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[192495_at]

Description R03E1.3 /REP_DB=WormBase Gene ID /WP=CE18903 /TR=Q9XTY8 /GB=CAB07402.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Neurotransmitter-gated ion-channel
Cluster 6grp_total > 91      4grp_total > 35      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 6.5
(-2.1)
A 		29.8
(3)
A 		2.5
(-3)
A 		8.7
(-1.6)
A 		27
B 17.1
(-0.1)
A 		29.7
(3)
A 		5.7
(-3)
A 		6.1
(-2.9)
A 		24
C 8
(-2.5)
A 		8.1
(-2.4)
A 		5.2
(-3)
A 		35.9
(3)
A 		31
avr 10.5
(-1) 		22.5
(3) 		4.5
(-3) 		16.9
(1.1) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10
1 2 3 4 5 6 range
A 8.7
(2.7)
A 		8.9
(3)
A 		5
(-3)
A 		5.5
(-2.2)
A 		7.8
(1.3)
A 		6.4
(-0.8)
A 		4
B 6.7
(-0.8)
A 		5.5
(-1.7)
A 		6.5
(-0.9)
A 		11.6
(3)
A 		6.2
(-1.2)
A 		3.8
(-3)
A 		8
C 7.4
(-0.6)
A 		8.6
(0.1)
A 		6.7
(-1)
A 		12.6
(2.4)
A 		13.7
(3)
A 		3.3
(-3)
A 		10
avr 7.6
(0.4) 		7.7
(0.6) 		6.1
(-1.2) 		9.9
(3) 		9.2
(2.2) 		4.5
(-3) 		5
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 2.4
(-1.2)
A 		6.5
(3)
A 		0.7
(-3)
A 		1.3
(-2.4)
A 		6
B 5.4
(1.1)
A 		7.3
(3)
A 		1.3
(-3)
A 		1.3
(-3)
A 		6
C 2.6
(-1.9)
A 		2.3
(-2.3)
A 		1.8
(-3)
A 		6.1
(3)
A 		4
avr 3.5
(0.2) 		5.4
(3) 		1.3
(-3) 		2.9
(-0.7) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 1.6
(-1.6)
A 		3.2
(3)
A 		1.1
(-3)
A 		1.4
(-2.1)
A 		2.3
(0.4)
A 		1.5
(-1.9)
A 		2
B 2.3
(0.2)
A 		1.8
(-1.6)
A 		1.6
(-2.3)
A 		3.1
(3)
A 		2.5
(0.9)
A 		1.4
(-3)
A 		2
C 2.8
(0.1)
A 		2.6
(-0.3)
A 		1.7
(-1.9)
A 		2.5
(-0.5)
A 		4.4
(3)
A 		1.1
(-3)
A 		3
avr 2.2
(0) 		2.5
(1) 		1.5
(-2.3) 		2.3
(0.3) 		3.1
(3) 		1.3
(-3) 		2
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192495_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17810
Sequence Type Exemplar sequence
Representative Public ID R03E1.3 NCBI
Target Description R03E1.3 /REP_DB=WormBase Gene ID /WP=CE18903 /TR=Q9XTY8 /GB=CAB07402.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Neurotransmitter-gated ion-channel
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_001029653(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029653 NCBI Caenorhabditis elegans R03E1.4 (R03E1.4) mRNA, complete cds. 10/11 None
GENEFINDER00000040388 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:14155035:14161557:-1 11/11 None
R03E1.4 ENSEMBL cdna:known chromosome:CEL140:X:14155035:14156933:-1 gene:R03E1.4 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000040382 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:14155034-14161557(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl R03E1.4
Entrez Gene 3565071 Entrez gene
SwissProt Q69YW8 EMBL-EBI
WormBase CE36660 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07402 Hypothetical protein R03E1.3 [Caenorhabditis elegans] ref|NP_510359.2| R03E1.3 [Caenorhabditis elegans] 0.0
blast AAF60813 Hypothetical protein Y58G8A.1 [Caenorhabditis elegans] ref|NP_503167.1| Y58G8A.1 [Caenorhabditis elegans] 1.0E-158
blast CAE66757 Hypothetical protein CBG12109 [Caenorhabditis briggsae] 1.0E-155
blast CAH10846 Hypothetical protein R03E1.4 [Caenorhabditis elegans] ref|NP_001024824.1| R03E1.4 [Caenorhabditis elegans] 5.0E-93
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999998002099E-12
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.00000003404354E-19
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-6
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-6
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.1E-24
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000040388 3 259-281,285-307,320-342
Sequence
Target Sequence 
>C. ELEGANS:192495_AT
acatcaagcgtaattctccatccgaaaaacttgttgaaagcaacaacatggagaagagta
aaaaaacgagacaaaattttaaaatagccgagttagggcttctgaaggagtcgtttgaaa
aagactcacaccctggaacttctgaaatgaatcgtcttgctggtttattgaatcgaaacg
aagctcagattaatcgctggttcaaggcaatgagagtaaaagtgaaaaaggcttccttaa
agatgtcgagagaagttacaagccaatcgggaagcaatgtagaactcctgggatcttcga
ttgttcccgagccaccgagtagtgaaatagtgtcatcgcaagctcaataccgattggaga
acatgaaactattaagcaatgttccggaaacttttaatgttgcaggaccgtcaaacagta
aaatggtacttctggaagcttacatgaacactgttcggcaaacttcgagtgttgttgggc
aatcaagcagtgaaatgcatacaactcctattgttccaattattcaagccaacaatgatc
tgctcactgtcaaaccacaagctccacccaatcagagtatcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACATCAAGCGTAATTCTCCATCCGA 705 103 1343 Antisense
GAAAAAGACTCACACCCTGGAACTT 450 355 1459 Antisense
ATCGTCTTGCTGGTTTATTGAATCG 18 37 1493 Antisense
GAAGCAATGTAGAACTCCTGGGATC 274 341 1613 Antisense
TGGGATCTTCGATTGTTCCCGAGCC 689 553 1631 Antisense
TAGTGTCATCGCAAGCTCAATACCG 165 655 1670 Antisense
GAACACTGTTCGGCAAACTTCGAGT 68 353 1788 Antisense
AATGCATACAACTCCTATTGTTCCA 686 165 1836 Antisense
AGCCAACAATGATCTGCTCACTGTC 661 83 1869 Antisense
TGCTCACTGTCAAACCACAAGCTCC 334 581 1883 Antisense
CAAGCTCCACCCAATCAGAGTATCG 623 185 1900 Antisense
Sequence Source Affymetrix Proprietary Database