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[193085_at] neurotransmitter transporter

Description W03G9.1 /REP_DB=WormBase Gene ID /WP=CE28503 /GEN=snf-1 /TR=O44752 /GB=AAB96735.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=neurotransmitter transporter
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 49      4grp_high_8_8 > 42      6grp_highest_nonorm > 75      6grp_total > 05      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 698
1 2 3 4 range
A 1082
(3)
P 		819.2
(0.3)
P 		701.7
(-0.9)
P 		495.5
(-3)
P 		587
B 1175.5
(3)
P 		776.4
(-0.4)
P 		746
(-0.7)
P 		477.7
(-3)
P 		698
C 1069.5
(3)
P 		904
(1.1)
P 		772.6
(-0.3)
P 		533.7
(-3)
P 		536
avr 1109
(3) 		833.2
(0.3) 		740.1
(-0.6) 		502.3
(-3) 		607

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 617
1 2 3 4 5 6 range
A 861.4
(2.1)
P 		896.4
(3)
P 		670.5
(-3)
P 		796.3
(0.3)
P 		814.8
(0.8)
P 		820.6
(1)
P 		226
B 929.2
(2)
P 		995.3
(3)
P 		746.7
(-0.8)
P 		707.6
(-1.4)
P 		729.4
(-1.1)
P 		601.4
(-3)
P 		394
C 1218.8
(3)
P 		796.5
(-1.8)
P 		989.6
(0.4)
P 		696.3
(-3)
P 		800.3
(-1.8)
P 		707.5
(-2.9)
P 		523
avr 1003.1
(3) 		896.1
(0.8) 		802.3
(-1.1) 		733.4
(-2.5) 		781.5
(-1.5) 		709.8
(-3) 		293
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 321
1 2 3 4 range
A 393.9
(3)
P 		177.8
(-1)
P 		183.4
(-0.9)
P 		72.5
(-3)
P 		321
B 374.9
(3)
P 		191.7
(-1)
P 		172.9
(-1.4)
P 		101.8
(-3)
P 		273
C 354
(3)
P 		259.9
(0.9)
P 		269.3
(1.1)
P 		90
(-3)
P 		264
avr 374.3
(3) 		209.8
(-0.4) 		208.5
(-0.5) 		88.1
(-3) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 312
1 2 3 4 5 6 range
A 158.8
(-2.6)
P 		318.8
(3)
P 		146
(-3)
P 		202
(-1.1)
P 		245.9
(0.5)
P 		199.8
(-1.1)
P 		173
B 323.3
(2.7)
P 		331.3
(3)
P 		181.3
(-3)
P 		187.4
(-2.8)
P 		296.3
(1.6)
P 		224.3
(-1.3)
P 		150
C 451.8
(3)
P 		243
(-1)
P 		251.9
(-0.8)
P 		140
(-3)
P 		259
(-0.7)
P 		236.8
(-1.1)
P 		312
avr 311.3
(3) 		297.7
(2.4) 		193.1
(-2.3) 		176.5
(-3) 		267.1
(1) 		220.3
(-1.1) 		135
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193085_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2015
Sequence Type Exemplar sequence
Representative Public ID W03G9.1 NCBI
Target Description W03G9.1 /REP_DB=WormBase Gene ID /WP=CE28503 /GEN=snf-1 /TR=O44752 /GB=AAB96735.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=neurotransmitter 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_059090(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059090 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-1) (snf-1) mRNA, complete cds. 11/11 A 
SNAP00000033395 ENSEMBL cdna:SNAP chromosome:CEL140:I:4980331:4983521:1 11/11 None
GENEFINDER00000033403 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4980331:4983521:1 11/11 None
W03G9.1.2 ENSEMBL cdna:known chromosome:CEL140:I:4980307:4983941:1 gene:W03G9.1 11/11 None
W03G9.1.1 ENSEMBL cdna:known chromosome:CEL140:I:4980308:4983955:1 gene:W03G9.1 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
chrI:4980330-4983521(+) 100.0 100.0
Public Domain and Genome References
Gene Title neurotransmitter transporter
Gene Symbol snf-1
Ensembl W03G9.1
Entrez Gene 172119 Entrez gene
SwissProt O44752 EMBL-EBI
WormBase CE30701 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_491491 Sodium:Neurotransmitter symporter Family family member (snf-1) [Caenorhabditis elegans] gb|AAB96735.3| Sodium:neurotransmitter symporter family protein 1 [Caenorhabditis elegans] 0.0
blast CAE65702 Hypothetical protein CBG10777 [Caenorhabditis briggsae] 0.0
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491491.2 13 30-47,54-76,86-105,112-134,208-230,235-257,277-299,320-342,372-394,415-437,452-470,491-513,533-555
W03G9.1.2 13 30-47,54-76,86-105,112-134,208-230,235-257,277-299,320-342,372-394,415-437,452-470,491-513,533-555
W03G9.1.1 13 30-47,54-76,86-105,112-134,208-230,235-257,277-299,320-342,372-394,415-437,452-470,491-513,533-555
SNAP00000033395 13 30-47,54-76,86-105,118-140,217-239,244-266,286-308,329-351,381-403,424-446,461-479,500-522,542-564
GENEFINDER00000033403 14 30-52,75-97,104-123,133-152,165-187,264-286,291-313,333-355,376-398,428-450,471-493,508-526,547-569,589-611
Sequence
Target Sequence 
>C. ELEGANS:193085_AT
tccaagtgctgtcgtcgattcttcctcgctttattcgtttgcctattctgcttcggattg
actgtatactttgcaacaaacgcgggtcgtcatgcttatgaacttgctactagaagcatc
aaatactgtacaatatatttcatactgacagctgaactttttgcgacagcttggttctat
tgtgctcacaaactcggaaaagatcttcacaacatgatgagatcaagatgctgctcctgt
ttcggacacttcttcctctacttcacctacttactgccaatattaccagcgggtgttgca
ttcctcaatgcactggactacaaattctcctcattctctgctccaattcacgagtggaaa
tattcggaatatgttggaatcgccatcgcaatggttccactgataccaattccgttgtat
ttcttcatgacgattctgtgcgcatgctgttgcaaagggaaggatcatgccaagacttgc
aagagaattcgaacagtattcgctgcacgacttcagaaccaccaccatcgagacgaaaaa
gcgcagccgattccccgatacacgtcgaatgctccaggctatttattacttccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAAGTGCTGTCGTCGATTCTTCC 667 587 1333 Antisense
GCTTTATTCGTTTGCCTATTCTGCT 172 305 1360 Antisense
GCAACAAACGCGGGTCGTCATGCTT 286 319 1405 Antisense
GACAGCTTGGTTCTATTGTGCTCAC 260 369 1497 Antisense
TACTTCACCTACTTACTGCCAATAT 557 645 1591 Antisense
GGACTACAAATTCTCCTCATTCTCT 136 525 1647 Antisense
CATTCTCTGCTCCAATTCACGAGTG 552 215 1664 Antisense
GGAATCGCCATCGCAATGGTTCCAC 302 531 1708 Antisense
GATTCTGTGCGCATGCTGTTGCAAA 73 433 1764 Antisense
GTATTCGCTGCACGACTTCAGAACC 267 453 1828 Antisense
GCTCCAGGCTATTTATTACTTCCAC 48 299 1903 Antisense
Sequence Source Affymetrix Proprietary Database