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[193854_s_at] acetylcholine receptor, beta precursor

Description T08G11.5 /REP_DB=WormBase Gene ID /WP=CE13451 /GEN=unc-29 /TR=SW:P48181 /GB=CAB02308.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=acetylcholine receptor, beta precursor
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 32      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 71      6grp_total > 31      4grp_total > 53      6grp_highest_sub > 02_03      6grp_cgc > 72      6grp_high1_sub > 02_03      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 152
1 2 3 4 range
A 332.1
(0.7)
P 		385.6
(3)
P 		293.4
(-0.9)
P 		245
(-3)
P 		141
B 373.1
(2.8)
P 		331.7
(-0.2)
P 		376.2
(3)
P 		293.4
(-3)
P 		83
C 397.1
(3)
P 		297.7
(-1.9)
P 		275.9
(-3)
P 		308.8
(-1.4)
P 		121
avr 367.4
(3) 		338.3
(0.9) 		315.2
(-0.7) 		282.4
(-3) 		85

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 269
1 2 3 4 5 6 range
A 326.7
(0.6)
P 		384
(2)
P 		427.9
(3)
P 		269.9
(-0.8)
P 		247.5
(-1.3)
P 		175.7
(-3)
P 		252
B 258.3
(-1.6)
P 		444.8
(3)
P 		354.6
(0.8)
P 		348.5
(0.6)
P 		254.1
(-1.7)
P 		201.4
(-3)
P 		243
C 317.6
(0.2)
P 		428.7
(3)
P 		362.3
(1.3)
P 		429.3
(3)
P 		228.7
(-2)
P 		187.6
(-3)
P 		242
avr 300.9
(-0.1) 		419.2
(3) 		381.6
(2) 		349.2
(1.2) 		243.4
(-1.6) 		188.2
(-3) 		231
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 96
1 2 3 4 range
A 120.9
(3)
P 		83.7
(0.4)
P 		76.7
(-0.1)
P 		35.9
(-3)
P 		85
B 119
(3)
P 		81.9
(-0.9)
P 		87.2
(-0.4)
P 		62.5
(-3)
P 		57
C 131.4
(3)
P 		85.6
(-0.5)
P 		96.2
(0.3)
P 		52.1
(-3)
P 		79
avr 123.8
(3) 		83.7
(-0.3) 		86.7
(-0) 		50.2
(-3) 		74

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 60.2
(-1.9)
P 		136.6
(3)
P 		93.2
(0.2)
P 		68.4
(-1.4)
P 		74.7
(-1)
P 		42.8
(-3)
P 		94
B 89.9
(-1.8)
P 		148.1
(3)
P 		86.1
(-2.1)
P 		92.3
(-1.6)
P 		103.2
(-0.7)
P 		75.1
(-3)
P 		73
C 117.7
(1.8)
P 		130.8
(3)
P 		92.2
(-0.4)
P 		86.3
(-0.9)
P 		74
(-2)
P 		62.8
(-3)
P 		68
avr 89.3
(-0.8) 		138.5
(3) 		90.5
(-0.7) 		82.3
(-1.3) 		84
(-1.2) 		60.2
(-3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193854_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.614
Sequence Type Exemplar sequence
Representative Public ID T08G11.5 NCBI
Target Description T08G11.5 /REP_DB=WormBase Gene ID /WP=CE13451 /GEN=unc-29 /TR=SW:P48181 /GB=CAB02308.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=acetylcholine receptor, beta precursor
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_059998(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059998 NCBI Caenorhabditis elegans UNCoordinated family member (unc-29) (unc-29) mRNA, complete cds. 11/11 None
SNAP00000035559 ENSEMBL cdna:SNAP chromosome:CEL140:I:8905880:8908343:-1 11/11 None
GENEFINDER00000035564 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8905880:8909981:-1 11/11 None
T08G11.5 ENSEMBL cdna:known chromosome:CEL140:I:8905756:8909559:-1 gene:T08G11.5 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
chrI:8905810-8909483(-) 100.0 100.0
Public Domain and Genome References
Gene Title acetylcholine receptor, beta precursor
Gene Symbol unc-29
Ensembl T08G11.5
Entrez Gene 172703 Entrez gene
SwissProt P48181 EMBL-EBI
WormBase CE13451 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
7274 neuromuscular synaptic transmission inferred from direct assay 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
45202 synapse inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4889 nicotinic acetylcholine-activated cation-selective channel activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel 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
15464 acetylcholine receptor activity inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB02308 Hypothetical protein T08G11.5 [Caenorhabditis elegans] ref|NP_492399.1| UNCoordinated family member (unc-29) [Caenorhabditis elegans] sp|P48181|ACH2_CAEEL Acetylcholine receptor, beta-type subunit unc-29 precursor (Uncoordinated protein 29) gb|AAB39358.1| non-alpha nicotinic acetylcholine receptor subunit precursor [Caenorhabditis elegans] 0.0
blast CAA58765 beta-1 subunit of nicotinic acetylcholine receptor [Caenorhabditis elegans] 0.0
blast CAE66991 Hypothetical protein CBG12389 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.4E-65
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.1E-86
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.4E-65
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.1E-58
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.4E-65
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.1E-86
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492399.1 5 7-24,233-255,262-284,297-319,446-468
T08G11.5 5 7-24,233-255,262-284,297-319,446-468
SNAP00000035559 4 139-161,171-193,206-228,357-379
GENEFINDER00000035564 4 290-312,319-341,354-376,503-525
Sequence
Target Sequence 
>C. ELEGANS:193854_S_AT
aggaccaagaactcatcggatgccacaatgggttcgagtcgtatttttgcagtttcttcc
aaaacttgtttgcatgaaacgcccaaaatcggcatctgagcgaagcgctgtccgttctgg
aatggcccaactaccaggagttggacagtttacattaagcccatcagctcatcatccact
atgtccatcagctgatgatcgaacaactacaattcgaaatactgcatcaaatgagacgtc
tgcatattatccattaagtactgatgctctacgagcaattgatgcaattgagtatattac
ggaacatttgaaaagagacgagcaacataaatcgttccgagacgattggaaatatgtggc
aatgataatcgatcgattgctgctttatgtattttttggaataactgttggaggaacatg
tggtattctgttttccgcgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGACCAAGAACTCATCGGATGCCA 348 55 972 Antisense
ATGCCACAATGGGTTCGAGTCGTAT 339 39 991 Antisense
GAGTCGTATTTTTGCAGTTTCTTCC 677 399 1007 Antisense
AACGCCCAAAATCGGCATCTGAGCG 111 147 1049 Antisense
ATCTGAGCGAAGCGCTGTCCGTTCT 587 33 1065 Antisense
GTTCTGGAATGGCCCAACTACCAGG 312 441 1085 Antisense
ACATTAAGCCCATCAGCTCATCATC 94 105 1123 Antisense
TCATCCACTATGTCCATCAGCTGAT 190 623 1143 Antisense
GAGACGTCTGCATATTATCCATTAA 632 393 1204 Antisense
ATCGATCGATTGCTGCTTTATGTAT 232 37 1339 Antisense
ACATGTGGTATTCTGTTTTCCGCGC 18 105 1387 Antisense
Sequence Source Affymetrix Proprietary Database