggtcaccta
tgcatacccagcaatttacacagtgctttgtcaaattggaattgccacttttccgtttga
tgatcaagtatacgttcagtttgcttcctgggcttacgatgaggataagattttgctcaa
tgcatcacataaaccgctactcaaaaactactctcccaacgaggaatgggcacttcaggt
cagctgttacaagggttttggaagatttttgaactttttgaaaacagatgtagacatggc
acgaaaagaatacgagcatgaagaaactgttgtcagtgagataatctattacatcaaagt
tgcccgcaaaccgttctactaccttatcagtcttgtggtacctagttatattatatgtgt
actatcaattgcgggactgttcgccaggttttcaacaaaacatgaaagacaggaacgatt
cacacttggagtcactgcaattctcagtatggctgtcttatcattggttgttactgaaaa
ggtaccacatagttcggaaaatgttccactcctcagtaagttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGCTCCTAGAAGCTGTTCGATCA 77 415 495 Antisense
GTCACCTATGCATACCCAGCAATTT 36 467 547 Antisense
AATTGCCACTTTTCCGTTTGATGAT 382 177 594 Antisense
TTCAGTTTGCTTCCTGGGCTTACGA 477 687 629 Antisense
AATGCATCACATAAACCGCTACTCA 169 165 673 Antisense
TACTCAAAAACTACTCTCCCAACGA 622 645 692 Antisense
GAATGGGCACTTCAGGTCAGCTGTT 289 333 718 Antisense
CAAACCGTTCTACTACCTTATCAGT 458 189 861 Antisense
AATTGCGGGACTGTTCGCCAGGTTT 519 175 921 Antisense
AGGAACGATTCACACTTGGAGTCAC 30 53 965 Antisense
AAATGTTCCACTCCTCAGTAAGTTT 211 119 1053 Antisense
Sequence Source Affymetrix Proprietary Database