[Home] | [Total List]

[191104_at] Acetylcholine receptor

Description C02C2.3 /REP_DB=WormBase Gene ID /WP=CE00029 /TR=SW:P34271 /GB=AAA27911.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Acetylcholine receptor
Cluster 6grp_highest_10_10 > 27      6grp_high1_10_10 > 71      4grp_highest_8_8 > 40      4grp_high_8_8 > 50      6grp_highest_nonorm > 53      6grp_total > 71      4grp_total > 53      6grp_highest_sub > 03_04      6grp_cgc > 84      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 382
1 2 3 4 range
A 638.1
(2.9)
P 		643.6
(3)
P 		404.3
(-1)
P 		285
(-3)
P 		359
B 624.8
(3)
P 		488.1
(0.2)
P 		449.1
(-0.7)
P 		336.8
(-3)
P 		288
C 666.9
(3)
P 		524.7
(0.8)
P 		620.7
(2.3)
P 		284.5
(-3)
P 		382
avr 643.3
(3) 		552.1
(1.4) 		491.4
(0.3) 		302.1
(-3) 		341

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1078
1 2 3 4 5 6 range
A 314.1
(-3)
P 		801.4
(-0.3)
P 		981.1
(0.7)
P 		1391.8
(3)
P 		749.1
(-0.6)
P 		421.9
(-2.4)
P 		1078
B 421.4
(-2.7)
P 		564.8
(-1.5)
P 		1094.5
(3)
P 		1008.3
(2.3)
P 		715.3
(-0.2)
P 		389.9
(-3)
P 		705
C 517.4
(-2)
P 		556.2
(-1.8)
P 		1004.1
(1.3)
P 		1243.5
(3)
P 		857.6
(0.3)
P 		377.7
(-3)
P 		866
avr 417.6
(-2.8) 		640.8
(-1.2) 		1026.6
(1.6) 		1214.5
(3) 		774
(-0.2) 		396.5
(-3) 		818
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 191
1 2 3 4 range
A 232.3
(3)
P 		139.7
(0.1)
P 		105.7
(-1)
P 		41.7
(-3)
P 		191
B 199.3
(3)
P 		120.6
(-0.7)
P 		104.1
(-1.5)
P 		71.8
(-3)
P 		128
C 220.8
(3)
P 		150.9
(0.6)
P 		216.3
(2.8)
P 		48
(-3)
P 		173
avr 217.5
(3) 		137.1
(0.1) 		142
(0.2) 		53.8
(-3) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 295
1 2 3 4 5 6 range
A 57.9
(-3)
P 		285
(1.6)
P 		213.7
(0.2)
P 		353
(3)
P 		226
(0.4)
P 		102.7
(-2.1)
P 		295
B 146.6
(-3)
P 		188
(-1.2)
P 		265.8
(2)
P 		267.1
(2)
P 		290.6
(3)
P 		145.4
(-3)
P 		145
C 191.8
(-0.4)
P 		169.7
(-1.3)
P 		255.6
(2.1)
P 		250.1
(1.9)
P 		277.5
(3)
P 		126.4
(-3)
P 		151
avr 132.1
(-2.7) 		214.2
(0.2) 		245
(1.4) 		290.1
(3) 		264.7
(2.1) 		124.8
(-3) 		165
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191104_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6159
Sequence Type Exemplar sequence
Representative Public ID C02C2.3 NCBI
Target Description C02C2.3 /REP_DB=WormBase Gene ID /WP=CE00029 /TR=SW:P34271 /GB=AAA27911.1 /SUBMIT=ST.LOUIS /CHR=3 /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_066309(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066309 NCBI Caenorhabditis elegans Coelomocyte UPtake defective family member (cup-4) (cup-4) mRNA, complete cds. 11/11 A 
GENEFINDER00000005407 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7865668:7870325:1 11/11 None
SNAP00000005401 ENSEMBL cdna:SNAP chromosome:CEL140:III:7866739:7868615:1 11/11 None
C02C2.3 ENSEMBL cdna:known chromosome:CEL140:III:7866431:7868651:1 gene:C02C2.3 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
chrIII:7865874-7868481(+) 100.0 100.0
Public Domain and Genome References
Gene Title Acetylcholine receptor
Gene Symbol cup-4
Ensembl C02C2.3
Entrez Gene 176104 Entrez gene
SwissProt P34271 EMBL-EBI
WormBase CE30416 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
Protein Similarities
Method ID Description E-Value
blast AAT42012 CUP-4 [Caenorhabditis elegans] gb|AAA27911.2| Coelomocyte uptake defective protein 4 [Caenorhabditis elegans] ref|NP_498710.2| Coelomocyte UPtake defective family member (cup-4) [Caenorhabditis elegans] sp|P34271|CUP4_CAEEL Acetylcholine receptor-like protein cup-4 precursor (Coelomocyte uptake defective protein 4) 0.0
blast CAE66892 Hypothetical protein CBG12273 [Caenorhabditis briggsae] 1.0E-148
blast CAE66892 Hypothetical protein CBG12273 [Caenorhabditis briggsae] 1.0E-145
blast CAE66892 Hypothetical protein CBG12273 [Caenorhabditis briggsae] 1.0E-130
blast AAF60813 Hypothetical protein Y58G8A.1 [Caenorhabditis elegans] ref|NP_503167.1| Y58G8A.1 [Caenorhabditis elegans] 3.0E-28
Protein Domains
Database ID Description E-Value
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-12
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.5E-12
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.0E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498710.2 4 280-302,304-323,343-365,410-432
C02C2.3 4 280-302,304-323,343-365,410-432
GENEFINDER00000005407 6 56-75,338-360,362-381,401-423,472-494,550-567
SNAP00000005401 2 215-237,345-367
Sequence
Target Sequence 
>C. ELEGANS:191104_AT
agaatttatatgccatcccaccaacactgagttttggctgggaagaacaaaaaatgaagc
gaataatatcggatttcaaaatccaaaacgtctcaagctcagcactttactacacaaacg
gaaacatcacttcatcggccccaattactggatttgatctgggctctacttggtctatgc
tggcagttactgtcagttttgtacggcattcccctttgtttgaagcggcagttgtgacac
cgtgtatagtagtagcatctctaatatccatgacgttctttatcgattcgctatcttcaa
catttctcttgatgatgcttcatttttatgttcaactgatattcctccatgatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAATTTATATGCCATCCCACCAAC 615 75 797 Antisense
ATCCAAAACGTCTCAAGCTCAGCAC 708 37 877 Antisense
GCTCAGCACTTTACTACACAAACGG 433 301 893 Antisense
TTCATCGGCCCCAATTACTGGATTT 397 687 927 Antisense
ACTGGATTTGATCTGGGCTCTACTT 22 95 943 Antisense
CTCTACTTGGTCTATGCTGGCAGTT 36 227 960 Antisense
ACTGTCAGTTTTGTACGGCATTCCC 151 97 985 Antisense
CATTCCCCTTTGTTTGAAGCGGCAG 51 217 1003 Antisense
GAAGCGGCAGTTGTGACACCGTGTA 491 343 1018 Antisense
ATGACGTTCTTTATCGATTCGCTAT 430 45 1066 Antisense
GTTCAACTGATATTCCTCCATGATC 642 445 1126 Antisense
Sequence Source Affymetrix Proprietary Database