[Home] | [Total List]

[190117_at] ion channel protein

Description Y58G8A.1 /REP_DB=WormBase Gene ID /WP=CE24478 /TR=Q9N4R6 /GB=AAF60813.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ion channel protein
Cluster 6grp_total > 22      4grp_total > 59      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 422
1 2 3 4 range
A 305.4
(0.3)
A 		259.8
(-0.6)
A 		451.3
(3)
A 		128.3
(-3)
A 		323
B 287.8
(-0.7)
A 		479.7
(3)
P 		351.9
(0.6)
P 		164.7
(-3)
A 		315
C 300.8
(-0.3)
A 		386.7
(0.9)
P 		533.2
(3)
M 		111.7
(-3)
A 		422
avr 298
(0.2) 		375.4
(1.6) 		445.5
(3) 		134.9
(-3) 		311

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 399
1 2 3 4 5 6 range
A 364.3
(0.3)
P 		500.2
(3)
P 		349.1
(0)
P 		406.4
(1.1)
P 		348.1
(-0)
A 		196.4
(-3)
A 		304
B 454.6
(1.6)
P 		539
(3)
P 		392.1
(0.6)
P 		394.9
(0.6)
P 		236
(-2)
A 		175.4
(-3)
A 		364
C 399.2
(0.9)
P 		440.9
(1.5)
P 		537
(3)
P 		523.7
(2.8)
P 		334.2
(-0.1)
M 		140.1
(-3)
A 		397
avr 406
(1.4) 		493.4
(3) 		426.1
(1.7) 		441.7
(2) 		306.1
(-0.5) 		170.6
(-3) 		323
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 167
1 2 3 4 range
A 111.2
(2.6)
A 		56.4
(-0.7)
A 		118
(3)
A 		18.8
(-3)
A 		99
B 91.8
(1.1)
A 		118.5
(3)
P 		81.5
(0.3)
P 		35.1
(-3)
A 		83
C 99.6
(-0.1)
A 		111.2
(0.3)
P 		185.8
(3)
M 		18.8
(-3)
A 		167
avr 100.9
(1.4) 		95.4
(1.1) 		128.4
(3) 		24.2
(-3) 		104

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 133
1 2 3 4 5 6 range
A 67.2
(-2.1)
P 		177.9
(3)
P 		76
(-1.7)
P 		103.1
(-0.4)
P 		105
(-0.4)
A 		47.8
(-3)
A 		130
B 158.2
(1.9)
P 		179.4
(3)
P 		95.2
(-1.4)
P 		104.6
(-0.9)
P 		95.9
(-1.4)
A 		65.4
(-3)
A 		114
C 148
(3)
P 		134.5
(2.2)
P 		136.7
(2.3)
P 		105.3
(0.5)
P 		108.1
(0.6)
M 		46.9
(-3)
A 		101
avr 124.5
(0.9) 		163.9
(3) 		102.6
(-0.3) 		104.3
(-0.2) 		103
(-0.3) 		53.4
(-3) 		111
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190117_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15691
Sequence Type Exemplar sequence
Representative Public ID Y58G8A.1 NCBI
Target Description Y58G8A.1 /REP_DB=WormBase Gene ID /WP=CE24478 /TR=Q9N4R6 /GB=AAF60813.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ion 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_070766(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070766 NCBI Caenorhabditis elegans Y58G8A.1 (Y58G8A.1) mRNA, complete cds. 11/11 None
SNAP00000024887 ENSEMBL cdna:SNAP chromosome:CEL140:V:267710:271096:1 9/11 None
GENEFINDER00000024894 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:259294:271593:1 11/11 None
Y58G8A.1 ENSEMBL cdna:known chromosome:CEL140:V:268135:271158:1 gene:Y58G8A.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
chrV:268170-271096(+) 100.0 100.0
Public Domain and Genome References
Gene Title ion channel protein
Ensembl Y58G8A.1
Entrez Gene 178554 Entrez gene
SwissProt Q9N4R6 EMBL-EBI
WormBase CE24478 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 AAF60813 Hypothetical protein Y58G8A.1 [Caenorhabditis elegans] ref|NP_503167.1| Y58G8A.1 [Caenorhabditis elegans] 0.0
blast NP_503166 Y58G8A.2 [Caenorhabditis elegans] 1.0E-166
blast CAE66757 Hypothetical protein CBG12109 [Caenorhabditis briggsae] 1.0E-162
blast CAE66757 Hypothetical protein CBG12109 [Caenorhabditis briggsae] 1.0E-159
blast CAE66757 Hypothetical protein CBG12109 [Caenorhabditis briggsae] 1.0E-155
blast CAB07402 Hypothetical protein R03E1.3 [Caenorhabditis elegans] ref|NP_510359.2| R03E1.3 [Caenorhabditis elegans] 1.0E-138
Protein Domains
Database ID Description E-Value
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.8E-20
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 5.7E-11
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.8E-34
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.8E-20
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503167.1 4 259-281,286-305,320-342,462-484
Y58G8A.1 4 259-281,286-305,320-342,462-484
SNAP00000024887 4 259-281,286-303,313-335,455-477
GENEFINDER00000024894 3 975-997,1002-1021,1036-1058
Sequence
Target Sequence 
>C. ELEGANS:190117_AT
cttccttatcactctcaacatagcattgcaagcaacctacggatccaacatactcagcag
aatgccgccaggaagtgggcgcactcctaaaattgtccatctctattcaattgggctttt
gataagcgcgtttcaagttgtgctgattgtgatgagcaacttcctaagagtacggctccc
gtcacactatgagttcgattttggatatgatattacagaaattccaaaaaagtttgggct
aaccagatttttcactacgaaagggctgtcttttgatccacaggaactccttaaccctgc
ccaactcacatctgaagctgagattcaaaaggaggcaagcacatcaatcggaatttcaaa
ccctcttgccgaatcaggctctgacaccgacctactgattaaccta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTCCTTATCACTCTCAACATAGCA 581 219 876 Antisense
GCAACCTACGGATCCAACATACTCA 490 319 907 Antisense
ACATACTCAGCAGAATGCCGCCAGG 127 105 923 Antisense
TGCCGCCAGGAAGTGGGCGCACTCC 621 583 938 Antisense
CGCACTCCTAAAATTGTCCATCTCT 217 255 955 Antisense
GCAACTTCCTAAGAGTACGGCTCCC 630 187 1031 Antisense
GCTCCCGTCACACTATGAGTTCGAT 394 299 1050 Antisense
GGGCTAACCAGATTTTTCACTACGA 666 491 1111 Antisense
GATCCACAGGAACTCCTTAACCCTG 657 413 1150 Antisense
TCAAACCCTCTTGCCGAATCAGGCT 693 627 1231 Antisense
TGACACCGACCTACTGATTAACCTA 608 571 1257 Antisense
Sequence Source Affymetrix Proprietary Database