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[190081_at] ion channel protein

Description F09G2.5 /REP_DB=WormBase Gene ID /WP=CE09300 /TR=O17402 /GB=AAB71323.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ion channel protein
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 60      6grp_total > 16      4grp_total > 46      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 545
1 2 3 4 range
A 708.5
(3)
P 		493
(-0.5)
P 		398.9
(-2.1)
P 		342
(-3)
P 		367
B 784.6
(3)
P 		465.8
(-0.5)
P 		239.9
(-3)
P 		369.5
(-1.6)
P 		545
C 651.8
(3)
P 		442.7
(-2)
P 		415.8
(-2.6)
P 		400.5
(-3)
P 		251
avr 715
(3) 		467.2
(-1.1) 		351.5
(-3) 		370.7
(-2.7) 		364

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 426
1 2 3 4 5 6 range
A 625.8
(3)
P 		528.2
(1.4)
P 		264.8
(-3)
P 		371.7
(-1.2)
P 		317.1
(-2.1)
P 		296.5
(-2.5)
P 		361
B 675.8
(3)
P 		523.2
(0.8)
P 		263.1
(-3)
P 		359.8
(-1.6)
P 		344.3
(-1.8)
P 		330.7
(-2)
P 		413
C 593.8
(3)
P 		538.5
(2)
P 		435.6
(0.2)
P 		366.3
(-1)
P 		250.3
(-3)
P 		308.1
(-2)
P 		344
avr 631.8
(3) 		530
(1.1) 		321.2
(-2.7) 		365.9
(-1.9) 		303.9
(-3) 		311.8
(-2.9) 		328
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 208
1 2 3 4 range
A 258
(3)
P 		107
(-1.4)
P 		104.3
(-1.4)
P 		50.1
(-3)
P 		208
B 250.2
(3)
P 		115
(-1.2)
P 		55.6
(-3)
P 		78.7
(-2.3)
P 		195
C 215.8
(3)
P 		127.3
(-0.6)
P 		144.9
(0.1)
P 		67.5
(-3)
P 		148
avr 241.3
(3) 		116.4
(-1.3) 		101.6
(-1.8) 		65.4
(-3) 		176

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 178
1 2 3 4 5 6 range
A 115.4
(-0.3)
P 		187.9
(3)
P 		57.7
(-3)
P 		94.3
(-1.3)
P 		95.7
(-1.2)
P 		72.2
(-2.3)
P 		130
B 235.2
(3)
P 		174.2
(0.9)
P 		63.9
(-3)
P 		95.3
(-1.9)
P 		139.9
(-0.3)
P 		123.3
(-0.9)
P 		171
C 220.1
(3)
P 		164.3
(0.7)
P 		110.9
(-1.5)
P 		73.7
(-3)
P 		81
(-2.7)
P 		103.1
(-1.8)
P 		146
avr 190.2
(3) 		175.5
(2.2) 		77.5
(-3) 		87.8
(-2.5) 		105.5
(-1.5) 		99.5
(-1.8) 		113
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190081_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11627
Sequence Type Exemplar sequence
Representative Public ID F09G2.5 NCBI
Target Description F09G2.5 /REP_DB=WormBase Gene ID /WP=CE09300 /TR=O17402 /GB=AAB71323.1 /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_072420(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072420 NCBI Caenorhabditis elegans F09G2.5 (F09G2.5) mRNA, complete cds. 11/11 None
SNAP00000025943 ENSEMBL cdna:SNAP chromosome:CEL140:V:7178162:7181282:1 11/11 None
GENEFINDER00000025954 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:7178162:7181282:1 11/11 None
F09G2.5 ENSEMBL cdna:known chromosome:CEL140:V:7178162:7181373:1 gene:F09G2.5 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:7178162-7181283(+) 100.0 100.0
Public Domain and Genome References
Gene Title ion channel protein
Ensembl F09G2.5
Entrez Gene 184265 Entrez gene
SwissProt O17402 EMBL-EBI
WormBase CE37627 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_504821 F09G2.5 [Caenorhabditis elegans] gb|AAB71323.3| Hypothetical protein F09G2.5 [Caenorhabditis elegans] 0.0
blast CAE72013 Hypothetical protein CBG19095 [Caenorhabditis briggsae] 0.0
blast CAA86760 Hypothetical protein C09G5.1 [Caenorhabditis elegans] ref|NP_496306.2| GABA/Glycine Receptor family (see gbr) family member (ggr-1) [Caenorhabditis elegans] sp|Q09453|GLRB4_CAEEL Glycine receptor beta-type chain 4 precursor 5.0E-65
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-26
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.6E-59
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.2E-20
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504821.3 4 4-26,335-357,401-423,534-556
F09G2.5 4 4-26,335-357,401-423,534-556
SNAP00000025943 4 4-26,335-357,401-423,534-556
GENEFINDER00000025954 2 416-438,549-571
Sequence
Target Sequence 
>C. ELEGANS:190081_AT
tggatgtcattctggttggacccgcgtgccagtccagcacgtatctcacttacaatcacc
tcattactcactttgacgacgatgagcaacggagcaagacaggatttgccgcaggtctcc
tatatcaaagcattggatatatggttgacattctcgcaagcgttgatctttttggtattg
ttggaatattcgtttgtttcgtattatatgacaaaaaggactacggattgttcacatcgg
aatatgttctatgaggaaagagtacaggaatgcaaaagggaggagaaggctcgaaagtcg
attgttaataacaacaagccagtaattgcgaataataccgagggatccgacctgaatcgg
aataaaaaatctcagcaattttctttgactcatggaatatccgcatgccttaatgaatca
tctgcgctgatgtcagtcactccggttccttctcgattattcaccaaatttgacaccaac
aaaccatgtgctcgatgctcggagaaaaacgaacgaatagcatttaaaattgacgaatat
agtcgatggttgtttccaacagttttttcgctattttgtgtttcctactggctcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGATGTCATTCTGGTTGGACCCGC 125 549 1189 Antisense
CGTGCCAGTCCAGCACGTATCTCAC 184 245 1213 Antisense
GTATCTCACTTACAATCACCTCATT 314 455 1229 Antisense
TCACCTCATTACTCACTTTGACGAC 191 625 1244 Antisense
TGCCGCAGGTCTCCTATATCAAAGC 550 585 1295 Antisense
TGGTTGACATTCTCGCAAGCGTTGA 552 547 1330 Antisense
ATACCGAGGGATCCGACCTGAATCG 259 23 1523 Antisense
TCATCTGCGCTGATGTCAGTCACTC 279 621 1606 Antisense
GGTTCCTTCTCGATTATTCACCAAA 272 507 1632 Antisense
CAACAAACCATGTGCTCGATGCTCG 567 189 1665 Antisense
TATTTTGTGTTTCCTACTGGCTCTA 501 663 1760 Antisense
Sequence Source Affymetrix Proprietary Database