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[190698_at] ligand-gated ion channel

Description C53D6.3 /REP_DB=WormBase Gene ID /WP=CE05488 /TR=Q18812 /GB=CAA94228.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=ligand-gated ion channel
Cluster 6grp_total > 24      4grp_total > 30      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 145
1 2 3 4 range
A 134.5
(3)
P 		36.9
(-1.8)
A 		11.7
(-3)
A 		101.2
(1.4)
M 		123
B 156.9
(3)
P 		89.7
(-1.6)
P 		68.3
(-3)
A 		105.1
(-0.5)
M 		89
C 126.9
(2.4)
P 		71.2
(-1.1)
P 		40
(-3)
A 		136.8
(3)
P 		97
avr 139.4
(3) 		65.9
(-1.4) 		40
(-3) 		114.4
(1.5) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 106
1 2 3 4 5 6 range
A 132.6
(3)
P 		82.1
(0.1)
P 		90.8
(0.6)
P 		26.5
(-3)
A 		57.4
(-1.3)
P 		29.3
(-2.8)
A 		106
B 116.4
(3)
P 		103.4
(2)
P 		109.5
(2.5)
P 		70.3
(-0.7)
P 		56.2
(-1.8)
P 		40.8
(-3)
A 		76
C 106.5
(3)
P 		100.4
(2.5)
P 		68.6
(0.1)
P 		81.5
(1.1)
P 		50.3
(-1.2)
A 		27.1
(-3)
A 		79
avr 118.5
(3) 		95.3
(1.4) 		89.6
(1) 		59.4
(-1.1) 		54.6
(-1.5) 		32.4
(-3) 		86
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 49
(3)
P 		8
(-2.4)
A 		3.1
(-3)
A 		14.8
(-1.5)
M 		46
B 50
(3)
P 		22.2
(-1.9)
P 		15.8
(-3)
A 		22.4
(-1.8)
M 		34
C 42
(3)
P 		20.5
(-1.6)
P 		13.9
(-3)
A 		23.1
(-1)
P 		28
avr 47
(3) 		16.9
(-2) 		10.9
(-3) 		20.1
(-1.5) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 34
1 2 3 4 5 6 range
A 24.4
(1.7)
P 		29.2
(3)
P 		19.8
(0.5)
P 		6.7
(-3)
A 		17.3
(-0.2)
P 		7.1
(-2.9)
A 		23
B 40.5
(3)
P 		34.4
(1.6)
P 		26.6
(-0.3)
P 		18.6
(-2.2)
P 		22.8
(-1.2)
P 		15.2
(-3)
A 		25
C 39.5
(3)
P 		30.6
(1.2)
P 		17.5
(-1.3)
P 		16.4
(-1.6)
P 		16.3
(-1.6)
A 		9.1
(-3)
A 		30
avr 34.8
(3) 		31.4
(2.2) 		21.3
(-0.3) 		13.9
(-2.2) 		18.8
(-1) 		10.5
(-3) 		24
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190698_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9516
Sequence Type Exemplar sequence
Representative Public ID C53D6.3 NCBI
Target Description C53D6.3 /REP_DB=WormBase Gene ID /WP=CE05488 /TR=Q18812 /GB=CAA94228.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=ligand-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_069166(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069166 NCBI Caenorhabditis elegans C53D6.3 (C53D6.3) mRNA, complete cds. 11/11 None
SNAP00000020663 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9016768:9019081:1 11/11 None
GENEFINDER00000020674 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9016768:9019081:1 11/11 None
C53D6.3 ENSEMBL cdna:known chromosome:CEL140:IV:9016768:9019081:1 gene:C53D6.3 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
chrIV:9016773-9019087(+) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ion channel
Ensembl C53D6.3
Entrez Gene 183758 Entrez gene
SwissProt Q18812 EMBL-EBI
WormBase CE05488 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
4890 GABA-A receptor 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 CAA94228 Hypothetical protein C53D6.3 [Caenorhabditis elegans] ref|NP_501567.1| C53D6.3 [Caenorhabditis elegans] 0.0
blast CAE74088 Hypothetical protein CBG21746 [Caenorhabditis briggsae] 0.0
blast CAA98509 Hypothetical protein K10D6.1 [Caenorhabditis elegans] ref|NP_505841.2| K10D6.1 [Caenorhabditis elegans] 1.0E-145
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.7E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.0E-68
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.7E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.3E-62
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501567.1 4 259-281,293-310,325-347,407-429
C53D6.3 4 259-281,293-310,325-347,407-429
SNAP00000020663 4 276-298,310-327,342-364,424-446
GENEFINDER00000020674 4 259-281,293-310,325-347,407-429
Sequence
Target Sequence 
>C. ELEGANS:190698_AT
gtgggacgagcttcatgttacaataatatttgagagacggtttatttggtatttcatgca
ggcatatctaccaacatatttgaccatttttataagctggatatcattctccctcggctc
acgtgcaattcctgctcgtacaatgctcggagttaatagccttttggcaattgttttctc
atttggaaatattatgaggaatctgccacgggtttcatatatcaaaggaattgatgtttg
gatgcttgtatcaatgacattcattttctgttcattgcttgaacttgctattgttggttt
tatggttcgagatgaaactgtagcgaagaaaaagcaacagaagaaaatttcagggaatat
ttcccgagaagaatctccacatggaattatatcagagcgtcgttttatgttcccaccggg
ttgctctgaatcttcaaaatctttgagctcatgcacaagtggttggactccggaacgaat
tgactcaatttccagtgtcatgttcccat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGGACGAGCTTCATGTTACAATA 609 487 747 Antisense
TTCATGCAGGCATATCTACCAACAT 340 687 799 Antisense
ATAAGCTGGATATCATTCTCCCTCG 406 25 838 Antisense
GCCTTTTGGCAATTGTTTTCTCATT 34 283 905 Antisense
TGAGGAATCTGCCACGGGTTTCATA 122 567 941 Antisense
GACATTCATTTTCTGTTCATTGCTT 350 371 1002 Antisense
ATCAGAGCGTCGTTTTATGTTCCCA 62 29 1137 Antisense
ACCGGGTTGCTCTGAATCTTCAAAA 555 85 1161 Antisense
CATGCACAAGTGGTTGGACTCCGGA 288 209 1196 Antisense
GGACTCCGGAACGAATTGACTCAAT 317 525 1211 Antisense
TCAATTTCCAGTGTCATGTTCCCAT 663 633 1231 Antisense
Sequence Source Affymetrix Proprietary Database