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[189368_at] channel protein

Description C04C3.2 /REP_DB=WormBase Gene ID /WP=CE16808 /TR=O44452 /GB=AAB92023.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=channel protein
Cluster 6grp_total > 19      4grp_total > 15      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 121
1 2 3 4 range
A 99.4
(3)
A 		4.1
(-3)
A 		10.6
(-2.6)
A 		61
(0.6)
A 		95
B 70.5
(0.1)
A 		12.9
(-3)
A 		31.5
(-2)
A 		125.1
(3)
A 		112
C 81.5
(0.7)
A 		29.7
(-3)
A 		37.3
(-2.5)
A 		114
(3)
M 		84
avr 83.8
(1.8) 		15.6
(-3) 		26.5
(-2.2) 		100
(3) 		84

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 67
1 2 3 4 5 6 range
A 71.8
(3)
A 		9.5
(-2.7)
A 		5.8
(-3)
A 		14.6
(-2.2)
A 		19.1
(-1.8)
A 		7
(-2.9)
A 		66
B 55.6
(3)
A 		11.2
(-2.4)
A 		6.4
(-3)
A 		52.4
(2.6)
A 		48.8
(2.2)
A 		29.5
(-0.2)
A 		49
C 17.9
(0.8)
A 		25.4
(3)
A 		4.5
(-3)
A 		8.5
(-1.9)
A 		8.5
(-1.9)
A 		8.9
(-1.7)
A 		21
avr 48.4
(3) 		15.4
(-1.6) 		5.6
(-3) 		25.2
(-0.3) 		25.5
(-0.2) 		15.1
(-1.7) 		43
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 35
1 2 3 4 range
A 36.2
(3)
A 		0.9
(-3)
A 		2.8
(-2.7)
A 		8.9
(-1.6)
A 		35
B 22.5
(1.9)
A 		3.2
(-3)
A 		7.3
(-2)
A 		26.7
(3)
A 		24
C 27
(3)
A 		8.5
(-3)
A 		13
(-1.5)
A 		19.2
(0.5)
M 		19
avr 28.6
(3) 		4.2
(-3) 		7.7
(-2.1) 		18.3
(0.5) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19
1 2 3 4 5 6 range
A 13.2
(3)
A 		3.4
(-1.9)
A 		1.3
(-3)
A 		3.7
(-1.8)
A 		5.8
(-0.7)
A 		1.7
(-2.8)
A 		12
B 19.4
(2.9)
A 		3.7
(-2.3)
A 		1.6
(-3)
A 		13.9
(1.1)
A 		19.8
(3)
A 		11
(0.1)
A 		18
C 6.7
(2.1)
A 		7.7
(3)
A 		1.1
(-3)
A 		1.7
(-2.5)
A 		2.7
(-1.5)
A 		3
(-1.3)
A 		7
avr 13.1
(3) 		4.9
(-1.2) 		1.3
(-3) 		6.4
(-0.4) 		9.4
(1.1) 		5.2
(-1) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189368_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11065
Sequence Type Exemplar sequence
Representative Public ID C04C3.2 NCBI
Target Description C04C3.2 /REP_DB=WormBase Gene ID /WP=CE16808 /TR=O44452 /GB=AAB92023.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=channel protein
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_067940(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067940 NCBI Caenorhabditis elegans C04C3.2 (C04C3.2) mRNA, complete cds. 11/11 None
SNAP00000029932 ENSEMBL cdna:SNAP chromosome:CEL140:IV:3415686:3419105:1 11/11 None
GENEFINDER00000029935 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:3415686:3419105:1 11/11 None
C04C3.2 ENSEMBL cdna:known chromosome:CEL140:IV:3415680:3419231:1 gene:C04C3.2 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:3415776-3419111(+) 99.39 100.0
Public Domain and Genome References
Gene Title channel protein
Ensembl C04C3.2
Entrez Gene 182195 Entrez gene
SwissProt O44452 EMBL-EBI
WormBase CE29558 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
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB92023 Hypothetical protein C04C3.2 [Caenorhabditis elegans] ref|NP_500341.1| C04C3.2 [Caenorhabditis elegans] 0.0
blast CAE73576 Hypothetical protein CBG21050 [Caenorhabditis briggsae] 0.0
blast CAE61536 Hypothetical protein CBG05440 [Caenorhabditis briggsae] 1.0E-127
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.8E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 8.4E-55
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.8E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.2E-50
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500341.1 4 246-268,281-303,313-335,431-453
C04C3.2 4 246-268,281-303,313-335,431-453
SNAP00000029932 4 240-262,275-297,307-329,425-447
GENEFINDER00000029935 4 246-268,281-303,313-335,431-453
Sequence
Target Sequence 
>C. ELEGANS:189368_AT
agtgtcactgggacttggttccctgctagccatgactgtcctcctggacattgtagctgg
cgccatgccaaaatccgacgccatcccccttctcgggtactacattatgcttgtcatcct
actctgcgccattggggtcgccgtgtcaatggctatgctctctatgtcacggagctgcat
acaaacttcgaaaatgccacccccgcactattatcgattactttttttgaatgtctgccg
ggtcgtcaaacagaatagtgggctgaatggagtggcgatgaatgagaagccaactgctat
cacaccccgtttcccggatctcatcgcgatttacaatcagctcatcgaagtggctcgggc
tcagaggacatatcgcgaacggatagaaaaacaaaagtggcagcatagagtagaaatcga
atggaacaaaatcttcgcgagaatcgatttcttcttcttgttccttttcgaaatgtttaa
cgtgcttattctggtactcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGTGTCACTGGGACTTGGTTCCCTG 536 57 771 Antisense
TCCTCCTGGACATTGTAGCTGGCGC 604 593 809 Antisense
TGGCGCCATGCCAAAATCCGACGCC 240 543 828 Antisense
CCCCCTTCTCGGGTACTACATTATG 354 261 855 Antisense
TACATTATGCTTGTCATCCTACTCT 283 645 871 Antisense
GTCAATGGCTATGCTCTCTATGTCA 692 463 915 Antisense
ACCCCCGCACTATTATCGATTACTT 338 89 969 Antisense
TCAGCTCATCGAAGTGGCTCGGGCT 417 623 1107 Antisense
GGCTCGGGCTCAGAGGACATATCGC 531 537 1122 Antisense
TCTTCTTCTTGTTCCTTTTCGAAAT 159 617 1220 Antisense
TAACGTGCTTATTCTGGTACTCTTC 593 637 1248 Antisense
Sequence Source Affymetrix Proprietary Database