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[183865_s_at] Sodium:neurotransmitter symporter family (2 domains) /// ---

Description Y43D4A.1 /REP_DB=WormBase Gene ID /WP=CE21874 /TR=Q9NF30 /GB=CAB60342.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 99      4grp_total > 26      6grp_cgc > 89      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 1.7
(-3)
A
26
(3)
A
3.6
(-2.5)
A
10.8
(-0.8)
A
24
B 7.6
(0.3)
A
12.7
(3)
A
2.6
(-2.4)
A
1.5
(-3)
A
11
C 1.7
(-3)
A
5.7
(-2.4)
A
9.4
(-1.9)
A
44.1
(3)
A
42
avr 3.7
(-3)
14.8
(1.4)
5.2
(-2.4)
18.8
(3)
15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 1.2
(-3)
A
4.1
(-2.4)
A
3
(-2.7)
A
1.1
(-3)
A
8.4
(-1.7)
A
33.8
(3)
A
33
B 21.6
(1.2)
A
14.8
(-0.2)
A
30.7
(3)
A
4.2
(-2.3)
A
17.9
(0.5)
A
0.5
(-3)
A
30
C 3.7
(-2.8)
A
7.3
(-2.2)
A
11.7
(-1.6)
A
2.2
(-3)
A
42.5
(3)
A
10.2
(-1.8)
A
40
avr 8.8
(-1.1)
8.7
(-1.2)
15.1
(0.7)
2.5
(-3)
22.9
(3)
14.8
(0.6)
20
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 0.6
(-3)
A
5.6
(3)
A
0.9
(-2.6)
A
1.6
(-1.8)
A
5
B 2.4
(1.5)
A
3.1
(3)
A
0.6
(-2.4)
A
0.3
(-3)
A
3
C 0.6
(-3)
A
1.6
(-2.1)
A
3.3
(-0.6)
A
7.4
(3)
A
7
avr 1.2
(-3)
3.4
(3)
1.6
(-1.9)
3.1
(2.2)
2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 0.2
(-3)
A
1.5
(-2)
A
0.7
(-2.6)
A
0.3
(-2.9)
A
2.5
(-1.3)
A
8.2
(3)
A
8
B 7.5
(3)
A
4.9
(0.9)
A
7.5
(3)
A
1.1
(-2.3)
A
7.3
(2.8)
A
0.2
(-3)
A
7
C 1.4
(-2.6)
A
2.2
(-2.2)
A
3
(-1.8)
A
0.4
(-3)
A
13.8
(3)
A
3.4
(-1.7)
A
13
avr 3
(-1)
2.9
(-1.1)
3.7
(-0.5)
0.6
(-3)
7.9
(3)
3.9
(-0.3)
7
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 183865_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8578
Sequence Type Exemplar sequence
Representative Public ID Y43D4A.1 NCBI
Target Description Y43D4A.1 /REP_DB=WormBase Gene ID /WP=CE21874 /TR=Q9NF30 /GB=CAB60342.1 /SUBMIT=HINXTON /CHR=4 /FEA=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_070582(11), NM_070676(11)
Transcript Assignments
Representative
Transcript
Description Matching Probes Related Probesets by Grade
NM_070582 NCBI Caenorhabditis elegans Y43D4A.1 (Y43D4A.1) mRNA, complete cds. 11/11 None
NM_070676 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-9) (snf-9) mRNA, complete cds. 11/11 A 
SNAP00000037216 ENSEMBL cdna:SNAP chromosome:CEL140:IV:16743789:16744120:1 11/11 None
GENEFINDER00000037223 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:16743810:16744438:1 11/11 None
SNAP00000040191 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17312379:17315384:1 11/11 None
GENEFINDER00000040210 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17312400:17315384:1 11/11 None
Y43D4A.1 ENSEMBL cdna:known chromosome:CEL140:IV:16743810:16744438:1 gene:Y43D4A.1 11/11 None
C49C3.1 ENSEMBL cdna:known chromosome:CEL140:IV:17312115:17315393:1 gene:C49C3.1 11/11 A 
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
chrIV:16743815-16744444(+) 77.99 100.0
Public Domain and Genome References
Gene Title Sodium:neurotransmitter symporter family (2 domains)

Gene Symbol snf-9
Ensembl Y43D4A.1
C49C3.1
Entrez Gene 178512 Entrez gene
189850 Entrez gene
SwissProt Q9XUG5 EMBL-EBI
Q9NF30 EMBL-EBI
WormBase CE18554 Wormbase
CE21874 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 CAB05153 Hypothetical protein C49C3.1 [Caenorhabditis elegans] ref|NP_503077.1| Sodium:Neurotransmitter symporter Family family member (snf-9) [Caenorhabditis elegans] 0.0
blast CAE57482 Hypothetical protein CBG00451 [Caenorhabditis briggsae] 0.0
blast CAE59375 Hypothetical protein CBG02728 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.8E-17
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.7E-40
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.8E-71
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.8E-17
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 5.7E-40
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.8E-71
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503077.1 12 53-72,82-104,125-147,261-280,285-307,335-357,369-391,429-451,472-494,499-521,551-573,593-615
C49C3.1 12 53-72,82-104,125-147,261-280,285-307,335-357,369-391,429-451,472-494,499-521,551-573,593-615
SNAP00000040191 12 60-79,89-111,132-154,268-287,292-314,342-364,376-398,436-458,479-501,506-528,558-580,600-622
GENEFINDER00000040210 12 53-72,82-104,125-147,261-280,285-307,335-357,369-391,429-451,472-494,499-521,551-573,593-615
Sequence
Target Sequence
>C. ELEGANS:183865_S_AT
acgcaacggagatcaccttccgactcgtcggctgcagaagatcagcgaattgcgacaact
attgtcagggactcgggaagttcgaaagagattgaggagagccaagcggatccgtgcaga
ggagcatggggaaatcagattgagtttctactttccacattaggaatggctgttggactt
ggaaatatctggagatttccgacgagagcttataat


BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position
Strandedness
ACGCAACGGAGATCACCTTCCGACT 197 91 25 Antisense
CCTTCCGACTCGTCGGCTGCAGAAG 61 271 40 Antisense
CGACTCGTCGGCTGCAGAAGATCAG 285 251 45 Antisense
GAAGATCAGCGAATTGCGACAACTA 386 337 61 Antisense
GACAACTATTGTCAGGGACTCGGGA 697 361 78 Antisense
GTCAGGGACTCGGGAAGTTCGAAAG 330 433 88 Antisense
TGAGGAGAGCCAAGCGGATCCGTGC 520 567 117 Antisense
GCGGATCCGTGCAGAGGAGCATGGG 145 293 130 Antisense
TTGAGTTTCTACTTTCCACATTAGG 379 703 164 Antisense
ATATCTGGAGATTTCCGACGAGAGC 289 21 209 Antisense
GAGATTTCCGACGAGAGCTTATAAT 248 395 216 Antisense
Sequence Source Affymetrix Proprietary Database