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[173230_s_at]

Description C52705_rc /REP_DB=TREMBL Accession /GB=C52705 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk271h3 : 3prime end, single read.
Cluster 6grp_total > 88      4grp_total > 17      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 4.5
(-2.3)
A 		18
(3)
A 		16.3
(2.3)
A 		2.6
(-3)
A 		15
B 3.7
(-2.7)
A 		4
(-2.7)
A 		2.3
(-3)
A 		35.2
(3)
A 		33
C 5.8
(1.1)
A 		5.3
(0.3)
A 		3.2
(-3)
A 		7
(3)
A 		4
avr 4.7
(-3) 		9.1
(-0.4) 		7.3
(-1.5) 		14.9
(3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 183
1 2 3 4 5 6 range
A 2.3
(-3)
A 		2.4
(-3)
A 		18.1
(-2.4)
A 		8.6
(-2.8)
A 		71.5
(-0.6)
A 		173.1
(3)
P 		171
B 2.2
(-3)
A 		5.1
(-2.9)
A 		3.5
(-3)
A 		18.6
(-2.4)
A 		70.8
(-0.5)
P 		165.1
(3)
P 		163
C 2.6
(-3)
A 		8.7
(-2.8)
A 		3.9
(-3)
A 		5.4
(-2.9)
A 		105.8
(0.4)
A 		185.4
(3)
P 		183
avr 2.4
(-3) 		5.4
(-2.9) 		8.5
(-2.8) 		10.9
(-2.7) 		82.7
(-0.2) 		174.5
(3) 		172
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 1.7
(-1)
A 		3.9
(2.4)
A 		4.3
(3)
A 		0.4
(-3)
A 		4
B 1.2
(-2.4)
A 		1
(-2.6)
A 		0.5
(-3)
A 		7.5
(3)
A 		7
C 1.9
(3)
A 		1.5
(0)
A 		1.1
(-3)
A 		1.2
(-2.3)
A 		1
avr 1.6
(-3) 		2.1
(-0.9) 		2
(-1.3) 		3
(3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 62
1 2 3 4 5 6 range
A 0.4
(-3)
A 		0.9
(-2.9)
A 		3.9
(-2.5)
A 		2.2
(-2.7)
A 		21.6
(0.1)
A 		42.1
(3)
P 		42
B 0.8
(-3)
A 		1.7
(-2.9)
A 		0.8
(-3)
A 		4.9
(-2.6)
A 		28.8
(-0.2)
P 		61.6
(3)
P 		61
C 1
(-3)
A 		2.7
(-2.8)
A 		1
(-3)
A 		1.1
(-3)
A 		34.2
(0.3)
A 		62.1
(3)
P 		61
avr 0.7
(-3) 		1.8
(-2.9) 		1.9
(-2.9) 		2.7
(-2.8) 		28.2
(0) 		55.3
(3) 		55
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173230_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27763
Sequence Type Exemplar sequence
Representative Public ID C52705 NCBI
Target Description C52705_rc /REP_DB=TREMBL Accession /GB=C52705 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk271h3 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
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_064334(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064334 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-5) (snf-5) mRNA, complete cds. 11/11 A 
SNAP00000039014 ENSEMBL cdna:SNAP chromosome:CEL140:II:12861983:12865147:-1 11/11 None
GENEFINDER00000039029 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12861983:12865147:-1 11/11 None
Y46G5A.30 ENSEMBL cdna:known chromosome:CEL140:II:12861882:12865718:-1 gene:Y46G5A.30 11/11 A 
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
chrII:12861991-12862308(-) 88.2 88.2
Public Domain and Genome References
Gene Title
Gene Symbol snf-5
Ensembl Y46G5A.30
Entrez Gene 174923 Entrez gene
SwissProt Q9U2E0 EMBL-EBI
WormBase CE29609 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6836 neurotransmitter transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5887 integral to plasma membrane inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5328 neurotransmitter:sodium symporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB60372 Hypothetical protein Y46G5A.30 [Caenorhabditis elegans] ref|NP_496735.1| Sodium:Neurotransmitter symporter Family family member (snf-5) [Caenorhabditis elegans] 0.0
blast CAE59375 Hypothetical protein CBG02728 [Caenorhabditis briggsae] 0.0
blast CAE57482 Hypothetical protein CBG00451 [Caenorhabditis briggsae] 1.0E-176
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.9E-26
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.7E-68
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.9E-26
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.7E-68
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496735.1 10 116-138,164-186,283-305,315-337,397-419,456-478,498-520,530-552,578-600,620-642
Y46G5A.30 10 116-138,164-186,283-305,315-337,397-419,456-478,498-520,530-552,578-600,620-642
SNAP00000039014 10 132-154,180-202,299-321,331-353,413-435,472-494,514-536,546-568,594-616,636-658
GENEFINDER00000039029 10 132-154,180-202,299-321,331-353,413-435,472-494,514-536,546-568,594-616,636-658
Sequence
Target Sequence 
>C. ELEGANS:173230_S_AT
agctatcgcacattgttcatgctccaaaagcagcacgcgtcgtaccgaagaatcgctgca
aantacagcaaagatcagcttgcgcttcaagatcaactacccgacaaggaaccttgggat
gaggaaaacgttgatttgaccgattcggagtactgagagccgtaacgctgcgagtggtga
tgtgccgattgatgatg

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCTATCGCACATTGTTCATGCTCC 211 79 91 Antisense
ATCGCACATTGTTCATGCTCCAAAA 301 37 95 Antisense
CATGCTCCAAAAGCAGCACGCGTCG 439 211 108 Antisense
CAGCACGCGTCGTACCGAAGAATCG 277 203 121 Antisense
ACAGCAAAGATCAGCTTGCGCTTCA 283 109 155 Antisense
TTGCGCTTCAAGATCAACTACCCGA 476 695 170 Antisense
TCAACTACCCGACAAGGAACCTTGG 264 627 183 Antisense
AAACGTTGATTTGACCGATTCGGAG 269 127 216 Antisense
CTGAGAGCCGTAACGCTGCGAGTGG 119 237 243 Antisense
AACGCTGCGAGTGGTGATGTGCCGA 431 145 254 Antisense
AGTGGTGATGTGCCGATTGATGATG 382 59 263 Antisense
Sequence Source Affymetrix Proprietary Database