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[175049_s_at] nicotinic acetylcholine receptor

Description CEK131G9R_rc /REP_DB=TREMBL Accession /GB=D65142 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk131g9 : 3prime end, single read.
Cluster 6grp_total > 29      4grp_total > 0      6grp_cgc > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 276
1 2 3 4 range
A 238.9
(-1.6)
A 		174.2
(-3)
A 		277.1
(-0.8)
A 		450.6
(3)
A 		276
B 240.1
(-0.5)
A 		223.2
(-1.3)
A 		191.7
(-3)
A 		305.6
(3)
P 		114
C 272.7
(2.5)
A 		176.1
(-3)
A 		270.8
(2.4)
A 		282.2
(3)
M 		106
avr 250.6
(-0.7) 		191.2
(-3) 		246.5
(-0.9) 		346.1
(3) 		155

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 328.7
(3)
P 		213.7
(-0.9)
A 		165.7
(-2.5)
A 		151.5
(-3)
A 		240.7
(0)
P 		204.8
(-1.2)
A 		177
B 258.1
(0.6)
M 		304.5
(3)
P 		186.2
(-3)
M 		269.4
(1.2)
P 		227.7
(-0.9)
P 		226
(-1)
P 		118
C 332
(3)
A 		196.3
(-2.7)
P 		269.8
(0.4)
M 		188.3
(-3)
M 		294.7
(1.4)
P 		229.4
(-1.3)
P 		144
avr 306.3
(3) 		238.2
(-1) 		207.2
(-2.8) 		203.1
(-3) 		254.4
(-0) 		220.1
(-2) 		103
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 57
1 2 3 4 range
A 87
(3)
A 		37.8
(-3)
A 		72.4
(1.2)
A 		66
(0.4)
A 		49
B 76.6
(3)
A 		55.1
(-1)
A 		44.4
(-3)
A 		65.1
(0.9)
P 		32
C 90.3
(2.5)
A 		50.6
(-2.6)
A 		94.4
(3)
A 		47.6
(-3)
M 		47
avr 84.6
(3) 		47.8
(-3) 		70.4
(0.7) 		59.6
(-1.1) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 87
1 2 3 4 5 6 range
A 60.6
(0.7)
P 		76
(3)
A 		36.1
(-3)
A 		38.4
(-2.7)
A 		72.6
(2.5)
P 		49.9
(-0.9)
A 		40
B 89.8
(1.8)
M 		101.3
(3)
P 		45.2
(-3)
M 		71.4
(-0.2)
P 		92.5
(2.1)
P 		84.3
(1.2)
P 		56
C 123.1
(3)
A 		59.9
(-1.5)
P 		68.7
(-0.8)
M 		37.9
(-3)
M 		95.4
(1)
P 		76.8
(-0.3)
P 		85
avr 91.2
(3) 		79.1
(1.3) 		50
(-2.9) 		49.2
(-3) 		86.8
(2.4) 		70.3
(0) 		42
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175049_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21826
Sequence Type Exemplar sequence
Representative Public ID CEK131G9R NCBI
Target Description CEK131G9R_rc /REP_DB=TREMBL Accession /GB=D65142 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk131g9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_073496(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073496 NCBI Caenorhabditis elegans DEGeneration of certain neurons family member (deg-3) (deg-3) mRNA, complete cds. 11/11 A 
SNAP00000002788 ENSEMBL cdna:SNAP chromosome:CEL140:V:11415668:11417734:-1 11/11 None
GENEFINDER00000002798 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11415668:11417734:-1 11/11 None
K03B8.9.1 ENSEMBL cdna:known chromosome:CEL140:V:11415458:11417747:-1 gene:K03B8.9 11/11 A 
K03B8.9.2 ENSEMBL cdna:known chromosome:CEL140:V:11415481:11417747:-1 gene:K03B8.9 11/11 A 
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:11415496-11415803(-) 100.0 100.0
Public Domain and Genome References
Gene Title nicotinic acetylcholine receptor
Gene Symbol deg-3
Ensembl K03B8.9
Entrez Gene 3565200 Entrez gene
WormBase CE06083 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
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA98507 Hypothetical protein K03B8.9 [Caenorhabditis elegans] ref|NP_505897.1| DEGeneration of certain neurons family member (deg-3) [Caenorhabditis elegans] sp|P54244|ACH3_CAEEL Acetylcholine receptor, alpha-type subunit deg-3 precursor gb|AAA92689.1| nicotinic acetylcholine receptor alpha subunit precursor gb|AAA92688.1| nicotinic acetylcholine receptor alpha subunit 0.0
blast CAE75242 Hypothetical protein CBG23194 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.1E-7
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.4E-78
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505897.1 4 267-289,302-319,334-356,528-550
K03B8.9.1 4 267-289,302-319,334-356,528-550
K03B8.9.2 4 267-289,302-319,334-356,528-550
SNAP00000002788 4 267-289,302-319,334-356,528-550
GENEFINDER00000002798 4 267-289,302-319,334-356,528-550
Sequence
Target Sequence 
>C. ELEGANS:175049_S_AT
ggttcctgttgatagttttcgtaggagcagtcgtcatcgtgacagctggcctcattctcg
ttggcagaatggcacaatacagttatgaccacccggatgaccgattctttaatgtctaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTTCCTGTTGATAGTTTTCGTAGG 673 505 30 Antisense
GTTTTCGTAGGAGCAGTCGTCATCG 626 441 44 Antisense
TTCGTAGGAGCAGTCGTCATCGTGA 42 693 47 Antisense
TAGGAGCAGTCGTCATCGTGACAGC 554 653 51 Antisense
TGGCCTCATTCTCGTTGGCAGAATG 558 543 76 Antisense
TCTCGTTGGCAGAATGGCACAATAC 595 609 85 Antisense
GGCACAATACAGTTATGACCACCCG 375 535 100 Antisense
ATACAGTTATGACCACCCGGATGAC 486 23 106 Antisense
TATGACCACCCGGATGACCGATTCT 373 657 113 Antisense
CCACCCGGATGACCGATTCTTTAAT 123 261 118 Antisense
GGATGACCGATTCTTTAATGTCTAA 202 513 124 Antisense
Sequence Source Affymetrix Proprietary Database