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[188990_at] ion channel

Description H35N03.1 /REP_DB=WormBase Gene ID /WP=CE19942 /TR=Q9TZI5 /GB=AAC67448.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=ion channel
Cluster 6grp_total > 02      4grp_total > 13      6grp_cgc > 52      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 41.3
(0.7)
A 		7.4
(-3)
A 		27.6
(-0.8)
A 		62
(3)
A 		55
B 41.2
(2.3)
M 		37.8
(1.8)
A 		7.6
(-3)
A 		45.4
(3)
P 		38
C 54.2
(-0.2)
M 		43.3
(-1)
A 		16.6
(-3)
A 		96.7
(3)
P 		80
avr 45.6
(0.3) 		29.5
(-1.6) 		17.3
(-3) 		68
(3) 		51

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 16.7
(-1.6)
A 		33.2
(3)
A 		24.5
(0.6)
A 		11.8
(-3)
A 		29
(1.8)
A 		22.5
(-0)
A 		21
B 45.6
(2)
P 		36.9
(0.6)
A 		30.7
(-0.4)
A 		41
(1.2)
P 		51.7
(3)
P 		15.1
(-3)
A 		37
C 31
(-0.4)
A 		52.6
(3)
A 		34.4
(0.2)
A 		37.7
(0.7)
A 		14.1
(-3)
A 		14.7
(-2.9)
A 		39
avr 31.1
(0.5) 		40.9
(3) 		29.9
(0.2) 		30.2
(0.3) 		31.6
(0.6) 		17.4
(-3) 		24
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 15
(3)
A 		1.6
(-3)
A 		7.2
(-0.5)
A 		9.1
(0.4)
A 		13
B 13.1
(3)
M 		9.3
(1)
A 		1.8
(-3)
A 		9.7
(1.2)
P 		11
C 17.9
(3)
M 		12.4
(0.3)
A 		5.8
(-3)
A 		16.3
(2.2)
P 		12
avr 15.3
(3) 		7.8
(-1.3) 		4.9
(-3) 		11.7
(0.9) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 3.1
(-2.9)
A 		11.8
(3)
A 		5.3
(-1.4)
A 		3
(-3)
A 		8.8
(1)
A 		5.5
(-1.3)
A 		9
B 15.9
(1)
P 		12.3
(-0.4)
A 		7.5
(-2.3)
A 		10.9
(-0.9)
P 		21
(3)
P 		5.6
(-3)
A 		15
C 11.5
(0.6)
A 		16
(3)
A 		8.8
(-0.8)
A 		7.6
(-1.4)
A 		4.6
(-3)
A 		4.9
(-2.8)
A 		11
avr 10.2
(0.6) 		13.4
(3) 		7.2
(-1.6) 		7.2
(-1.6) 		11.5
(1.6) 		5.3
(-3) 		8
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188990_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5404
Sequence Type Exemplar sequence
Representative Public ID H35N03.1 NCBI
Target Description H35N03.1 /REP_DB=WormBase Gene ID /WP=CE19942 /TR=Q9TZI5 /GB=AAC67448.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=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_062828(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062828 NCBI Caenorhabditis elegans EXPulsion defective (defecation) family member (exp-1) (exp-1) mRNA, complete cds. 11/11 None
SNAP00000038629 ENSEMBL cdna:SNAP chromosome:CEL140:II:6157185:6160996:-1 11/11 None
GENEFINDER00000038631 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6157185:6160975:-1 11/11 None
H35N03.1 ENSEMBL cdna:known chromosome:CEL140:II:6157120:6160975:-1 gene:H35N03.1 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
chrII:6157854-6159938(-) 100.0 100.0
Public Domain and Genome References
Gene Title ion channel
Gene Symbol exp-1
Ensembl H35N03.1
Entrez Gene 186801 Entrez gene
SwissProt Q9TZI5 EMBL-EBI
WormBase CE37026 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 AAC67448 Expulsion defective (defecation) protein 1 [Caenorhabditis elegans] ref|NP_495229.3| EXPulsion defective (defecation) family member (exp-1) [Caenorhabditis elegans] gb|AAQ96595.1| excitatory GABA receptor EXP-1B [Caenorhabditis elegans] 0.0
blast AAQ96594 excitatory GABA receptor EXP-1A [Caenorhabditis elegans] 0.0
blast CAE59254 Hypothetical protein CBG02582 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.0E-10
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-62
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.9E-10
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.0E-10
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-62
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.9E-10
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.9E-62
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495229.3 4 317-336,343-360,375-394,492-514
H35N03.1 4 317-336,343-360,375-394,492-514
SNAP00000038629 4 318-337,344-361,376-395,493-515
GENEFINDER00000038631 4 311-330,337-354,369-388,486-508
Sequence
Target Sequence 
>C. ELEGANS:188990_AT
gattcgattgccagactttacgattcaagaagcgtatgttacaagtcaaatggaaagtta
tgctacgggaaattattctcgactttatgtatgctttgtattttcccgatcttctggatt
ctgttttcttcaacttatcattccatctacggcagttgtaataacttcatgggtttcatt
atggatggagactgaaacagaatttcaggatatgatatcaattattctggcaattacttt
cctaatcttctcgtacaatgaaatgatgccacgtgtcagttatatcaaagcaatggatat
ttacttaggagtctgttttatgattgtttttctctccctgataaagttggcacttgtaaa
atatatgcgccagaaaatcatgttgacaagcgacagcgggaattctcttcgtgaaatgtc
acagatgtcaacgaggcagcgactgagggcccggaagacgtcaaacatga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATTCGATTGCCAGACTTTACGATT 337 431 603 Antisense
TATTCTCGACTTTATGTATGCTTTG 645 663 676 Antisense
GTATTTTCCCGATCTTCTGGATTCT 296 453 700 Antisense
TCTTCTGGATTCTGTTTTCTTCAAC 195 617 712 Antisense
CTTCAACTTATCATTCCATCTACGG 690 221 730 Antisense
ATTATTCTGGCAATTACTTTCCTAA 637 13 823 Antisense
CTTTCCTAATCTTCTCGTACAATGA 247 223 839 Antisense
GTTTTATGATTGTTTTTCTCTCCCT 335 449 917 Antisense
AGCGACAGCGGGAATTCTCTTCGTG 86 83 991 Antisense
CAACGAGGCAGCGACTGAGGGCCCG 27 185 1031 Antisense
AGGGCCCGGAAGACGTCAAACATGA 647 1 1048 Antisense
Sequence Source Affymetrix Proprietary Database