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[192309_at]

Description R06A4.10 /REP_DB=WormBase Gene ID /WP=CE21114 /TR=Q9U398 /GB=CAB51466.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=nicotinic acetylcholine receptor
Cluster 6grp_total > 25      4grp_total > 47      6grp_cgc > 43      6grp_cgc_sub > 02      6grp_total_sub > Decrease      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 86
(3)
A 		9
(-3)
A 		18.2
(-2.3)
A 		33.8
(-1.1)
A 		77
B 102.4
(3)
A 		10.6
(-3)
A 		36.3
(-1.3)
A 		33.7
(-1.5)
A 		92
C 125.6
(3)
A 		19.6
(-2.4)
A 		39.2
(-1.4)
A 		7.1
(-3)
A 		119
avr 104.7
(3) 		13.1
(-3) 		31.2
(-1.8) 		24.9
(-2.2) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 67
1 2 3 4 5 6 range
A 24.9
(-0.8)
A 		62.3
(3)
A 		3.8
(-3)
A 		4.1
(-3)
A 		10.3
(-2.3)
A 		12.7
(-2.1)
A 		59
B 66.9
(3)
A 		54
(1.8)
A 		36.3
(0)
A 		8.1
(-2.7)
A 		12.3
(-2.3)
A 		4.9
(-3)
A 		62
C 44.2
(0.6)
A 		70.5
(3)
A 		16.7
(-1.9)
A 		4.8
(-2.9)
A 		6.7
(-2.8)
A 		4
(-3)
A 		67
avr 45.3
(1.2) 		62.3
(3) 		18.9
(-1.6) 		5.7
(-3) 		9.8
(-2.6) 		7.2
(-2.8) 		57
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 31.3
(3)
A 		2
(-3)
A 		4.8
(-2.4)
A 		4.9
(-2.4)
A 		29
B 32.7
(3)
A 		2.6
(-3)
A 		8.4
(-1.8)
A 		7.2
(-2.1)
A 		30
C 41.6
(3)
A 		5.6
(-2.3)
A 		13.7
(-1.1)
A 		1.2
(-3)
A 		40
avr 35.2
(3) 		3.4
(-3) 		9
(-1.9) 		4.4
(-2.8) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 23
1 2 3 4 5 6 range
A 4.6
(-1.9)
A 		22.1
(3)
A 		0.8
(-3)
A 		1
(-2.9)
A 		3.1
(-2.4)
A 		3.1
(-2.4)
A 		21
B 23.3
(3)
A 		18
(1.5)
A 		8.8
(-1)
A 		2.1
(-2.9)
A 		5
(-2.1)
A 		1.8
(-3)
A 		22
C 16.4
(1.5)
A 		21.5
(3)
A 		4.2
(-2.1)
A 		1
(-3)
A 		2.2
(-2.6)
A 		1.3
(-2.9)
A 		21
avr 14.8
(1.2) 		20.5
(3) 		4.6
(-2) 		1.4
(-3) 		3.4
(-2.4) 		2.1
(-2.8) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192309_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3223
Sequence Type Exemplar sequence
Representative Public ID R06A4.10 NCBI
Target Description R06A4.10 /REP_DB=WormBase Gene ID /WP=CE21114 /TR=Q9U398 /GB=CAB51466.1 /SUBMIT=HINXTON /CHR=2 /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_001027102(11), NM_001027101(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027102 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-20) (acr-20) mRNA, complete cds. 11/11 None
NM_001027101 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-20) (acr-20) mRNA, complete cds. 11/11 None
SNAP00000043982 ENSEMBL cdna:SNAP chromosome:CEL140:II:14373878:14377017:-1 10/11 None
GENEFINDER00000043990 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14373878:14378991:-1 11/11 None
R06A4.10a ENSEMBL cdna:known chromosome:CEL140:II:14373752:14376733:-1 gene:R06A4.10 11/11 None
R06A4.10b ENSEMBL cdna:known chromosome:CEL140:II:14373752:14379004:-1 gene:R06A4.10 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
chrII:14373874-14377764(-) 100.0 100.0
Public Domain and Genome References
Ensembl R06A4.10
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAE46678 Hypothetical protein R06A4.10b [Caenorhabditis elegans] ref|NP_001022273.1| AcetylCholine Receptor family member (acr-20) [Caenorhabditis elegans] 0.0
blast AAR98637 acetylcholine receptor 20 (63.9 kD) alternative variant a [Caenorhabditis elegans] 0.0
blast CAB51466 Hypothetical protein R06A4.10a [Caenorhabditis elegans] ref|NP_001022272.1| AcetylCholine Receptor family member (acr-20) [Caenorhabditis elegans] 0.0
blast CAE65920 Hypothetical protein CBG11088 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.6E-9
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.3E-73
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.6E-9
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 5.3E-73
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.6E-9
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.9E-65
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022273.1 4 197-219,232-249,264-286,483-505
NP_001022272.1 4 197-219,232-249,264-286,486-508
R06A4.10a 4 197-219,232-249,264-286,486-508
R06A4.10b 4 197-219,232-249,264-286,483-505
SNAP00000043982 4 233-255,268-285,300-322,517-539
GENEFINDER00000043990 4 333-355,368-385,400-422,674-696
Sequence
Target Sequence 
>C. ELEGANS:192309_AT
ggatgtcacttgcataagcgactccgggatcgtcgcgatgggagttccgacgttggcttc
tgaggatgatgatcaggatgtgtctctgttggagctggagacgacgcccacgcccgcaat
gcagagacccactcggttgcataaagcttccacttgcggaagcttcgatagtatgatgtt
caggcagattgaagtgccagtatccccccgaaccgcccgaaatttggctgaaatcgagta
cgactggctcgccgcactgctcgagcgaatatttctcatcaccttcttgttcattttcgt
tttgacctctattgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATGTCACTTGCATAAGCGACTCC 230 515 1494 Antisense
AAGCGACTCCGGGATCGTCGCGATG 111 149 1509 Antisense
AGTTCCGACGTTGGCTTCTGAGGAT 342 63 1536 Antisense
CTGTTGGAGCTGGAGACGACGCCCA 436 217 1579 Antisense
CCGCAATGCAGAGACCCACTCGGTT 190 261 1607 Antisense
CACTCGGTTGCATAAAGCTTCCACT 210 159 1623 Antisense
GCAGATTGAAGTGCCAGTATCCCCC 234 313 1677 Antisense
GAAATCGAGTACGACTGGCTCGCCG 32 363 1723 Antisense
TCGCCGCACTGCTCGAGCGAATATT 618 599 1742 Antisense
AGCGAATATTTCTCATCACCTTCTT 67 83 1757 Antisense
CATTTTCGTTTTGACCTCTATTGGA 333 215 1785 Antisense
Sequence Source Affymetrix Proprietary Database