[Home] | [Total List]

[193834_at] sodium/chloride-dependent GABA transporter

Description T13B5.1 /REP_DB=WormBase Gene ID /WP=CE13605 /GEN=snf-3 /TR=O17372 /GB=AAB71293.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=sodium-chloride-dependent GABA transporter
Cluster 6grp_highest_10_10 > 90      6grp_high1_10_10 > 09      4grp_highest_8_8 > 31      4grp_high_8_8 > 20      6grp_highest_nonorm > 74      6grp_total > 29      4grp_total > 20      6grp_cgc > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 556
1 2 3 4 range
A 687.9
(-0.3)
P 		569.1
(-1.7)
P 		456.9
(-3)
P 		973.6
(3)
P 		517
B 630.1
(-0.9)
P 		650.3
(-0.5)
P 		502.3
(-3)
P 		860.3
(3)
P 		358
C 612.5
(-2)
P 		678.9
(-1.2)
P 		535.9
(-3)
P 		1013
(3)
P 		477
avr 643.5
(-1.1) 		632.8
(-1.2) 		498.4
(-3) 		949
(3) 		451

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 502
1 2 3 4 5 6 range
A 687
(2.6)
P 		671.9
(2.3)
P 		417.1
(-3)
P 		633.4
(1.5)
P 		706.9
(3)
P 		614.4
(1.1)
P 		290
B 666.5
(1.7)
P 		562.1
(-0.4)
P 		507.8
(-1.4)
P 		658
(1.6)
P 		729.1
(3)
P 		430.5
(-3)
P 		299
C 918.6
(3)
P 		558.4
(-2.3)
P 		712.7
(-0)
P 		511.6
(-3)
P 		806
(1.3)
P 		545
(-2.5)
P 		407
avr 757.4
(3) 		597.5
(-1.2) 		545.9
(-2.6) 		601
(-1.1) 		747.3
(2.7) 		530
(-3) 		227
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 250.5
(3)
P 		123.5
(-2.8)
P 		119.4
(-3)
P 		142.5
(-1.9)
P 		131
B 200.9
(3)
P 		160.6
(0.1)
P 		116.4
(-3)
P 		183.3
(1.8)
P 		85
C 202.8
(3)
P 		195.2
(1.6)
P 		186.8
(0)
P 		170.8
(-3)
P 		32
avr 218.1
(3) 		159.8
(-1.5) 		140.9
(-3) 		165.5
(-1.1) 		77

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 250
1 2 3 4 5 6 range
A 126.6
(-1.6)
P 		239
(3)
P 		90.8
(-3)
P 		160.6
(-0.2)
P 		213.3
(2)
P 		149.6
(-0.6)
P 		148
B 231.9
(0.8)
P 		187.1
(-0.8)
P 		123.3
(-3)
P 		174.3
(-1.2)
P 		296.2
(3)
P 		160.5
(-1.7)
P 		173
C 340.5
(3)
P 		170.4
(-1.3)
P 		181.4
(-1)
P 		102.9
(-3)
P 		260.8
(1)
P 		182.4
(-1)
P 		238
avr 233
(1.9) 		198.8
(0.2) 		131.8
(-3) 		145.9
(-2.3) 		256.8
(3) 		164.2
(-1.4) 		125
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193834_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5727
Sequence Type Exemplar sequence
Representative Public ID T13B5.1 NCBI
Target Description T13B5.1 /REP_DB=WormBase Gene ID /WP=CE13605 /GEN=snf-3 /TR=O17372 /GB=AAB71293.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=sodium-chloride-dependent GABA transporter
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_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
SNAP00000003623 ENSEMBL cdna:SNAP chromosome:CEL140:II:1092016:1097557:1 11/11 None
GENEFINDER00000003630 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:1092016:1097557:1 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:1092480-1097556(+) 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
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.5E-52
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
SNAP00000003623 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
GENEFINDER00000003630 13 37-59,66-88,98-120,125-147,250-272,281-303,330-352,365-387,421-443,464-481,496-518,539-563,578-600
Sequence
Target Sequence 
>C. ELEGANS:193834_AT
ggcgttggaagacgctttcccgatcctcagaaaatacaaaaagcagtcacttggaatatt
ctgcctgttcttcttctgcatcggaattcctatggttacacattccggctcccactggct
cacccttttcgatgcttatggtgcatcgggctatgctctcctctttgtcgtattctttga
agtagtcggtctggcttacggttttggagcccataacatcagaaaagcactccatgaaat
gattggtgtaaccctgccaaaaggtatcgagtacgtctggaaattctgtgctccggctac
gagtttggtgctcttcgtgttctgcgttgtgtactatcacccagtcaagtacccggacgg
aaaggatttcccgttctgggctaacgctttcggatggttcttgtcttcgtgctccatggt
tgtcatcccaggatatgctatctattatctcttcttcacaaacaaacatctgacactcaa
agagcgcgttcgcaaggggctcaacttggatggttccttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCGTTGGAAGACGCTTTCCCGATC 359 541 1251 Antisense
TTGGAATATTCTGCCTGTTCTTCTT 315 709 1301 Antisense
TTCCTATGGTTACACATTCCGGCTC 376 693 1337 Antisense
TCTCCTCTTTGTCGTATTCTTTGAA 277 611 1407 Antisense
GAAGTAGTCGGTCTGGCTTACGGTT 146 331 1429 Antisense
ACGTCTGGAAATTCTGTGCTCCGGC 417 95 1523 Antisense
GGCTACGAGTTTGGTGCTCTTCGTG 549 537 1545 Antisense
TGCGTTGTGTACTATCACCCAGTCA 278 579 1573 Antisense
AACGCTTTCGGATGGTTCTTGTCTT 389 145 1633 Antisense
TGCTATCTATTATCTCTTCTTCACA 39 581 1686 Antisense
GGGGCTCAACTTGGATGGTTCCTTC 696 497 1746 Antisense
Sequence Source Affymetrix Proprietary Database