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[193076_at] sodium-dependent transporter

Description M01G5.5 /REP_DB=WormBase Gene ID /WP=CE19539 /GEN=snf-6 /TR=O76689 /GB=AAC26944.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=sodium-dependent transporter
Cluster 6grp_total > 52      4grp_total > 34      6grp_cgc > 92      6grp_cgc_sub > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 80
1 2 3 4 range
A 2.3
(-3)
A 		33.3
(-0.3)
A 		59.2
(2)
P 		70
(3)
A 		68
B 54.3
(1.3)
A 		63.4
(3)
A 		55.1
(1.4)
A 		31.3
(-3)
A 		32
C 55.5
(0.3)
A 		81.9
(3)
A 		22.2
(-3)
A 		64.7
(1.3)
A 		60
avr 37.4
(-3) 		59.5
(3) 		45.5
(-0.8) 		55.3
(1.9) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 15.1
(-3)
A 		58.1
(2.2)
P 		64.6
(3)
A 		42.6
(0.3)
A 		44.4
(0.6)
A 		47.6
(0.9)
A 		50
B 64.8
(2.9)
A 		56.1
(1.7)
A 		65.8
(3)
P 		51
(1.1)
A 		20.1
(-3)
A 		36.4
(-0.9)
A 		46
C 33.5
(-2.8)
A 		32.7
(-3)
A 		57.9
(2.9)
P 		58.3
(3)
A 		46.4
(0.2)
A 		48
(0.6)
P 		26
avr 37.8
(-2.8) 		49
(-0.2) 		62.8
(3) 		50.6
(0.2) 		37
(-3) 		44
(-1.4) 		26
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 0.9
(-3)
A 		7.2
(-0.4)
A 		15.5
(3)
P 		10.2
(0.8)
A 		15
B 17.3
(3)
A 		15.7
(2.1)
A 		12.8
(0.5)
A 		6.7
(-3)
A 		11
C 18.4
(1)
A 		23.6
(3)
A 		7.7
(-3)
A 		10.9
(-1.8)
A 		16
avr 12.2
(-0.2) 		15.5
(3) 		12
(-0.4) 		9.3
(-3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 20
1 2 3 4 5 6 range
A 2.8
(-3)
A 		20.7
(3)
P 		14.1
(0.8)
A 		10.8
(-0.3)
A 		13.4
(0.6)
A 		11.6
(-0.1)
A 		18
B 22.6
(3)
A 		18.7
(1.4)
A 		16
(0.3)
P 		13.5
(-0.8)
A 		8.2
(-3)
A 		13.6
(-0.8)
A 		14
C 12.4
(-0.6)
A 		10
(-3)
A 		14.7
(1.6)
P 		11.7
(-1.3)
A 		15
(1.9)
A 		16.1
(3)
P 		6
avr 12.6
(-2.2) 		16.5
(3) 		14.9
(0.9) 		12
(-3) 		12.2
(-2.7) 		13.8
(-0.6) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193076_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8266
Sequence Type Exemplar sequence
Representative Public ID M01G5.5 NCBI
Target Description M01G5.5 /REP_DB=WormBase Gene ID /WP=CE19539 /GEN=snf-6 /TR=O76689 /GB=AAC26944.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=sodium-dependent 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_065015(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065015 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-6) (snf-6) mRNA, complete cds. 11/11 None
GENEFINDER00000031214 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:1520214:1528199:-1 11/11 None
M01G5.5 ENSEMBL cdna:known chromosome:CEL140:III:1520214:1532758:-1 gene:M01G5.5 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
chrIII:1521512-1531822(-) 100.0 100.0
Public Domain and Genome References
Gene Title sodium-dependent transporter
Gene Symbol snf-6
Ensembl M01G5.5
Entrez Gene 191768 Entrez gene
SwissProt O76689 EMBL-EBI
WormBase CE37392 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.27957.1.S1_AT similar to Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (Amino acid transporter ATB0+) (Solute carrier family 6 member 14) cfa
CHICKEN:GGAAFFX.3708.3.S1_S_AT similar to Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (Amino acid transporter ATB0+) (Colonic system B0+ amino acid transporter CATB0+) (Solute carrier family 6 member 14) gga
HG-U133_PLUS_2:219795_AT solute carrier family 6 (amino acid transporter), member 14 hs
HG-U133A:219795_AT solute carrier family 6 (amino acid transporter), member 14 hs
HG-FOCUS:219795_AT solute carrier family 6 (amino acid transporter), member 14 hs
HG-U133A_2:219795_AT solute carrier family 6 (amino acid transporter), member 14 hs
HUGENEFL:Z96810_AT solute carrier family 6 (amino acid transporter), member 14 hs
U133_X3P:G6005714_3P_AT solute carrier family 6 (amino acid transporter), member 14 hs
HG-U95D:68793_AT solute carrier family 6 (amino acid transporter), member 14 hs
MOUSE430_2:1420504_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MOE430A:1420504_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MOUSE430A_2:1420504_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MOUSE430_2:1420503_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MOE430A:1420503_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MOUSE430A_2:1420503_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MG-U74BV2:110453_R_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MG-U74BV2:110452_I_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
MG-U74CV2:134826_AT solute carrier family 6 (neurotransmitter transporter), member 14 mm
RAE230B:1385107_AT similar to colonic system B0+ amino acid transporter rn
RAT230_2:1385107_AT similar to colonic system B0+ amino acid transporter 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 NP_497416 Sodium:Neurotransmitter symporter Family family member (snf-6) [Caenorhabditis elegans] gb|AAC26944.3| Sodium:neurotransmitter symporter family protein 6 [Caenorhabditis elegans] sp|O76689|SNF6_CAEEL Sodium-dependent acetylcholine transporter 0.0
blast AAV70493 acetylcholine/choline transporter [Caenorhabditis elegans] 0.0
blast CAE66445 Hypothetical protein CBG11720 [Caenorhabditis briggsae] 0.0
blast CAE66445 Hypothetical protein CBG11720 [Caenorhabditis briggsae] 1.0E-147
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 6.0E-43
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 2.4E-42
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.8E-33
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 3.5E-22
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 8.6E-24
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.7E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497416.3 12 72-94,99-118,149-171,255-277,286-308,335-357,369-391,419-441,475-497,501-523,544-566,581-603
M01G5.5 12 72-94,99-118,149-171,255-277,286-308,335-357,369-391,419-441,475-497,501-523,544-566,581-603
GENEFINDER00000031214 8 52-74,84-106,214-236,266-288,317-339,349-371,449-471,486-508
Sequence
Target Sequence 
>C. ELEGANS:193076_AT
tattccattttgtctctcatctgggctcttctggatggagcttctcacccaatttgtgct
cacttggccactggttgtcattgcatttttagagtgtatggctattaattgggtatacgg
agttgataatatgctggataatgctaaatggattgttggctactggccgccgtgttatat
tttttggaagattttattcaaattcatttgtcctatggtatatctggcgattctttgctt
cctttggcttgattggaactcaattcaatacgaatcctatcaattcccgtattggtcaat
tctgacagcatggtgcatcgccagttttccgctaatcctcattccaatcgtcggaatctg
gcaattttgtatcgctaagggtacaattacccaaaaatggtggagggtactgtacccgga
cgacgcttggggacccgcgatggcaatacatcgagccgaaaaatttccgctacaaattcc
agaggcccggaggttgctgctgccgccagaagtcgaaattgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATTCCATTTTGTCTCTCATCTGGG 270 665 1089 Antisense
GGGCTCTTCTGGATGGAGCTTCTCA 531 493 1111 Antisense
GAGCTTCTCACCCAATTTGTGCTCA 291 389 1126 Antisense
TCACTTGGCCACTGGTTGTCATTGC 647 627 1148 Antisense
TACTGGCCGCCGTGTTATATTTTTT 336 647 1249 Antisense
GTATATCTGGCGATTCTTTGCTTCC 414 453 1306 Antisense
TCTTTGCTTCCTTTGGCTTGATTGG 483 615 1320 Antisense
GAATCCTATCAATTCCCGTATTGGT 231 329 1360 Antisense
CTGACAGCATGGTGCATCGCCAGTT 280 225 1390 Antisense
AAATTCCAGAGGCCCGGAGGTTGCT 258 113 1562 Antisense
GCTGCCGCCAGAAGTCGAAATTGCC 584 297 1587 Antisense
Sequence Source Affymetrix Proprietary Database