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[187058_at]

Description Y105C5B.16 /REP_DB=WormBase Gene ID /WP=CE24065 /TR=Q9NAM5 /GB=CAB54361.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 43      4grp_total > 43      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 71
1 2 3 4 range
A 52.3
(-2.3)
A 		92.4
(3)
A 		46.6
(-3)
A 		58.9
(-1.4)
A 		46
B 71.3
(1.7)
A 		81.5
(3)
A 		69.8
(1.5)
A 		34.8
(-3)
A 		47
C 82
(-0.9)
A 		106
(3)
A 		70.1
(-2.8)
A 		68.7
(-3)
A 		37
avr 68.5
(-0.8) 		93.3
(3) 		62.2
(-1.8) 		54.1
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 57.8
(-0.5)
A 		50.1
(-1.1)
A 		101.2
(3)
P 		55.7
(-0.7)
A 		34.9
(-2.4)
A 		26.9
(-3)
A 		74
B 63.7
(1)
A 		75.3
(2.3)
M 		81.6
(3)
P 		28.3
(-3)
A 		53.5
(-0.2)
A 		44.1
(-1.2)
A 		53
C 36.5
(-2.1)
A 		89.1
(3)
M 		77.1
(1.8)
A 		62
(0.4)
A 		27.5
(-3)
A 		54.7
(-0.4)
A 		62
avr 52.7
(-1.2) 		71.5
(1.1) 		86.6
(3) 		48.7
(-1.7) 		38.6
(-3) 		41.9
(-2.6) 		48
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 19
(2.4)
A 		20.1
(3)
A 		12.2
(-1.1)
A 		8.6
(-3)
A 		12
B 22.8
(3)
A 		20.1
(1.9)
A 		16.2
(0.4)
A 		7.4
(-3)
A 		15
C 27.2
(2)
A 		30.5
(3)
A 		24.4
(1.1)
A 		11.6
(-3)
A 		19
avr 23
(2.8) 		23.6
(3) 		17.6
(0.5) 		9.2
(-3) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 21
1 2 3 4 5 6 range
A 10.7
(-1.4)
A 		17.8
(1.4)
A 		22
(3)
P 		14.1
(-0.1)
A 		10.5
(-1.5)
A 		6.6
(-3)
A 		15
B 22.2
(2)
A 		25.1
(3)
M 		19.8
(1.2)
P 		7.5
(-3)
A 		21.7
(1.8)
A 		16.4
(0)
A 		18
C 13.5
(-1.5)
A 		27.2
(3)
M 		19.6
(0.5)
A 		12.5
(-1.8)
A 		8.9
(-3)
A 		18.3
(0.1)
A 		18
avr 15.5
(-1) 		23.4
(3) 		20.5
(1.6) 		11.4
(-3) 		13.7
(-1.9) 		13.8
(-1.8) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187058_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10360
Sequence Type Exemplar sequence
Representative Public ID Y105C5B.16 NCBI
Target Description Y105C5B.16 /REP_DB=WormBase Gene ID /WP=CE24065 /TR=Q9NAM5 /GB=CAB54361.1 /SUBMIT=HINXTON /CHR=4 /FEA=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_070504(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070504 NCBI Caenorhabditis elegans Y105C5B.16 (Y105C5B.16) mRNA, complete cds. 11/11 None
SNAP00000018400 ENSEMBL cdna:SNAP chromosome:CEL140:IV:15956533:15958192:-1 9/11 None
GENEFINDER00000018440 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:15956533:15962674:-1 11/11 None
Y105C5B.16 ENSEMBL cdna:known chromosome:CEL140:IV:15956533:15962674:-1 gene:Y105C5B.16 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
chrIV:15956538-15962680(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y105C5B.16
Entrez Gene 190895 Entrez gene
SwissProt Q9NAM5 EMBL-EBI
WormBase CE24065 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
Protein Similarities
Method ID Description E-Value
blast CAB54361 Hypothetical protein Y105C5B.16 [Caenorhabditis elegans] ref|NP_502905.1| Y105C5B.16 [Caenorhabditis elegans] 0.0
blast CAE57396 Hypothetical protein CBG00348 [Caenorhabditis briggsae] 1.0E-170
blast CAA91537 Hypothetical protein T01H10.2 [Caenorhabditis elegans] ref|NP_510024.2| T01H10.2 [Caenorhabditis elegans] 1.0E-132
blast CAB54361 Hypothetical protein Y105C5B.16 [Caenorhabditis elegans] ref|NP_502905.1| Y105C5B.16 [Caenorhabditis elegans] 2.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.5E-30
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 0.018
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502905.1 4 260-282,289-308,318-340,345-367
Y105C5B.16 4 260-282,289-308,318-340,345-367
SNAP00000018400 4 58-80,90-107,119-141,173-195
GENEFINDER00000018440 4 260-282,289-308,318-340,345-367
Sequence
Target Sequence 
>C. ELEGANS:187058_AT
ctgtcaaattcgtttctgtcttccaatcttttatcgggttcaggtggacattttgaacga
gatttatgaagaaattatggatgagaggatatttaagactatgggaaactctgaatggaa
gctgttaaacctgacgaatcgtgttgaagcattagtgtacaatgataatatgggaactat
ggatttggcgatttttgagattacaattagaagaaaccctttatattacatttatatgat
agtttttccctcgtttatcattaattttgtgtcgattgtcggagttttcctgaatggagc
tgataaaatgtcgaggctaaacgtcgggctcaccaacatcatgacaatgacgttcatcct
cggagtgatggctgacaaaattccgagaactggaaatattccgctacttgggatttatat
cattataaatttggtgatcatagctcaactggaatcatttctgggtcgtccattggagta
taccagtgcaattatattggaattaatgacatgtgccaactttctagtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGTCAAATTCGTTTCTGTCTTCCA 31 241 567 Antisense
GTCTTCCAATCTTTTATCGGGTTCA 72 469 584 Antisense
AGCTGTTAAACCTGACGAATCGTGT 517 27 686 Antisense
ATATGATAGTTTTTCCCTCGTTTAT 582 21 800 Antisense
GTCGGAGTTTTCCTGAATGGAGCTG 428 471 844 Antisense
TGTCGAGGCTAAACGTCGGGCTCAC 294 557 875 Antisense
GGGCTCACCAACATCATGACAATGA 259 491 892 Antisense
CAATGACGTTCATCCTCGGAGTGAT 69 179 911 Antisense
GGAAATATTCCGCTACTTGGGATTT 513 525 958 Antisense
GAATCATTTCTGGGTCGTCCATTGG 551 327 1018 Antisense
AATGACATGTGCCAACTTTCTAGTT 366 163 1071 Antisense
Sequence Source Affymetrix Proprietary Database