[Home] | [Total List]

[188937_at] ion channel

Description Y39A3B.2 /REP_DB=WormBase Gene ID /WP=CE21643 /TR=Q9N517 /GB=AAF60513.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ion channel
Cluster 6grp_total > 0      4grp_total > 09      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 50
1 2 3 4 range
A 1.4
(-3)
A 		2.9
(-0.8)
A 		2
(-2.1)
A 		5.4
(3)
A 		4
B 3.3
(-3)
A 		5.8
(2.6)
A 		6
(3)
A 		4.1
(-1.2)
A 		3
C 2.3
(-3)
A 		2.8
(-2.9)
A 		3.5
(-2.9)
A 		51.6
(3)
A 		49
avr 2.3
(-3) 		3.8
(-2.5) 		3.8
(-2.5) 		20.4
(3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 2.9
(-2.2)
A 		10.4
(3)
A 		1.8
(-3)
A 		3.6
(-1.7)
A 		1.9
(-2.9)
A 		6.7
(0.4)
A 		9
B 1.2
(-3)
A 		2.9
(2.4)
A 		2.1
(-0.2)
A 		3.1
(3)
A 		2.7
(1.7)
A 		1.8
(-1.1)
A 		2
C 1.5
(-3)
A 		2.9
(0.2)
A 		4.1
(3)
A 		2.1
(-1.6)
A 		2.7
(-0.2)
A 		2.7
(-0.2)
A 		3
avr 1.9
(-3) 		5.4
(3) 		2.7
(-1.6) 		2.9
(-1.3) 		2.4
(-2.1) 		3.7
(0.1) 		4
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8
1 2 3 4 range
A 0.5
(-3)
A 		0.6
(-1)
A 		0.5
(-3)
A 		0.8
(3)
A 		0
B 1.1
(-0.6)
A 		1.4
(3)
A 		1.4
(3)
A 		0.9
(-3)
A 		0
C 0.8
(-3)
A 		0.8
(-3)
A 		1.2
(-2.7)
A 		8.7
(3)
A 		8
avr 0.8
(-3) 		0.9
(-2.8) 		1
(-2.6) 		3.5
(3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 0.5
(-2.8)
A 		3.7
(3)
A 		0.4
(-3)
A 		0.9
(-2.1)
A 		0.6
(-2.6)
A 		1.6
(-0.8)
A 		3
B 0.4
(-3)
A 		1
(2.1)
A 		0.5
(-2.1)
A 		0.8
(0.4)
A 		1.1
(3)
A 		0.7
(-0.4)
A 		1
C 0.6
(-1.3)
A 		0.9
(1.3)
A 		1.1
(3)
A 		0.4
(-3)
A 		0.9
(1.3)
A 		0.9
(1.3)
A 		1
avr 0.5
(-3) 		1.9
(3) 		0.7
(-2.1) 		0.7
(-2.1) 		0.9
(-1.3) 		1.1
(-0.4) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188937_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8177
Sequence Type Exemplar sequence
Representative Public ID Y39A3B.2 NCBI
Target Description Y39A3B.2 /REP_DB=WormBase Gene ID /WP=CE21643 /TR=Q9N517 /GB=AAF60513.1 /SUBMIT=ST.LOUIS /CHR=3 /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_065088(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065088 NCBI Caenorhabditis elegans Y39A3B.2 (Y39A3B.2) mRNA, complete cds. 10/11 None
GENEFINDER00000018251 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:1998309:2002434:1 11/11 None
Y39A3B.2 ENSEMBL cdna:known chromosome:CEL140:III:1998309:2002426:1 gene:Y39A3B.2 10/11 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
chrIII:1998308-2002426(+) 100.0 100.0
Public Domain and Genome References
Gene Title ion channel
Ensembl Y39A3B.2
Entrez Gene 189722 Entrez gene
SwissProt Q9N517 EMBL-EBI
WormBase CE35080 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 NP_497489 Y39A3B.2 [Caenorhabditis elegans] gb|AAF60513.2| Hypothetical protein Y39A3B.2 [Caenorhabditis elegans] 0.0
blast CAE69099 Hypothetical protein CBG15124 [Caenorhabditis briggsae] 0.0
blast CAA90332 Hypothetical protein C39B10.2 [Caenorhabditis elegans] ref|NP_509753.2| C39B10.2 [Caenorhabditis elegans] 1.0E-110
blast CAA90332 Hypothetical protein C39B10.2 [Caenorhabditis elegans] ref|NP_509753.2| C39B10.2 [Caenorhabditis elegans] 1.0E-103
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.0E-31
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-41
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.6E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497489.2 4 200-222,229-251,266-288,355-374
Y39A3B.2 4 200-222,229-251,266-288,355-374
GENEFINDER00000018251 3 200-222,229-251,266-288
Sequence
Target Sequence 
>C. ELEGANS:188937_AT
gtacactttaacacacaattcctcaagagtcggcgaattttcgtgtctgctgggaatgtt
gaagctgaaacgggcaattggattccatttagtgcagagttatatcccaacggggcttat
tgtggccatatcgtgggtttcgttttggatcgatcggcgagcggttccggcaagagttag
cttgtcatttactactttattgacgttgagtacacagggtaatggtatacgatatgcact
gccggcggtttcatatgccaaagctattgattatttctacggagtgtgcatgctgttcat
attcggtgttctgttggagtttgcggcggtgaacagttacatgcgacgagccaacaagta
taatcatatggctgaaaaaattcagagcgcctatggtggaaagcctataattgcagctga
ctatgattccgactacgaggagggtccgaccaaatactatggcaatttgaacaaaaactc
ggctcatttgatgtacaaagcactgaaattttcgagaaaagcattatcgatcgataaagc
agcacggtttgcgtttccat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTACACTTTAACACACAATTCCTCA 414 461 537 Antisense
GCGAATTTTCGTGTCTGCTGGGAAT 427 287 569 Antisense
ATATCCCAACGGGGCTTATTGTGGC 230 19 638 Antisense
TTGGATCGATCGGCGAGCGGTTCCG 145 707 681 Antisense
ATGCACTGCCGGCGGTTTCATATGC 277 43 770 Antisense
CATGCTGTTCATATTCGGTGTTCTG 322 211 825 Antisense
CGGTGTTCTGTTGGAGTTTGCGGCG 572 243 840 Antisense
GGTGAACAGTTACATGCGACGAGCC 158 501 864 Antisense
GCAGCTGACTATGATTCCGACTACG 556 313 949 Antisense
TCCGACTACGAGGAGGGTCCGACCA 563 569 964 Antisense
AAAGCAGCACGGTTTGCGTTTCCAT 491 121 1072 Antisense
Sequence Source Affymetrix Proprietary Database