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[193410_at] neurotransmitter-gated ion-channel protein

Description Y73F8A.2 /REP_DB=WormBase Gene ID /WP=CE22973 /TR=Q9NA62 /GB=CAB60529.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=neurotransmitter-gated ion-channel protein
Cluster 6grp_total > 14      4grp_total > 39      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 88
1 2 3 4 range
A 96.4
(3)
P 		44.8
(-2.9)
A 		43.5
(-3)
A 		63
(-0.8)
A 		53
B 84.2
(3)
A 		25.9
(-1.6)
A 		8.4
(-3)
A 		16
(-2.4)
A 		76
C 78.7
(3)
A 		9.3
(-3)
A 		22.8
(-1.8)
A 		56.8
(1.1)
A 		69
avr 86.4
(3) 		26.7
(-2.8) 		24.9
(-3) 		45.3
(-1) 		62

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 119
1 2 3 4 5 6 range
A 123.8
(3)
A 		42.7
(-1.1)
A 		39.5
(-1.3)
A 		29.8
(-1.7)
A 		5
(-3)
A 		5
(-3)
A 		119
B 101
(3)
A 		76.8
(1.4)
P 		33.6
(-1.3)
A 		49.7
(-0.3)
A 		16.9
(-2.4)
A 		8
(-3)
A 		93
C 52.3
(0.7)
A 		74.2
(3)
A 		26.3
(-2)
A 		34.2
(-1.2)
A 		16.7
(-3)
A 		29.2
(-1.7)
A 		58
avr 92.4
(3) 		64.6
(0.9) 		33.1
(-1.5) 		37.9
(-1.1) 		12.9
(-3) 		14.1
(-2.9) 		80
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 35.1
(3)
P 		9.7
(-2.9)
A 		11.4
(-2.5)
A 		9.2
(-3)
A 		26
B 26.8
(3)
A 		6.4
(-1.9)
A 		1.9
(-3)
A 		3.4
(-2.6)
A 		25
C 26.1
(3)
A 		2.7
(-3)
A 		8
(-1.6)
A 		9.6
(-1.2)
A 		23
avr 29.3
(3) 		6.3
(-3) 		7.1
(-2.8) 		7.4
(-2.7) 		23

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 34
1 2 3 4 5 6 range
A 22.8
(3)
A 		15.2
(0.9)
A 		8.6
(-0.9)
A 		7.6
(-1.2)
A 		1.5
(-2.9)
A 		1.2
(-3)
A 		22
B 35.1
(3)
A 		25.6
(1.2)
P 		8.1
(-2)
A 		13.2
(-1.1)
A 		6.9
(-2.3)
A 		3
(-3)
A 		32
C 19.4
(1.9)
A 		22.6
(3)
A 		6.7
(-2.5)
A 		6.9
(-2.5)
A 		5.4
(-3)
A 		9.8
(-1.5)
A 		17
avr 25.8
(3) 		21.1
(1.7) 		7.8
(-2.1) 		9.2
(-1.7) 		4.6
(-3) 		4.7
(-3) 		21
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193410_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10009
Sequence Type Exemplar sequence
Representative Public ID Y73F8A.2 NCBI
Target Description Y73F8A.2 /REP_DB=WormBase Gene ID /WP=CE22973 /TR=Q9NA62 /GB=CAB60529.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=neurotransmitter-gated 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_070438(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070438 NCBI Caenorhabditis elegans Y73F8A.2 (Y73F8A.2) mRNA, complete cds. 11/11 None
SNAP00000030801 ENSEMBL cdna:SNAP chromosome:CEL140:IV:15238982:15243637:1 11/11 None
GENEFINDER00000030901 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:15236856:15243637:1 11/11 None
Y73F8A.2 ENSEMBL cdna:known chromosome:CEL140:IV:15236856:15243637:1 gene:Y73F8A.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:15236861-15243643(+) 100.0 100.0
Public Domain and Genome References
Gene Title neurotransmitter-gated ion-channel protein
Ensembl Y73F8A.2
Entrez Gene 190669 Entrez gene
SwissProt Q9NA62 EMBL-EBI
WormBase CE36678 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 CAB60529 Hypothetical protein Y73F8A.2 [Caenorhabditis elegans] ref|NP_502839.2| Y73F8A.2 [Caenorhabditis elegans] 0.0
blast CAB60529 Hypothetical protein Y73F8A.2 [Caenorhabditis elegans] ref|NP_502839.2| Y73F8A.2 [Caenorhabditis elegans] 1.0E-106
blast CAE60301 Hypothetical protein CBG03886 [Caenorhabditis briggsae] 1.0E-105
blast CAE59048 Hypothetical protein CBG02331 [Caenorhabditis briggsae] 1.0E-104
blast CAE60301 Hypothetical protein CBG03886 [Caenorhabditis briggsae] 1.0E-101
blast CAE59048 Hypothetical protein CBG02331 [Caenorhabditis briggsae] 1.0E-100
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.9E-15
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.7E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.4E-58
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.9E-15
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.7E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.2E-15
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.9E-15
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.7E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.1E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.1E-40
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502839.2 4 262-284,291-313,328-350,404-426
Y73F8A.2 4 262-284,291-313,328-350,404-426
SNAP00000030801 4 167-189,196-218,233-255,309-331
GENEFINDER00000030901 4 292-314,321-343,358-380,434-456
Sequence
Target Sequence 
>C. ELEGANS:193410_AT
ggaatgtggcatcgactgtcagtatccatacatttcgagcgtctctacggtttctatatt
ctccaaatgtacctacctacctacatatcagttttcatatcatggatagcattttggatg
gatacaaaggctcttcctgcgagaattacactctccgtctcttcactgatggcactgact
tttcaatttggaaatattgtcaaatcactgccaaaggcatcctacgtaaaagccatcgat
atttggatgttcagttgtgttggattcatatttttctccctaatcgagcttgcaatcgtc
gcctacaatgataaaatgcacgaccaacgactacgagaagtccggtgttcggttggaaat
ttgaattcaaatggaataggacaatataattcaactacaaggagaagtttcgtggagctc
agtgctcggcgagcaaaggggagcgagcttggagcatcgatcgatcgggtagctagcatg
ttgtttcctacgatgtttgccctattcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAATGTGGCATCGACTGTCAGTAT 215 533 844 Antisense
GTATCCATACATTTCGAGCGTCTCT 548 455 865 Antisense
AGCGTCTCTACGGTTTCTATATTCT 699 81 881 Antisense
GTACCTACCTACCTACATATCAGTT 12 451 912 Antisense
AAGGCTCTTCCTGCGAGAATTACAC 513 161 970 Antisense
CGTCTCTTCACTGATGGCACTGACT 69 247 999 Antisense
TAATCGAGCTTGCAATCGTCGCCTA 522 633 1124 Antisense
TTCGTGGAGCTCAGTGCTCGGCGAG 394 695 1252 Antisense
GGGGAGCGAGCTTGGAGCATCGATC 667 497 1281 Antisense
CGATCGATCGGGTAGCTAGCATGTT 307 249 1301 Antisense
TTCCTACGATGTTTGCCCTATTCAA 532 699 1328 Antisense
Sequence Source Affymetrix Proprietary Database