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[193534_at] nicotinic acetylcholine receptor

Description K03B8.9 /REP_DB=WormBase Gene ID /WP=CE06083 /GEN=deg-3 /TR=SW:P54244 /GB=CAA98507.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nicotinic acetylcholine receptor
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 50      4grp_highest_8_8 > 56      4grp_high_8_8 > 27      6grp_highest_nonorm > 90      6grp_total > 51      4grp_total > 37      6grp_highest_sub > 03_04      6grp_cgc > 84      6grp_high1_sub > 03_04      6grp_cgc_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 104
1 2 3 4 range
A 155.6
(3)
P 		143.8
(2.1)
P 		72.5
(-3)
P 		121.5
(0.5)
P 		83
B 139.4
(0.4)
P 		176
(3)
P 		131.9
(-0.2)
P 		92.1
(-3)
P 		84
C 153.5
(1.7)
P 		108.8
(-3)
P 		123.6
(-1.5)
P 		166.3
(3)
P 		58
avr 149.5
(3) 		142.9
(2) 		109.3
(-3) 		126.6
(-0.4) 		40

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 134
1 2 3 4 5 6 range
A 119.9
(-2)
P 		170.8
(3)
P 		146.8
(0.6)
P 		162.6
(2.2)
P 		162.8
(2.2)
P 		109.8
(-3)
P 		61
B 144
(1.1)
P 		143.3
(1)
P 		177.6
(3)
P 		146.7
(1.2)
P 		114.9
(-0.6)
P 		74.2
(-3)
P 		103
C 189.7
(2)
P 		95
(-3)
P 		202.9
(2.7)
P 		208.6
(3)
P 		149.3
(-0.1)
P 		101.7
(-2.6)
P 		114
avr 151.2
(1.2) 		136.4
(0.1) 		175.8
(3) 		172.6
(2.8) 		142.3
(0.5) 		95.2
(-3) 		81
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 39
1 2 3 4 range
A 56.7
(3)
P 		31.2
(-0.9)
P 		19
(-2.8)
P 		17.8
(-3)
P 		39
B 44.5
(3)
P 		43.5
(2.8)
P 		30.6
(-0.3)
P 		19.6
(-3)
P 		25
C 50.8
(3)
P 		31.3
(-2.1)
P 		43.1
(1)
P 		28
(-3)
P 		23
avr 50.7
(3) 		35.3
(-0.2) 		30.9
(-1.1) 		21.8
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 48
1 2 3 4 5 6 range
A 22.1
(-3)
P 		60.8
(3)
P 		32
(-1.5)
P 		41.2
(-0)
P 		49.1
(1.2)
P 		26.7
(-2.3)
P 		39
B 50.1
(3)
P 		47.7
(2.4)
P 		43.1
(1.1)
P 		38.8
(-0)
P 		46.7
(2.1)
P 		27.7
(-3)
P 		22
C 70.3
(3)
P 		29
(-3)
P 		51.6
(0.3)
P 		41.9
(-1.1)
P 		48.3
(-0.2)
P 		34
(-2.3)
P 		41
avr 47.5
(2.8) 		45.8
(2.3) 		42.2
(1.1) 		40.6
(0.6) 		48
(3) 		29.5
(-3) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193534_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14408
Sequence Type Exemplar sequence
Representative Public ID K03B8.9 NCBI
Target Description K03B8.9 /REP_DB=WormBase Gene ID /WP=CE06083 /GEN=deg-3 /TR=SW:P54244 /GB=CAA98507.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nicotinic acetylcholine receptor
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_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:11415667-11417734(-) 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:193534_AT
agaaatcctccacaattcattcgttatatcttcttcgttctccttcctcaagtcctattg
ctcaatgtacctccaccacttcaaactctttggggagaacttgatgatgatccattgaat
gttcgaagaaggaaaaagtcacattatttatcaagaaatgtgaataatggatcaactaaa
atggcatctccaatgtccacattgcgagtgccacagtcggctggaagtgtttctgaaaag
cggcaatccttccaaatgattgatgtaacatctccaaattctccaaatacagccaggtca
cgtgcaccatctcttgctccatcaactgccaaagctacaatgtgggagggaacaatgtca
gcacttgctggaacaaatactcaattacgaagaacttccaatgtattcaataaggaagtg
gacgagatgcgaagaaaacggcagtgctccctcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAAATCCTCCACAATTCATTCGTT 282 73 1105 Antisense
TCATTCGTTATATCTTCTTCGTTCT 582 619 1121 Antisense
CTTCCTCAAGTCCTATTGCTCAATG 231 219 1147 Antisense
CTCCACCACTTCAAACTCTTTGGGG 19 237 1175 Antisense
AATGGCATCTCCAATGTCCACATTG 193 163 1284 Antisense
CCACATTGCGAGTGCCACAGTCGGC 148 273 1301 Antisense
GAAAAGCGGCAATCCTTCCAAATGA 425 351 1339 Antisense
CAAATACAGCCAGGTCACGTGCACC 241 193 1388 Antisense
TGCTCCATCAACTGCCAAAGCTACA 136 583 1419 Antisense
GAGGGAACAATGTCAGCACTTGCTG 701 401 1450 Antisense
CGAAGAAAACGGCAGTGCTCCCTCG 320 247 1534 Antisense
Sequence Source Affymetrix Proprietary Database