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[176580_at] ACHR

Description R13A5.4 /REP_DB=WormBase Gene ID /WP=CE01376 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ACHR
Cluster 6grp_highest_10_10 > 04      6grp_high1_10_10 > 21      4grp_highest_8_8 > 54      4grp_high_8_8 > 18      6grp_highest_nonorm > 90      6grp_total > 41      4grp_total > 22      6grp_high1_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 146.9
(0.8)
P 		117.8
(-0.5)
P 		61
(-3)
P 		196.8
(3)
P 		136
B 180.3
(3)
P 		83.2
(-2.5)
P 		75.2
(-3)
P 		168.9
(2.3)
P 		105
C 191.1
(3)
P 		143.2
(-0.2)
P 		102.2
(-3)
P 		148.3
(0.1)
P 		89
avr 172.8
(3) 		114.7
(-0.7) 		79.5
(-3) 		171.3
(2.9) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 130
1 2 3 4 5 6 range
A 159.8
(1.7)
P 		175
(2.7)
P 		180.4
(3)
P 		173.2
(2.5)
P 		112.5
(-1.3)
P 		85.6
(-3)
P 		95
B 134.4
(1.3)
P 		165.8
(3)
P 		166.4
(3)
P 		124.3
(0.7)
P 		120.9
(0.5)
P 		55.5
(-3)
P 		111
C 140.3
(0.8)
P 		127.7
(0.2)
P 		185.3
(3)
P 		163.4
(1.9)
P 		85.8
(-1.9)
P 		63.6
(-3)
P 		122
avr 144.8
(1.2) 		156.2
(1.8) 		177.4
(3) 		153.6
(1.7) 		106.4
(-0.9) 		68.2
(-3) 		109
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 53.5
(3)
P 		25.6
(-1.5)
P 		15.9
(-3)
P 		28.8
(-0.9)
P 		38
B 57.5
(3)
P 		20.5
(-2.5)
P 		17.4
(-3)
P 		36
(-0.2)
P 		40
C 63.3
(3)
P 		41.2
(-0.5)
P 		35.6
(-1.3)
P 		25
(-3)
P 		38
avr 58.1
(3) 		29.1
(-2) 		23
(-3) 		29.9
(-1.8) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 29.5
(-1.7)
P 		62.2
(3)
P 		39.3
(-0.3)
P 		43.9
(0.3)
P 		34
(-1.1)
P 		20.8
(-3)
P 		41
B 46.8
(1.5)
P 		55.2
(3)
P 		40.4
(0.4)
P 		32.9
(-0.9)
P 		49.1
(1.9)
P 		20.7
(-3)
P 		35
C 52
(3)
P 		39
(0.5)
P 		47.2
(2.1)
P 		32.9
(-0.7)
P 		27.7
(-1.7)
P 		21.3
(-3)
P 		31
avr 42.8
(1.2) 		52.1
(3) 		42.3
(1.1) 		36.6
(0) 		36.9
(0.1) 		20.9
(-3) 		31
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176580_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6275
Sequence Type Exemplar sequence
Representative Public ID R13A5.4 NCBI
Target Description R13A5.4 /REP_DB=WormBase Gene ID /WP=CE01376 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ACHR
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_066255(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066255 NCBI Caenorhabditis elegans R13A5.4 (ACHR) mRNA, complete cds. 11/11 None
SNAP00000038243 ENSEMBL cdna:SNAP chromosome:CEL140:III:7561931:7564447:1 11/11 None
GENEFINDER00000038257 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7561931:7564447:1 11/11 None
R13A5.4 ENSEMBL cdna:known chromosome:CEL140:III:7562090:7564447:1 gene:R13A5.4 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
chrIII:7562087-7564445(+) 100.0 100.0
Public Domain and Genome References
Gene Title ACHR
Ensembl R13A5.4
Entrez Gene 187855 Entrez gene
SwissProt Q95Y94 EMBL-EBI
WormBase CE01376 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
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK84465 Hypothetical protein R13A5.4 [Caenorhabditis elegans] ref|NP_498656.1| R13A5.4 [Caenorhabditis elegans] 0.0
blast CAE70225 Hypothetical protein CBG16705 [Caenorhabditis briggsae] 0.0
blast AAF99957 Acetylcholine receptor protein 22 [Caenorhabditis elegans] ref|NP_509270.1| AcetylCholine Receptor family member (acr-22) [Caenorhabditis elegans] gb|AAR89633.1| acetylcholine receptor (51.1 kD) (acr-22) [Caenorhabditis elegans] 0.0
blast AAF99957 Acetylcholine receptor protein 22 [Caenorhabditis elegans] ref|NP_509270.1| AcetylCholine Receptor family member (acr-22) [Caenorhabditis elegans] gb|AAR89633.1| acetylcholine receptor (51.1 kD) (acr-22) [Caenorhabditis elegans] 1.0E-160
blast AAK84465 Hypothetical protein R13A5.4 [Caenorhabditis elegans] ref|NP_498656.1| R13A5.4 [Caenorhabditis elegans] 1.0E-159
blast CAE70225 Hypothetical protein CBG16705 [Caenorhabditis briggsae] 1.0E-158
blast CAE64450 Hypothetical protein CBG09157 [Caenorhabditis briggsae] 1.0E-143
Protein Domains
Database ID Description E-Value
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.7E-35
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 4.8E-48
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.2E-19
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 8.1E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498656.1 4 196-218,231-249,264-286,366-385
R13A5.4 4 196-218,231-249,264-286,366-385
SNAP00000038243 4 183-205,218-236,251-273,353-372
GENEFINDER00000038257 4 245-267,280-298,313-335,415-434
Sequence
Target Sequence 
>C. ELEGANS:176580_AT
gaagtccgcagaaaaccactctactacattgttgtgattttaattccaacttttctaatc
gtaacagtatcaaacatcggattgttcactccacatggagtacatggagacagagaagag
catgtttccctgggacttaccactatgcttacaatggctgttattctagatatggtcact
ggacaaatgccgaaaagtagtgaaggaattcccttacttgggatgtatgttttaatagag
tttgccctgtcaattatggccgttttggtgtcagtactgataatatttgctcacgaaaga
atgctctacatggatgcaatgccgccattctggattttcagattattctcgaaacataaa
aatcaaatcccactggctgaaatggaatacgatgatttacgttcaagcccagtcgatttg
gctcaagagctccgattttgtattgaaaaagttagaaaacacttggaagatttggattcc
aaagataagaatgagttgatttggcagagatttttctcgtgtgcagatattatttgtggt
tcatgcttcttttttgttaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGTCCGCAGAAAACCACTCTACT 87 337 580 Antisense
ACATCGGATTGTTCACTCCACATGG 448 105 653 Antisense
AGAGCATGTTTCCCTGGGACTTACC 19 71 696 Antisense
GGGACTTACCACTATGCTTACAATG 208 495 711 Antisense
GAGTTTGCCCTGTCAATTATGGCCG 505 397 817 Antisense
TATGGCCGTTTTGGTGTCAGTACTG 371 655 834 Antisense
GCTCTACATGGATGCAATGCCGCCA 18 301 882 Antisense
CAATGCCGCCATTCTGGATTTTCAG 156 183 896 Antisense
ATTTACGTTCAAGCCCAGTCGATTT 100 3 974 Antisense
TTGGCTCAAGAGCTCCGATTTTGTA 251 709 997 Antisense
GTGGTTCATGCTTCTTTTTTGTTAA 143 489 1115 Antisense
Sequence Source Affymetrix Proprietary Database