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[193580_at] ligand-gated ionic channel protein

Description D2092.3 /REP_DB=WormBase Gene ID /WP=CE09102 /GEN=acr-11 /TR=P91197 /GB=AAB42223.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel protein
Cluster 4grp_high_8_8 > 18      6grp_total > 24      4grp_total > 30      6grp_cgc > 34      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 144.1
(1.6)
P 		62.8
(-3)
P 		100.8
(-0.8)
M 		168.3
(3)
P 		106
B 167.5
(3)
P 		136.5
(-0.3)
P 		110.6
(-3)
P 		127.4
(-1.2)
P 		57
C 153.8
(3)
P 		131.3
(1.2)
P 		79.7
(-3)
P 		134.7
(1.5)
P 		74
avr 155.1
(3) 		110.2
(-1.6) 		97
(-3) 		143.5
(1.8) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 111
1 2 3 4 5 6 range
A 106.1
(3)
P 		100.9
(2.2)
P 		103.6
(2.6)
P 		101.4
(2.3)
P 		67.1
(-3)
A 		85.3
(-0.2)
P 		39
B 116.7
(2.3)
P 		128.2
(3)
P 		85.5
(0.2)
P 		65.9
(-1)
P 		35.1
(-3)
M 		63.2
(-1.2)
P 		93
C 146.4
(3)
P 		125.4
(1.6)
P 		128.9
(1.8)
P 		88.1
(-1)
P 		64.9
(-2.6)
A 		59.3
(-3)
A 		87
avr 123.1
(3) 		118.2
(2.6) 		106
(1.5) 		85.1
(-0.4) 		55.7
(-3) 		69.3
(-1.8) 		67
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 52.5
(3)
P 		13.6
(-3)
P 		26.3
(-1)
M 		24.6
(-1.3)
P 		39
B 53.4
(3)
P 		33.7
(-1.3)
P 		25.6
(-3)
P 		27.1
(-2.7)
P 		28
C 50.9
(3)
P 		37.8
(0.2)
P 		27.8
(-1.9)
P 		22.7
(-3)
P 		28
avr 52.3
(3) 		28.4
(-2.2) 		26.6
(-2.6) 		24.8
(-3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 40
1 2 3 4 5 6 range
A 19.6
(-3)
P 		35.9
(3)
P 		22.6
(-1.9)
P 		25.7
(-0.8)
P 		20.2
(-2.8)
A 		20.8
(-2.6)
P 		16
B 40.6
(2.6)
P 		42.7
(3)
P 		20.8
(-1.6)
P 		17.4
(-2.3)
P 		14.3
(-3)
M 		23.6
(-1)
P 		28
C 54.3
(3)
P 		38.3
(0.4)
P 		32.8
(-0.5)
P 		17.7
(-3)
P 		21
(-2.5)
A 		19.8
(-2.7)
A 		37
avr 38.2
(2.8) 		39
(3) 		25.4
(-1) 		20.3
(-2.5) 		18.5
(-3) 		21.4
(-2.2) 		21
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193580_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.612
Sequence Type Exemplar sequence
Representative Public ID D2092.3 NCBI
Target Description D2092.3 /REP_DB=WormBase Gene ID /WP=CE09102 /GEN=acr-11 /TR=P91197 /GB=AAB42223.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel protein
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_059505(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059505 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-11) (acr-11) mRNA, complete cds. 11/11 None
SNAP00000030849 ENSEMBL cdna:SNAP chromosome:CEL140:I:6629821:6632758:-1 11/11 None
GENEFINDER00000030861 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6629821:6633028:-1 11/11 None
D2092.3 ENSEMBL cdna:known chromosome:CEL140:I:6629821:6633028:-1 gene:D2092.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:6629749-6632957(-) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel protein
Gene Symbol acr-11
Ensembl D2092.3
Entrez Gene 191599 Entrez gene
SwissProt P91197 EMBL-EBI
WormBase CE09102 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1632622_AT nicotinic Acetylcholine Receptor 18C dm
DROSGENOME1:145365_AT nicotinic Acetylcholine Receptor 18C dm
DROSGENOME1:145364_AT nicotinic Acetylcholine Receptor 18C dm
CHICKEN:GGA.664.1.S1_AT mature protein gga
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
15464 acetylcholine receptor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB42223 Acetylcholine receptor protein 11 [Caenorhabditis elegans] ref|NP_491906.1| AcetylCholine Receptor family member (acr-11) [Caenorhabditis elegans] 0.0
blast CAE67246 Hypothetical protein CBG12686 [Caenorhabditis briggsae] 0.0
blast AAC25796 Acetylcholine receptor protein 16, isoform a [Caenorhabditis elegans] emb|CAA58764.1| alpha-1 subunit of nicotinic acetylcholine receptor [Caenorhabditis elegans] ref|NP_505207.1| AcetylCholine Receptor family member (acr-16) [Caenorhabditis elegans] sp|P48180|ACH1_CAEEL Acetylcholine receptor-like protein, alpha-type subunit precursor gb|AAR98633.1| acetylcholine receptor (57.1 kD) alternative variant 1 [Caenorhabditis elegans] 1.0E-131
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.0E-49
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-100
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.0E-49
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.0E-47
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491906.1 5 239-261,271-288,301-323,338-355,438-460
D2092.3 5 239-261,271-288,301-323,338-355,438-460
SNAP00000030849 5 126-148,158-175,188-210,225-242,325-347
GENEFINDER00000030861 5 239-261,271-288,301-323,338-355,438-460
Sequence
Target Sequence 
>C. ELEGANS:193580_AT
tggattcatgtttccaccagacgctggagagaaaataactcttgaggttacaatcctgtt
ggcaatcgtgttcttcctgagtatggtttccgaaatgacgccgccaacgtcggaagcagt
gccattaattggagtattcttctcctgctgtatgctcgttgtttctgcttcggttgtctt
caccattgttgtccttaatttacacttcagaagtgctgatagtcacgagatgaatcctct
agtacgtcgtgtacttctggaattccttccttggcttctctttatgtcacgtcctggata
caaatttgtgaaagctaatgtgattgatagcactgacaaaatgccgaaaaagccaaaaaa
tccactggactgcaatcttccatctaatcatgctggatatgaagcacaaattctacttct
tcattcggttcatacagaattaagaagagttgttgctttttataacaaggaagaacatga
tgaaaggattcaaacggattggagattcgcggcgatggtcgtcgatagagcgtgtcttct
acttttcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGATTCATGTTTCCACCAGACGCT 411 551 789 Antisense
GCAATCGTGTTCTTCCTGAGTATGG 539 321 850 Antisense
TATGGTTTCCGAAATGACGCCGCCA 203 655 870 Antisense
TGGAGTATTCTTCTCCTGCTGTATG 694 549 918 Antisense
TTCGGTTGTCTTCACCATTGTTGTC 498 695 957 Antisense
GATGAATCCTCTAGTACGTCGTGTA 83 413 1017 Antisense
GTACTTCTGGAATTCCTTCCTTGGC 44 461 1039 Antisense
GACTGCAATCTTCCATCTAATCATG 496 375 1156 Antisense
ATTCTACTTCTTCATTCGGTTCATA 387 11 1198 Antisense
GGAGATTCGCGGCGATGGTCGTCGA 563 517 1289 Antisense
ATAGAGCGTGTCTTCTACTTTTCAC 242 23 1313 Antisense
Sequence Source Affymetrix Proprietary Database