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[192412_at] acetylcholine receptor

Description F28F8.1 /REP_DB=WormBase Gene ID /WP=CE09755 /GEN=acr-18 /TR=O17848 /GB=CAB03014.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=acetylcholine receptor
Cluster 6grp_highest_10_10 > 89      6grp_high1_10_10 > 99      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 91      6grp_total > 84      4grp_total > 13      6grp_highest_sub > In      6grp_cgc > 78      6grp_cgc_sub > In      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 150.6
(-1)
P 		126.5
(-2.2)
P 		111.2
(-3)
P 		227.1
(3)
P 		116
B 152.7
(0.7)
P 		116.8
(-1.5)
P 		92.8
(-3)
P 		188.9
(3)
P 		96
C 200.1
(3)
P 		115.4
(-2.3)
P 		103.4
(-3)
P 		189.7
(2.4)
P 		97
avr 167.8
(0.9) 		119.6
(-2) 		102.5
(-3) 		201.9
(3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 167
1 2 3 4 5 6 range
A 180.1
(-2.3)
P 		172.6
(-3)
P 		194.7
(-1)
P 		197.2
(-0.7)
P 		237.5
(3)
P 		184.2
(-1.9)
P 		65
B 129.5
(-3)
P 		173.9
(-1.4)
P 		200.6
(-0.4)
P 		194.1
(-0.7)
P 		296
(3)
P 		276.3
(2.3)
P 		167
C 140.5
(-3)
P 		181.1
(-0.7)
P 		185.6
(-0.5)
P 		247.3
(3)
P 		247.9
(3)
P 		234
(2.2)
P 		107
avr 150
(-3) 		175.9
(-1.6) 		193.6
(-0.6) 		212.9
(0.4) 		260.5
(3) 		231.5
(1.4) 		111
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 45
1 2 3 4 range
A 54.8
(3)
P 		27.5
(-3)
P 		29.1
(-2.6)
P 		33.2
(-1.7)
P 		27
B 48.7
(3)
P 		28.9
(-1.4)
P 		21.5
(-3)
P 		40.2
(1.1)
P 		27
C 66.2
(3)
P 		33.2
(-2.8)
P 		36
(-2.3)
P 		32
(-3)
P 		34
avr 56.6
(3) 		29.9
(-2.8) 		28.9
(-3) 		35.1
(-1.7) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 87
1 2 3 4 5 6 range
A 33.2
(-3)
P 		61.4
(1.4)
P 		42.4
(-1.6)
P 		50
(-0.4)
P 		71.7
(3)
P 		44.9
(-1.2)
P 		39
B 45.1
(-3)
P 		57.9
(-2)
P 		48.7
(-2.7)
P 		51.4
(-2.5)
P 		120.2
(3)
P 		103
(1.6)
P 		75
C 52.1
(-2.1)
P 		55.3
(-1.5)
P 		47.2
(-3)
P 		49.7
(-2.5)
P 		80.2
(3)
P 		78.3
(2.7)
P 		33
avr 43.5
(-3) 		58.2
(-1.1) 		46.1
(-2.7) 		50.4
(-2.1) 		90.7
(3) 		75.4
(1.1) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192412_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13681
Sequence Type Exemplar sequence
Representative Public ID F28F8.1 NCBI
Target Description F28F8.1 /REP_DB=WormBase Gene ID /WP=CE09755 /GEN=acr-18 /TR=O17848 /GB=CAB03014.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=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_074467(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074467 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-18) (acr-18) mRNA, complete cds. 11/11 None
SNAP00000036071 ENSEMBL cdna:SNAP chromosome:CEL140:V:15553823:15556424:-1 11/11 None
GENEFINDER00000036089 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15553823:15561731:-1 11/11 None
F28F8.1 ENSEMBL cdna:known chromosome:CEL140:V:15553744:15561731:-1 gene:F28F8.1 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
chrV:15553822-15557261(-) 100.0 100.0
Public Domain and Genome References
Gene Title acetylcholine receptor
Gene Symbol acr-18
Ensembl F28F8.1
Entrez Gene 191604 Entrez gene
SwissProt O17848 EMBL-EBI
WormBase CE36645 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
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
Protein Similarities
Method ID Description E-Value
blast CAB03014 Hypothetical protein F28F8.1 [Caenorhabditis elegans] ref|NP_506868.2| AcetylCholine Receptor family member (acr-18) [Caenorhabditis elegans] gb|AAR98635.1| acetylcholine receptor, one of nine alpha a7-like nicotinic acetylcholine receptor subunits (58.6 kD) (acr-18) [Caenorhabditis elegans] 0.0
blast CAE71629 Hypothetical protein CBG18595 [Caenorhabditis briggsae] 0.0
blast AAT48618 Acetylcholine receptor protein 17, isoform b [Caenorhabditis elegans] ref|NP_001023961.1| AcetylCholine Receptor family member (acr-17) [Caenorhabditis elegans] 1.0E-114
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.6E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.0E-76
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.6E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.9E-32
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506868.2 4 238-260,273-290,300-322,474-491
F28F8.1 4 238-260,273-290,300-322,474-491
SNAP00000036071 4 115-137,150-167,177-199,351-368
GENEFINDER00000036089 4 238-260,273-290,300-322,474-491
Sequence
Target Sequence 
>C. ELEGANS:192412_AT
ttatggccgcattcacaacgacacttactctatcctaccaaatgagaggaaatagcggac
aagaagttgatcctcgagttcgtgacttcttcttttaccaaatcgcagcaaatccttgta
tttcgtgggctttctcgtttcaactaccaaagaagcttttgagatcggatcaccggaaac
agagcttcttcttcaccaacggagccgcccatgtgaacggctactcaaaaggcgcacttc
acccgaacacccctccagctcacattgtgaaaatggaggagataaccggtggtggaagtg
ttaaaagttttgtgatgtctcaagaatctgcggcaacatcgacactgttgacatcgtcgc
taatgaaaataaaagttgttttggatgacatgaaagcatcaattcatgcagaacgcgaac
taaagcgaataaaattcgagtggcaacaagtgacccgtcttatcgatcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTATGGCCGCATTCACAACGACACT 44 681 1052 Antisense
ACACTTACTCTATCCTACCAAATGA 306 109 1072 Antisense
TGATCCTCGAGTTCGTGACTTCTTC 186 565 1119 Antisense
GTGACTTCTTCTTTTACCAAATCGC 277 477 1133 Antisense
ATCCTTGTATTTCGTGGGCTTTCTC 424 39 1163 Antisense
GGCTTTCTCGTTTCAACTACCAAAG 483 505 1179 Antisense
CGGAAACAGAGCTTCTTCTTCACCA 246 243 1225 Antisense
CGGAGCCGCCCATGTGAACGGCTAC 690 241 1251 Antisense
GAACGGCTACTCAAAAGGCGCACTT 271 347 1266 Antisense
GACACTGTTGACATCGTCGCTAATG 347 367 1392 Antisense
ACAAGTGACCCGTCTTATCGATCGA 635 111 1497 Antisense
Sequence Source Affymetrix Proprietary Database