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[193728_at] Na(+)/Cl(-)-dependent GABA transporter

Description T03F7.1 /REP_DB=WormBase Gene ID /WP=CE06344 /GEN=snf-11 /TR=Q22116 /GB=CAA98519.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Na(+)-Cl(-)-dependent GABA transporter
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 15      4grp_highest_8_8 > 41      4grp_high_8_8 > 50      6grp_highest_nonorm > 40      6grp_total > 15      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 23      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 606
1 2 3 4 range
A 815.1
(3)
P 		496.1
(-0.4)
P 		469.5
(-0.7)
P 		249.9
(-3)
P 		565
B 535.5
(3)
P 		472.9
(1.6)
P 		449
(1.1)
P 		260.2
(-3)
P 		275
C 715.4
(3)
P 		629.1
(2)
P 		580.9
(1.4)
P 		209.3
(-3)
P 		506
avr 688.7
(3) 		532.7
(0.9) 		499.8
(0.5) 		239.8
(-3) 		449

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 923
1 2 3 4 5 6 range
A 1135.3
(3)
P 		859.8
(1.1)
P 		512.3
(-1.4)
P 		412.5
(-2.1)
P 		406
(-2.1)
P 		281.8
(-3)
P 		854
B 1063.3
(3)
P 		900.6
(1.7)
P 		492.3
(-1.4)
P 		465.4
(-1.6)
P 		346.1
(-2.5)
P 		283.7
(-3)
P 		780
C 1007.5
(3)
P 		946
(2.5)
P 		598.1
(-0.1)
P 		455.6
(-1.2)
P 		297.7
(-2.4)
P 		212.8
(-3)
P 		795
avr 1068.7
(3) 		902.1
(1.8) 		534.2
(-1) 		444.5
(-1.6) 		349.9
(-2.3) 		259.4
(-3) 		809
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 262
1 2 3 4 range
A 296.8
(3)
P 		107.7
(-1.4)
P 		122.7
(-1)
P 		36.6
(-3)
P 		260
B 170.8
(3)
P 		116.8
(0.2)
P 		104
(-0.5)
P 		55.4
(-3)
P 		115
C 236.8
(3)
P 		180.9
(1.3)
P 		202.5
(2)
P 		35.3
(-3)
P 		202
avr 234.8
(3) 		135.1
(-0.1) 		143.1
(0.1) 		42.4
(-3) 		192

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 305
1 2 3 4 5 6 range
A 209.3
(0.6)
P 		305.8
(3)
P 		111.6
(-1.9)
P 		104.6
(-2.1)
P 		122.5
(-1.6)
P 		68.6
(-3)
P 		237
B 370
(3)
P 		299.8
(1.4)
P 		119.5
(-2.7)
P 		123.3
(-2.6)
P 		140.6
(-2.2)
P 		105.8
(-3)
P 		264
C 373.4
(3)
P 		288.7
(1.3)
P 		152.2
(-1.4)
P 		91.6
(-2.6)
P 		96.3
(-2.5)
P 		71.2
(-3)
P 		302
avr 317.6
(3) 		298.1
(2.5) 		127.8
(-1.8) 		106.5
(-2.4) 		119.8
(-2) 		81.9
(-3) 		236
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193728_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13495
Sequence Type Exemplar sequence
Representative Public ID T03F7.1 NCBI
Target Description T03F7.1 /REP_DB=WormBase Gene ID /WP=CE06344 /GEN=snf-11 /TR=Q22116 /GB=CAA98519.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Na(+)-Cl(-)-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_073472(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073472 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-11) (snf-11) mRNA, complete cds. 11/11 None
SNAP00000015851 ENSEMBL cdna:SNAP chromosome:CEL140:V:11307942:11311028:-1 11/11 None
GENEFINDER00000015855 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11307942:11311028:-1 11/11 None
T03F7.1.2 ENSEMBL cdna:known chromosome:CEL140:V:11307610:11311650:-1 gene:T03F7.1 11/11 None
T03F7.1.1 ENSEMBL cdna:known chromosome:CEL140:V:11307657:11311650:-1 gene:T03F7.1 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
chrV:11307941-11311650(-) 100.0 100.0
Public Domain and Genome References
Gene Title Na(+)/Cl(-)-dependent GABA transporter
Gene Symbol snf-11
Ensembl T03F7.1
Entrez Gene 191770 Entrez gene
SwissProt Q22116 EMBL-EBI
WormBase CE06344 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.8481.1.S1_AT similar to solute carrier family 6 (neurotransmitter transporter, GABA), member 1 cfa
CANINE_2:CFAAFFX.8482.1.S1_S_AT similar to solute carrier family 6 (neurotransmitter transporter, GABA), member 1 cfa
DROSOPHILA_2:1633033_S_AT dm
DROSGENOME1:150984_AT dm
CHICKEN:GGA.10380.1.S1_S_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 gga
CHICKEN:GGAAFFX.26357.1.S1_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 gga
CHICKEN:GGAAFFX.26357.2.S1_S_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 gga
HU35KSUBB:RC_R52822_I_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HUGENEFL:X54673_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
U133_X3P:HS.22003.0.S2_3P_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U133A_2:205152_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-FOCUS:205152_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U133_PLUS_2:205152_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U133A:205152_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U95AV2:39599_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U95B:42987_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HG-U95D:84930_AT Solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
HU35KSUBC:RC_N63505_AT Solute carrier family 6 (neurotransmitter transporter, GABA), member 1 hs
MOUSE430_2:1457183_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MOE430B:1457183_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MU11KSUBA:M92378_S_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MG-U74CV2:138510_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MG-U74AV2:161059_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MG-U74CV2:170648_F_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MOE430A:1452142_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MOUSE430A_2:1452142_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
MOUSE430_2:1452142_AT solute carrier family 6 (neurotransmitter transporter, GABA), member 1 mm
RN-U34:RC_AI228669_AT GABA transporter protein rn
RG-U34A:RC_AI228669_AT GABA transporter protein rn
RAE230A:1368170_AT GABA transporter protein rn
RAT230_2:1368170_AT GABA transporter protein rn
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 CAA98519 Hypothetical protein T03F7.1 [Caenorhabditis elegans] ref|NP_505873.1| Sodium:Neurotransmitter symporter Family family member (snf-11) [Caenorhabditis elegans] 0.0
blast AAT02634 GABA transporter protein [Caenorhabditis elegans] 0.0
blast CAE75218 Hypothetical protein CBG23167 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-72
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-126
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.1E-26
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 6.4E-37
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-126
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-72
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505873.1 14 7-24,39-61,66-88,92-114,121-140,239-261,270-292,319-341,354-376,403-425,456-478,488-510,531-550,570-592
T03F7.1.2 14 7-24,39-61,66-88,92-114,121-140,239-261,270-292,319-341,354-376,403-425,456-478,488-510,531-550,570-592
T03F7.1.1 14 7-24,39-61,66-88,92-114,121-140,239-261,270-292,319-341,354-376,403-425,456-478,488-510,531-550,570-592
SNAP00000015851 12 13-35,102-124,145-167,271-293,302-324,351-373,386-408,435-457,488-510,520-542,563-582,602-624
GENEFINDER00000015855 12 12-34,44-66,87-109,217-239,248-270,297-319,332-354,381-403,434-456,466-488,509-528,548-570
Sequence
Target Sequence 
>C. ELEGANS:193728_AT
tcaccgctatcattgacgagttcccacaaattcgacgaaaaaaatacggacgagaaatat
ttgtgggagtgatctgcgttatatcatatcttattgggttgactacagtaaccgaaggtg
gtttttatgtattccaactgtttgatttctatgcagcatctggatgggcacttttatggc
ttcttttctttgaatgtattgcaatttcatggagtttaggaatcgatcgttggtatgaac
atatgaagagtatgattggttattatccaagtgcttggtggaagttttgctgggtttttg
caacaccgtctgtatgtttcggagttcttttattcggactaattaaatatcaaccacttc
gtattgatgcctacaattatgactacccggtatggggacatatcttcggatggttcttat
cgctttcttcaatgctttgtattcccggatatgctatttggatatggttcaaaactccag
gaactgttcaagagaaaatcaaattgctgtgccgacccgacattgaaatcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCACCGCTATCATTGACGAGTTCCC 33 627 1319 Antisense
GACGAGTTCCCACAAATTCGACGAA 560 375 1333 Antisense
GGGCACTTTTATGGCTTCTTTTCTT 415 493 1484 Antisense
TGGGTTTTTGCAACACCGTCTGTAT 371 553 1609 Antisense
CGTCTGTATGTTTCGGAGTTCTTTT 389 245 1625 Antisense
CAACCACTTCGTATTGATGCCTACA 157 187 1669 Antisense
GATGCCTACAATTATGACTACCCGG 338 415 1684 Antisense
GGGGACATATCTTCGGATGGTTCTT 695 497 1712 Antisense
TGGTTCTTATCGCTTTCTTCAATGC 467 551 1729 Antisense
TCTTCAATGCTTTGTATTCCCGGAT 215 617 1744 Antisense
TGTGCCGACCCGACATTGAAATCAA 16 555 1826 Antisense
Sequence Source Affymetrix Proprietary Database