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[174045_s_at] neurotransmitter transporter

Description C63932 /REP_DB=TREMBL Accession /GB=C63932 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk324b9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 25      4grp_highest_8_8 > 49      4grp_high_8_8 > 41      6grp_highest_nonorm > 90      6grp_total > 15      4grp_total > 54      6grp_highest_sub > 01_02      6grp_cgc > 32      6grp_high1_sub > 01_02      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 189
1 2 3 4 range
A 290
(3)
P 		158.2
(-1.2)
P 		144.4
(-1.6)
P 		101.5
(-3)
P 		189
B 249.8
(3)
P 		176.6
(0)
P 		144.1
(-1.3)
P 		102.8
(-3)
P 		147
C 254
(3)
P 		214.1
(0.7)
P 		178.5
(-1.4)
P 		151.4
(-3)
P 		103
avr 264.6
(3) 		183
(-0.4) 		155.7
(-1.5) 		118.6
(-3) 		146

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 153
1 2 3 4 5 6 range
A 160.7
(-1)
P 		190.4
(3)
P 		176
(1.1)
P 		145.5
(-3)
P 		145.5
(-3)
P 		146.9
(-2.8)
P 		45
B 209.3
(1.6)
P 		239
(3)
P 		163.9
(-0.6)
P 		146.1
(-1.4)
P 		162.7
(-0.6)
P 		112.9
(-3)
P 		126
C 265.8
(3)
P 		245.4
(2.2)
P 		123.4
(-2.8)
P 		119.7
(-3)
P 		151.4
(-1.7)
P 		147.4
(-1.9)
P 		146
avr 211.9
(2.1) 		224.9
(3) 		154.4
(-1.7) 		137.1
(-2.9) 		153.2
(-1.8) 		135.7
(-3) 		89
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 105.6
(3)
P 		34.3
(-1.7)
P 		37.8
(-1.5)
P 		14.9
(-3)
P 		91
B 79.7
(3)
P 		43.6
(-0.7)
P 		33.4
(-1.8)
P 		21.9
(-3)
P 		58
C 84.1
(3)
P 		61.6
(0.7)
P 		62.2
(0.8)
P 		25.5
(-3)
P 		59
avr 89.8
(3) 		46.5
(-0.8) 		44.5
(-0.9) 		20.8
(-3) 		69

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 29.6
(-3)
P 		67.7
(3)
P 		38.3
(-1.6)
P 		36.9
(-1.9)
P 		43.9
(-0.7)
P 		35.8
(-2)
P 		38
B 72.8
(2)
P 		79.5
(3)
P 		39.8
(-2.8)
P 		38.7
(-3)
P 		66.1
(1)
P 		42.1
(-2.5)
P 		41
C 98.5
(3)
P 		74.9
(1.1)
P 		31.4
(-2.4)
P 		24.1
(-3)
P 		49
(-1)
P 		49.3
(-1)
P 		74
avr 67
(2) 		74
(3) 		36.5
(-2.5) 		33.2
(-3) 		53
(-0.1) 		42.4
(-1.6) 		41
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174045_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20295
Sequence Type Exemplar sequence
Representative Public ID C63932 NCBI
Target Description C63932 /REP_DB=TREMBL Accession /GB=C63932 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk324b9 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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 10/11 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:4980394-4981235(+) 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:174045_S_AT
gtggccgtcaaaaatcgaattcattgtgtcagcaatggcatatttgttcgcaatgacaaa
cttccttaacttgccaaaattgatactcgaaaatggaggagtagcatttgcggctgcata
tgcaatagtcgttggggttctatgtatgccaacaatggttatggagatgtcaattggaca
agtgaccggacgagcgcctgttcttgctttttatcatctgtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGCCGTCAAAAATCGAATTCATT 387 491 17 Antisense
AAAATCGAATTCATTGTGTCAGCAA 272 133 27 Antisense
GTCAGCAATGGCATATTTGTTCGCA 653 465 44 Antisense
GTTCGCAATGACAAACTTCCTTAAC 640 441 62 Antisense
TGACAAACTTCCTTAACTTGCCAAA 213 571 70 Antisense
GGAGGAGTAGCATTTGCGGCTGCAT 140 515 111 Antisense
GCGGCTGCATATGCAATAGTCGTTG 564 293 126 Antisense
TAGTCGTTGGGGTTCTATGTATGCC 586 653 142 Antisense
GGGGTTCTATGTATGCCAACAATGG 45 499 150 Antisense
TTGGACAAGTGACCGGACGAGCGCC 365 709 190 Antisense
CTGTTCTTGCTTTTTATCATCTGTT 478 239 214 Antisense
Sequence Source Affymetrix Proprietary Database