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[193536_at] sodium dependent neurotransporter

Description T25B6.7 /REP_DB=WormBase Gene ID /WP=CE14176 /GEN=snf-12 /TR=O45813 /GB=AAC48222.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=sodium dependent neurotransporter
Cluster 6grp_highest_10_10 > 42      6grp_high1_10_10 > 24      4grp_high_8_8 > 33      6grp_highest_nonorm > 70      6grp_total > 02      4grp_total > 38      6grp_highest_sub > 02      6grp_cgc > 42      6grp_high1_sub > 02      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 199
1 2 3 4 range
A 247.5
(3)
P 		174.1
(-3)
P 		184.4
(-2.2)
P 		230.5
(1.6)
M 		73
B 342.9
(3)
P 		223.2
(-0.6)
P 		144.4
(-3)
P 		157.6
(-2.6)
P 		199
C 324.5
(3)
P 		185.6
(-3)
P 		191.4
(-2.7)
P 		207.8
(-2)
M 		139
avr 305
(3) 		194.3
(-2) 		173.4
(-3) 		198.6
(-1.9) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 221
1 2 3 4 5 6 range
A 318.7
(-0)
P 		398.5
(3)
P 		240.9
(-3)
P 		256.2
(-2.4)
P 		267.7
(-2)
P 		252.6
(-2.6)
P 		158
B 316.1
(1.3)
P 		371.4
(3)
P 		268.8
(-0.2)
P 		177.2
(-3)
P 		270.9
(-0.1)
P 		221.5
(-1.6)
P 		194
C 306.7
(2.1)
P 		326.7
(3)
P 		274.6
(0.7)
P 		189.4
(-3)
P 		305.8
(2.1)
P 		196.3
(-2.7)
P 		137
avr 313.8
(1) 		365.5
(3) 		261.4
(-1) 		207.6
(-3) 		281.5
(-0.2) 		223.5
(-2.4) 		158
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 76
1 2 3 4 range
A 90.1
(3)
P 		37.8
(-2.6)
P 		48.2
(-1.5)
P 		33.7
(-3)
M 		56
B 109.3
(3)
P 		55.1
(-1.3)
P 		33.5
(-3)
P 		33.6
(-3)
P 		76
C 107.4
(3)
P 		53.4
(-1.5)
P 		66.7
(-0.4)
P 		35
(-3)
M 		72
avr 102.3
(3) 		48.8
(-1.7) 		49.5
(-1.6) 		34.1
(-3) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 104
1 2 3 4 5 6 range
A 58.7
(-2.6)
P 		141.7
(3)
P 		52.5
(-3)
P 		65
(-2.2)
P 		80.8
(-1.1)
P 		61.5
(-2.4)
P 		89
B 110
(1.9)
P 		123.6
(3)
P 		65.3
(-1.6)
P 		46.9
(-3)
P 		110.1
(1.9)
P 		82.6
(-0.2)
P 		77
C 113.7
(3)
P 		99.7
(1.9)
P 		69.9
(-0.5)
P 		38.1
(-3)
P 		98.9
(1.8)
P 		65.7
(-0.8)
P 		76
avr 94.1
(0.7) 		121.7
(3) 		62.6
(-1.9) 		50
(-3) 		96.6
(0.9) 		69.9
(-1.3) 		72
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193536_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17296
Sequence Type Exemplar sequence
Representative Public ID T25B6.7 NCBI
Target Description T25B6.7 /REP_DB=WormBase Gene ID /WP=CE14176 /GEN=snf-12 /TR=O45813 /GB=AAC48222.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=sodium dependent neurotransporter
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_077126(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077126 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-12) (snf-12) mRNA, complete cds. 11/11 None
SNAP00000006429 ENSEMBL cdna:SNAP chromosome:CEL140:X:9029413:9033850:1 11/11 None
GENEFINDER00000006436 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9029413:9033850:1 11/11 None
T25B6.7 ENSEMBL cdna:known chromosome:CEL140:X:9029413:9033850:1 gene:T25B6.7 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
chrX:9029411-9033849(+) 100.0 100.0
Public Domain and Genome References
Gene Title sodium dependent neurotransporter
Gene Symbol snf-12
Ensembl T25B6.7
Entrez Gene 181143 Entrez gene
SwissProt O45813 EMBL-EBI
WormBase CE29353 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 NP_509527 Sodium:Neurotransmitter symporter Family family member (snf-12) [Caenorhabditis elegans] gb|AAC48222.2| Sodium:neurotransmitter symporter family protein 12 [Caenorhabditis elegans] 0.0
blast CAE57292 Hypothetical protein CBG00201 [Caenorhabditis briggsae] 0.0
blast XP_395746 PREDICTED: similar to ENSANGP00000017838 [Apis mellifera] 2.0E-72
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.0E-84
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 3.5E-60
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 2.4E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509527.1 10 166-185,195-217,238-260,338-360,445-467,504-526,547-569,584-601,642-664,679-698
T25B6.7 10 166-185,195-217,238-260,338-360,445-467,504-526,547-569,584-601,642-664,679-698
SNAP00000006429 10 166-185,195-217,238-260,355-377,454-473,506-528,549-571,586-603,644-666,681-700
GENEFINDER00000006436 10 166-185,195-217,238-260,338-360,445-467,504-526,547-569,584-601,642-664,679-698
Sequence
Target Sequence 
>C. ELEGANS:193536_AT
atttggttcgccacctgcaatattaggagatgacgagaaaataatgacaaccagattttc
ggaatcgatgcctgtaaactataaatgtcgtaatgttgaagtgccaagaataccaaacaa
gctaccacaaaatatggaaaggatggctcgtaaaacacgcaagaagcgaagtagcccatc
ggcatccgatccacccgtcccgacaagtccactccctccaccgcccaaattacaacactg
ccgatctgagcccccaatgatgaacagcaaagagtcacactctcctgaaatcatcacacc
aggtgatgattcaccgtcaatttctaactcatctgacgactcatccgatgactgctttcg
tagagctacagtcatccgacggaaaacctccgacgacgacgcattcactcatttctctac
agcaaccgctgaatcaatttccattacacccttggactttcccagacagcgctctttgag
ttcagtggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTGGTTCGCCACCTGCAATATTA 357 17 2556 Antisense
GAAGCGAAGTAGCCCATCGGCATCC 682 343 2718 Antisense
AATTACAACACTGCCGATCTGAGCC 210 173 2783 Antisense
GATCTGAGCCCCCAATGATGAACAG 129 419 2798 Antisense
GTCACACTCTCCTGAAATCATCACA 340 465 2829 Antisense
GATTCACCGTCAATTTCTAACTCAT 97 431 2863 Antisense
TTCTAACTCATCTGACGACTCATCC 510 685 2877 Antisense
ACTCATCCGATGACTGCTTTCGTAG 76 99 2894 Antisense
GTAGAGCTACAGTCATCCGACGGAA 637 455 2915 Antisense
GCTGAATCAATTTCCATTACACCCT 198 295 2983 Antisense
GACAGCGCTCTTTGAGTTCAGTGGC 80 367 3020 Antisense
Sequence Source Affymetrix Proprietary Database