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[190334_at] ion-channel protein

Description Y110A7A.3 /REP_DB=WormBase Gene ID /WP=CE24123 /TR=Q9N587 /GB=AAF60421.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ion-channel protein
Cluster 6grp_total > 05      4grp_total > 28      6grp_cgc > 32      6grp_cgc_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 61.1
(1)
A 		36.3
(-0.9)
A 		8.5
(-3)
A 		87.2
(3)
A 		79
B 33.9
(-2.6)
A 		64.5
(3)
A 		31.9
(-3)
A 		55
(1.3)
A 		33
C 61.3
(2.6)
A 		52.5
(1)
A 		31.3
(-3)
A 		63.4
(3)
A 		32
avr 52.1
(0.8) 		51.1
(0.7) 		23.9
(-3) 		68.5
(3) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 59
1 2 3 4 5 6 range
A 79.2
(3)
A 		73.9
(2.4)
A 		50.6
(0)
A 		21.8
(-3)
A 		35.7
(-1.5)
A 		42.2
(-0.9)
A 		57
B 76.9
(3)
A 		68.9
(2.1)
A 		52.5
(0.2)
A 		24.7
(-3)
A 		56.7
(0.7)
P 		25.7
(-2.9)
A 		52
C 70.9
(2.9)
A 		71.8
(3)
P 		29.5
(-1.9)
A 		25.2
(-2.5)
A 		47.2
(0.1)
A 		20.5
(-3)
A 		51
avr 75.7
(3) 		71.5
(2.5) 		44.2
(-0.6) 		23.9
(-3) 		46.5
(-0.4) 		29.5
(-2.4) 		52
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 22.2
(3)
A 		7.9
(-1.3)
A 		2.2
(-3)
A 		12.8
(0.2)
A 		20
B 10.8
(-0.6)
A 		15.9
(3)
A 		7.4
(-3)
A 		11.7
(0)
A 		9
C 20.3
(3)
A 		15.1
(-0.3)
A 		10.9
(-2.9)
A 		10.7
(-3)
A 		10
avr 17.8
(3) 		13
(0.4) 		6.8
(-3) 		11.7
(-0.3) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 14.6
(-0.4)
A 		26.3
(3)
A 		11
(-1.4)
A 		5.5
(-3)
A 		10.8
(-1.5)
A 		10.3
(-1.6)
A 		21
B 26.8
(3)
A 		22.9
(1.8)
A 		12.7
(-1.2)
A 		6.5
(-3)
A 		23
(1.9)
P 		9.6
(-2.1)
A 		20
C 26.3
(3)
A 		21.9
(1.8)
P 		7.5
(-2.3)
A 		5.1
(-3)
A 		15.3
(-0.1)
A 		6.9
(-2.5)
A 		21
avr 22.6
(2.6) 		23.7
(3) 		10.4
(-1.4) 		5.7
(-3) 		16.4
(0.6) 		8.9
(-1.9) 		18
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190334_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.513
Sequence Type Exemplar sequence
Representative Public ID Y110A7A.3 NCBI
Target Description Y110A7A.3 /REP_DB=WormBase Gene ID /WP=CE24123 /TR=Q9N587 /GB=AAF60421.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ion-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_059132(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059132 NCBI Caenorhabditis elegans UNCoordinated family member (unc-63) (unc-63) mRNA, complete cds. 11/11 None
SNAP00000029216 ENSEMBL cdna:SNAP chromosome:CEL140:I:5143719:5149119:1 11/11 None
GENEFINDER00000029226 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5146074:5149119:1 11/11 None
Y110A7A.3 ENSEMBL cdna:known chromosome:CEL140:I:5141678:5149229:1 gene:Y110A7A.3 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
chrI:5141681-5149119(+) 100.0 100.0
Public Domain and Genome References
Gene Title ion-channel protein
Gene Symbol unc-63
Ensembl Y110A7A.3
Entrez Gene 172150 Entrez gene
SwissProt Q9N587 EMBL-EBI
WormBase CE30706 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.9107.1.S1_AT similar to Neuronal acetylcholine receptor protein, alpha-6 subunit precursor cfa
CANINE_2:CFAAFFX.9118.1.S1_AT similar to Neuronal acetylcholine receptor protein, alpha-6 subunit precursor cfa
CANINE_2:CFAAFFX.9118.1.S1_S_AT similar to Neuronal acetylcholine receptor protein, alpha-6 subunit precursor cfa
DROSOPHILA_2:1629258_AT nicotinic Acetylcholine Receptor alpha 7E dm
DROSGENOME1:143810_AT nicotinic Acetylcholine Receptor alpha 7E dm
CHICKEN:GGA.340.1.S1_AT cholinergic receptor, nicotinic, alpha polypeptide 6 gga
HG-U133_PLUS_2:207568_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
HG-U133A:207568_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
HG-FOCUS:207568_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
HG-U133A_2:207568_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
HG-U95AV2:31703_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
HU35KSUBA:U62435_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
U133_X3P:G4757981_3P_AT cholinergic receptor, nicotinic, alpha polypeptide 6 hs
MOUSE430_2:1450426_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MOE430A:1450426_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MOUSE430A_2:1450426_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MG-U74AV2:96996_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MG-U74CV2:138177_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MOE430A:1450427_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MOUSE430A_2:1450427_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
MOUSE430_2:1450427_AT cholinergic receptor, nicotinic, alpha polypeptide 6 mm
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 AAK83056 nicotinic acetylcholine receptor alpha subunit [Caenorhabditis elegans] gb|AAF60421.3| Uncoordinated protein 63 [Caenorhabditis elegans] ref|NP_491533.2| UNCoordinated family member (unc-63) [Caenorhabditis elegans] 0.0
blast CAE56135 Hypothetical protein CBG23747 [Caenorhabditis briggsae] 0.0
blast CAA04053 nicotinic acetylcholine receptor, alpha2 subunit [Locusta migratoria] 1.0E-138
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-91
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 6.5E-102
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-91
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.2E-71
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-91
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.3E-33
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491533.2 4 262-284,291-313,326-348,472-494
Y110A7A.3 4 262-284,291-313,326-348,472-494
SNAP00000029216 4 179-201,208-230,243-265,389-411
GENEFINDER00000029226 4 113-135,142-164,177-199,323-345
Sequence
Target Sequence 
>C. ELEGANS:190334_AT
ttatctcgttgactgttttcttccttctgctcgtagagattattccatcaacatcacttg
tgattccattaattggaaaatatcttctatttacaatggttcttgtcacattatctgtgg
tggttactgtagttacattgaatgtacattatcgatccccaacaacacatacaatgccaa
aatggatgaagcggttattcgtggattttctgccaaaatatcttctcatgacacgaccgc
aacctcctggtcatcatagcaaaccaaatcggaagttcgactcccgtgcatcaacattca
gtattggagtgaatcatgtattgggacagaattctgaattattatcaccaggactcaatt
ccaatagggaagagtcttcatttactttaccacgcgacaactcgccagttcgatctgctg
tcgaaagtgttgcctatatagcggatcatttgaaaaacgaggaagatgataaacaggtaa
tcgaggactggaaatacatatcagtcgtcatggatcgaatatttttaatcacattcactt
ttgcttgtgcttttggaaccgttgtgattattgcacgtgcaccgtcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTATCTCGTTGACTGTTTTCTTCCT 505 679 1241 Antisense
TGAATGTACATTATCGATCCCCAAC 558 575 1379 Antisense
AGCGGTTATTCGTGGATTTTCTGCC 47 83 1430 Antisense
AAATATCTTCTCATGACACGACCGC 673 115 1456 Antisense
GCAACCTCCTGGTCATCATAGCAAA 594 319 1479 Antisense
CAAATCGGAAGTTCGACTCCCGTGC 378 191 1505 Antisense
ACTCCCGTGCATCAACATTCAGTAT 517 99 1520 Antisense
GTCTTCATTTACTTTACCACGCGAC 304 469 1614 Antisense
GATCTGCTGTCGAAAGTGTTGCCTA 379 419 1652 Antisense
TTGCTTGTGCTTTTGGAACCGTTGT 498 699 1781 Antisense
TGTGATTATTGCACGTGCACCGTCC 238 555 1803 Antisense
Sequence Source Affymetrix Proprietary Database