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[174111_at] sodium/chloride-dependent GABA transporter

Description C51467_rc /REP_DB=TREMBL Accession /GB=C51467 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk200d4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 90      6grp_high1_10_10 > 19      4grp_highest_8_8 > 23      4grp_high_8_8 > 13      6grp_highest_nonorm > 50      6grp_total > 29      4grp_total > 02      6grp_cgc > 02      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 475
1 2 3 4 range
A 364.6
(-0.9)
P 		268.2
(-3)
P 		368.9
(-0.8)
P 		544.5
(3)
P 		276
B 393.7
(-2.6)
P 		414
(-2.3)
P 		372.2
(-3)
P 		738.6
(3)
P 		366
C 420.8
(-2)
P 		436.7
(-1.8)
P 		356.3
(-3)
P 		742.9
(3)
P 		387
avr 393
(-2.5) 		373
(-2.9) 		365.8
(-3) 		675.3
(3) 		310

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 453
1 2 3 4 5 6 range
A 507.7
(0.2)
P 		503.9
(0.1)
P 		568.5
(1.3)
P 		358.5
(-2.6)
P 		655.4
(3)
P 		339.9
(-3)
P 		316
B 649.1
(2.5)
P 		431.7
(-0.4)
P 		236.9
(-3)
P 		435.9
(-0.4)
P 		690.1
(3)
P 		535.7
(1)
P 		453
C 611.3
(3)
P 		591.1
(2.6)
P 		294.3
(-3)
P 		328.5
(-2.4)
P 		549.7
(1.8)
P 		303
(-2.8)
P 		317
avr 589.4
(2) 		508.9
(0.2) 		366.6
(-3) 		374.3
(-2.8) 		631.7
(3) 		392.9
(-2.4) 		265
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 99
1 2 3 4 range
A 132.8
(3)
P 		58.2
(-3)
P 		96.4
(0.1)
P 		79.7
(-1.3)
P 		75
B 125.5
(0.3)
P 		102.3
(-1.6)
P 		86.2
(-3)
P 		157.4
(3)
P 		71
C 139.3
(3)
P 		125.6
(-2.4)
P 		124.2
(-3)
P 		125.3
(-2.6)
P 		15
avr 132.5
(3) 		95.4
(-3) 		102.3
(-1.9) 		120.8
(1.1) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 223
1 2 3 4 5 6 range
A 93.6
(-2.4)
P 		179.2
(2)
P 		123.8
(-0.9)
P 		90.9
(-2.6)
P 		197.8
(3)
P 		82.7
(-3)
P 		115
B 225.9
(1.5)
P 		143.7
(-0.7)
P 		57.5
(-3)
P 		115.4
(-1.4)
P 		280.4
(3)
P 		199.8
(0.8)
P 		223
C 226.6
(3)
P 		180.4
(1.3)
P 		74.9
(-2.7)
P 		66.1
(-3)
P 		177.9
(1.2)
P 		101.4
(-1.7)
P 		161
avr 182
(1.3) 		167.8
(0.7) 		85.4
(-3) 		90.8
(-2.8) 		218.7
(3) 		128
(-1.1) 		133
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174111_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20869
Sequence Type Exemplar sequence
Representative Public ID C51467 NCBI
Target Description C51467_rc /REP_DB=TREMBL Accession /GB=C51467 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk200d4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic 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_061509(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061509 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-3) (snf-3) mRNA, complete cds. 11/11 None
T13B5.1 ENSEMBL cdna:known chromosome:CEL140:II:1092012:1097897:1 gene:T13B5.1 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:1097559-1097863(+) 100.0 100.0
Public Domain and Genome References
Gene Title sodium/chloride-dependent GABA transporter
Gene Symbol snf-3
Ensembl T13B5.1
Entrez Gene 173493 Entrez gene
SwissProt O17372 EMBL-EBI
WormBase CE30176 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 AAB71293 Sodium:neurotransmitter symporter family protein 3 [Caenorhabditis elegans] ref|NP_493910.2| Sodium:Neurotransmitter symporter Family family member (snf-3) [Caenorhabditis elegans] gb|AAZ23105.1| sodium-coupled betaine transporter protein [Caenorhabditis elegans] 0.0
blast CAE62990 Hypothetical protein CBG07219 [Caenorhabditis briggsae] 0.0
blast P48065 Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter) (BGT-1) gb|AAA66574.1| betaine/GABA transporter 1.0E-128
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493910.2 13 37-59,66-88,98-120,125-147,206-228,237-259,286-308,321-343,377-399,420-437,452-474,495-519,534-556
T13B5.1 13 37-59,66-88,98-120,125-147,206-228,237-259,286-308,321-343,377-399,420-437,452-474,495-519,534-556
Sequence
Target Sequence 
>C. ELEGANS:174111_AT
cccccgcaatactgagattcttcaatgatcttttgctgtttatttcttcatattttccct
gaattttgtccattttcagacaagctttatcttctcctcttcccgttcatttttccattc
caatatgagctttttctattacttctccagctggttacccccctgacccccgtatttttc
aacaaaaaaaccgattatcaattgaaattcactttgttaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCCCCGCAATACTGAGATTCTTCAA 407 259 66 Antisense
GATTCTTCAATGATCTTTTGCTGTT 476 431 81 Antisense
ATGATCTTTTGCTGTTTATTTCTTC 311 47 90 Antisense
TTCTTCATATTTTCCCTGAATTTTG 617 689 109 Antisense
TATTTTCCCTGAATTTTGTCCATTT 177 663 116 Antisense
GAATTTTGTCCATTTTCAGACAAGC 398 325 126 Antisense
TCAGACAAGCTTTATCTTCTCCTCT 631 623 141 Antisense
TTTCCATTCCAATATGAGCTTTTTC 666 669 177 Antisense
CAATATGAGCTTTTTCTATTACTTC 188 181 186 Antisense
TTCTATTACTTCTCCAGCTGGTTAC 292 691 199 Antisense
ATCAATTGAAATTCACTTTGTTACA 96 25 262 Antisense
Sequence Source Affymetrix Proprietary Database