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[193648_at]

Description F25G6.3 /REP_DB=WormBase Gene ID /WP=CE09639 /GEN=acr-16 /TR=SW:P48180 /GB=AAC25796.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ion channel subunit
Cluster 6grp_highest_10_10 > 20      6grp_high1_10_10 > 11      4grp_high_8_8 > 42      6grp_highest_nonorm > 80      6grp_total > 13      4grp_total > 45      6grp_highest_sub > De      6grp_cgc > 60      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 167
1 2 3 4 range
A 155.6
(3)
P 		131.4
(1.5)
P 		98.4
(-0.6)
P 		59.1
(-3)
A 		97
B 226.2
(3)
P 		99.1
(-2.3)
P 		83.6
(-2.9)
P 		81.2
(-3)
P 		145
C 161.6
(2.2)
P 		174.4
(3)
P 		125.9
(-0.2)
P 		83.5
(-3)
A 		91
avr 181.1
(3) 		135
(0.4) 		102.6
(-1.4) 		74.6
(-3) 		107

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 180
1 2 3 4 5 6 range
A 263.8
(3)
P 		182.4
(0.3)
P 		172.2
(-0.1)
P 		183.7
(0.3)
P 		159.4
(-0.5)
P 		83.8
(-3)
P 		180
B 195.6
(2.2)
P 		189.3
(1.9)
P 		210.7
(3)
P 		128.9
(-1.3)
P 		137.2
(-0.9)
P 		97.2
(-3)
P 		114
C 232.4
(3)
P 		221.3
(2.5)
P 		181.1
(0.8)
P 		232.5
(3)
P 		150.2
(-0.5)
P 		90.3
(-3)
P 		142
avr 230.6
(3) 		197.7
(1.6) 		188
(1.2) 		181.7
(0.9) 		148.9
(-0.5) 		90.4
(-3) 		140
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 56.6
(3)
P 		28.5
(-0.5)
P 		25.7
(-0.9)
P 		8.6
(-3)
A 		48
B 72.1
(3)
P 		24.5
(-2.2)
P 		19.4
(-2.8)
P 		17.3
(-3)
P 		55
C 53.5
(3)
P 		50.1
(2.5)
P 		43.9
(1.5)
P 		14.1
(-3)
A 		39
avr 60.7
(3) 		34.4
(-0.3) 		29.7
(-0.9) 		13.3
(-3) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 66
1 2 3 4 5 6 range
A 48.6
(0.8)
P 		64.9
(3)
P 		37.5
(-0.7)
P 		46.6
(0.5)
P 		48.1
(0.7)
P 		20.4
(-3)
P 		45
B 68.1
(3)
P 		63
(2.1)
P 		51.2
(0)
P 		34.1
(-3)
P 		55.8
(0.8)
P 		36.2
(-2.6)
P 		34
C 86.2
(3)
P 		67.5
(1)
P 		46.1
(-1.3)
P 		46.8
(-1.2)
P 		48.6
(-1)
P 		30.2
(-3)
P 		56
avr 67.6
(3) 		65.1
(2.6) 		44.9
(-0.5) 		42.5
(-0.9) 		50.8
(0.4) 		28.9
(-3) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193648_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11983
Sequence Type Exemplar sequence
Representative Public ID F25G6.3 NCBI
Target Description F25G6.3 /REP_DB=WormBase Gene ID /WP=CE09639 /GEN=acr-16 /TR=SW:P48180 /GB=AAC25796.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ion channel subunit
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_072806(11), NM_001028676(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072806 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-16) (acr-16) mRNA, complete cds. 11/11 None
NM_001028676 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-16) (acr-16) mRNA, complete cds. 9/11 None
SNAP00000003980 ENSEMBL cdna:SNAP chromosome:CEL140:V:8563857:8566661:1 11/11 None
GENEFINDER00000003989 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:8565367:8566661:1 11/11 None
F25G6.3a ENSEMBL cdna:known chromosome:CEL140:V:8563804:8566933:1 gene:F25G6.3 11/11 None
F25G6.3b ENSEMBL cdna:known chromosome:CEL140:V:8563857:8566214:1 gene:F25G6.3 9/11 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:8563857-8566662(+) 100.0 100.0
Public Domain and Genome References
Ensembl F25G6.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
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] 0.0
blast CAE58366 Hypothetical protein CBG01491 [Caenorhabditis briggsae] 0.0
blast AAN84815 Acetylcholine receptor protein 16, isoform b [Caenorhabditis elegans] ref|NP_001023847.1| AcetylCholine Receptor family member (acr-16) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.1E-56
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-106
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.4E-44
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-10
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.5E-31
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.9E-23
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505207.1 5 229-251,261-278,291-313,328-342,473-495
NP_001023847.1 3 229-251,261-278,291-313
F25G6.3a 5 229-251,261-278,291-313,328-342,473-495
F25G6.3b 3 229-251,261-278,291-313
SNAP00000003980 3 231-253,263-285,444-466
GENEFINDER00000003989 2 10-32,225-247
Sequence
Target Sequence 
>C. ELEGANS:193648_AT
ggttactgcatcgacagtcttcaccgtctacgttctcaacttacattaccgtactccgga
gacccacgatatgggaccatggacacgtaacctccttctctattggattccatggattct
tcgaatgaaacgacccggtcacaacttgacatatgcttcacttccatcattattttccac
taagccaaatcgtcactcggaatcattgatccgtaacatcaaagacaatgaacattcact
ttcacgagcaaactcatttgatgccgattgtcgattgaatcaatatattatgacacaatc
tgttagtaatgggttgacaagtcttggcagtattccaagtacaatgatttcatcaaatgg
tacaactacagacgtctcacaacaggcgacacttctgattcttcacagaatataccatga
attgaagattgttacgaagagaatgatagaaggtgataaggaagaacaggcatgcaataa
ttggaaatttgcggccatggttgtggaccgcctttgtttatacgtcttca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTTACTGCATCGACAGTCTTCACC 10 507 918 Antisense
GTCTACGTTCTCAACTTACATTACC 352 469 943 Antisense
TACATTACCGTACTCCGGAGACCCA 589 641 959 Antisense
ATGGGACCATGGACACGTAACCTCC 213 49 988 Antisense
GTAACCTCCTTCTCTATTGGATTCC 69 461 1004 Antisense
TCACTTCCATCATTATTTTCCACTA 408 627 1075 Antisense
TTCCACTAAGCCAAATCGTCACTCG 31 697 1092 Antisense
GGTACAACTACAGACGTCTCACAAC 289 503 1276 Antisense
ACAGGCGACACTTCTGATTCTTCAC 519 107 1299 Antisense
TTGCGGCCATGGTTGTGGACCGCCT 256 701 1406 Antisense
GACCGCCTTTGTTTATACGTCTTCA 692 381 1423 Antisense
Sequence Source Affymetrix Proprietary Database