[Home] | [Total List]

[192579_at] neurotransmitter-gated ion channel

Description C50B6.11 /REP_DB=WormBase Gene ID /WP=CE08880 /TR=P91985 /GB=CAB02858.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=neurotransmitter-gated ion channel
Cluster 6grp_total > 58      4grp_total > 26      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 8.2
(-3)
A 		24
(-1.1)
A 		43.5
(1.2)
A 		58.4
(3)
A 		50
B 18
(-3)
A 		40.7
(1.7)
A 		27.4
(-1)
A 		46.8
(3)
A 		29
C 51.2
(2.5)
A 		55.1
(3)
A 		7.5
(-3)
A 		47.7
(2.1)
A 		48
avr 25.8
(-3) 		39.9
(0.4) 		26.1
(-2.9) 		51
(3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 62
1 2 3 4 5 6 range
A 68.6
(3)
A 		35.6
(-1.6)
A 		48.7
(0.2)
A 		32.3
(-2.1)
A 		25.7
(-3)
A 		57.8
(1.5)
A 		43
B 43.7
(1.7)
A 		30
(0)
A 		32.6
(0.3)
A 		6.4
(-3)
A 		24.1
(-0.8)
A 		53.6
(3)
A 		47
C 12.7
(-3)
A 		29.3
(-0.5)
A 		32.6
(-0)
A 		44.1
(1.7)
A 		53
(3)
A 		47.3
(2.2)
A 		40
avr 41.7
(0.3) 		31.6
(-2.1) 		38
(-0.5) 		27.6
(-3) 		34.3
(-1.4) 		52.9
(3) 		25
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 3
(-3)
A 		5.2
(-1.4)
A 		11.4
(3)
A 		8.6
(1)
A 		8
B 5.7
(-3)
A 		10.1
(3)
A 		6.4
(-2)
A 		10
(2.9)
A 		4
C 17
(3)
A 		15.8
(2.5)
A 		2.6
(-3)
A 		8
(-0.8)
A 		14
avr 8.6
(-0) 		10.4
(3) 		6.8
(-3) 		8.9
(0.5) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 12.6
(1.6)
A 		12.7
(1.7)
A 		10.6
(-0.3)
A 		8.2
(-2.6)
A 		7.8
(-3)
A 		14.1
(3)
A 		6
B 15.2
(1.4)
A 		10
(-0.3)
A 		7.9
(-1)
A 		1.7
(-3)
A 		9.8
(-0.3)
A 		20
(3)
A 		18
C 4.7
(-3)
A 		8.9
(-1)
A 		8.3
(-1.3)
A 		8.9
(-1)
A 		17.1
(3)
A 		15.8
(2.4)
A 		12
avr 10.8
(-0.4) 		10.5
(-0.6) 		8.9
(-1.5) 		6.3
(-3) 		11.6
(0.1) 		16.6
(3) 		10
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192579_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12778
Sequence Type Exemplar sequence
Representative Public ID C50B6.11 NCBI
Target Description C50B6.11 /REP_DB=WormBase Gene ID /WP=CE08880 /TR=P91985 /GB=CAB02858.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=neurotransmitter-gated ion channel
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_073907
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000011272 ENSEMBL cdna:SNAP chromosome:CEL140:V:13342832:13345102:1 None
NM_073907 NCBI Caenorhabditis elegans C50B6.11 (C50B6.11) mRNA, complete cds. None
GENEFINDER00000011293 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13342647:13345296:1 None
C50B6.11 ENSEMBL cdna:known chromosome:CEL140:V:13342647:13345308:1 gene:C50B6.11 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:13342646-13345308(+) 100.0 100.0
Public Domain and Genome References
Gene Title neurotransmitter-gated ion channel
Ensembl C50B6.11
Entrez Gene 183638 Entrez gene
SwissProt P91985 EMBL-EBI
WormBase CE36634 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
Protein Similarities
Method ID Description E-Value
blast CAB02858 Hypothetical protein C50B6.11 [Caenorhabditis elegans] ref|NP_506308.2| C50B6.11 [Caenorhabditis elegans] 0.0
blast CAB02858 Hypothetical protein C50B6.11 [Caenorhabditis elegans] ref|NP_506308.2| C50B6.11 [Caenorhabditis elegans] 1.0E-151
blast CAE62615 Hypothetical protein CBG06736 [Caenorhabditis briggsae] 1.0E-150
blast CAE62615 Hypothetical protein CBG06736 [Caenorhabditis briggsae] 1.0E-149
blast CAE62615 Hypothetical protein CBG06736 [Caenorhabditis briggsae] 1.0E-120
blast CAA98509 Hypothetical protein K10D6.1 [Caenorhabditis elegans] ref|NP_505841.2| K10D6.1 [Caenorhabditis elegans] 1.0E-108
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.0E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 7.1E-70
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.4E-63
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506308.2 3 280-302,314-331,346-368
C50B6.11 3 280-302,314-331,346-368
SNAP00000011272 2 231-253,265-282
GENEFINDER00000011293 3 280-302,314-331,346-368
Sequence
Target Sequence 
>C. ELEGANS:192579_AT
tagttttttccctttgacacatgttatattccacgtttcacctgccctctttcgatcttc
aatcattgttttcagctttacttacaacaatgaagaagtccgacttcaatggaacagtca
acgatcaccagtattcgctttacaagagattagaatcgcagacttctggcttaaagacat
cacaccagcagtcatcaaaagggactatccagctggattatgggatgaacttgttgtgac
atttgtctttgaacgacgatacatgtggtacttccttcaagcatatcttcccacgttctt
ctccatttttatcagttggattgcattctcattaggacctcaagcaatcactccgcgaac
tatgattggtgtcaatgcgttgctttcaatgatattccactttggatcaattatgaaaaa
tttgccaagagtttcttatattaaggcaattgatgtctggatgctgagttcaatgacatt
tgtctttctgtcacttattga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAGTTTTTTCCCTTTGACACATGTT 699 653 711 Antisense
CATGTTATATTCCACGTTTCACCTG 535 209 730 Antisense
CCCTCTTTCGATCTTCAATCATTGT 383 259 755 Antisense
GTCAACGATCACCAGTATTCGCTTT 676 463 827 Antisense
AAGACATCACACCAGCAGTCATCAA 396 153 884 Antisense
GACGATACATGTGGTACTTCCTTCA 321 377 965 Antisense
TACTTCCTTCAAGCATATCTTCCCA 472 645 979 Antisense
GGATTGCATTCTCATTAGGACCTCA 241 509 1028 Antisense
TTAGGACCTCAAGCAATCACTCCGC 672 681 1042 Antisense
GATTGGTGTCAATGCGTTGCTTTCA 179 435 1074 Antisense
CATTTGTCTTTCTGTCACTTATTGA 412 215 1187 Antisense
Sequence Source Affymetrix Proprietary Database