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[193953_s_at] Sodium:neurotransmitter symporter family (2 domains)

Description C49C3.1 /REP_DB=WormBase Gene ID /WP=CE18554 /GEN=snf-9 /TR=Q9XUG5 /GB=CAB05153.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Sodium:neurotransmitter symporter family (2 domains)
Cluster 6grp_total > 99      4grp_total > 19      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 3.6
(-2.3)
A 		7.3
(3)
A 		3.1
(-3)
A 		5.4
(0.3)
A 		4
B 4.8
(2.8)
A 		2.4
(-1.8)
A 		4.9
(3)
A 		1.8
(-3)
A 		3
C 4.8
(-2.3)
A 		8.2
(-1.3)
A 		2.4
(-3)
A 		22.8
(3)
A 		20
avr 4.4
(-2.2) 		6
(-0.7) 		3.5
(-3) 		10
(3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 158
1 2 3 4 5 6 range
A 7.6
(-2.8)
A 		3.7
(-3)
A 		3
(-3)
A 		4.9
(-2.9)
A 		130.3
(1.9)
P 		159.9
(3)
P 		157
B 4.1
(-2.9)
A 		2.1
(-3)
A 		4.8
(-2.9)
A 		4.5
(-2.9)
A 		157.2
(3)
P 		134.8
(2.1)
P 		155
C 3.6
(-3)
A 		6.5
(-2.9)
A 		4.6
(-3)
A 		10.2
(-2.7)
A 		133.2
(3)
P 		132.9
(3)
P 		130
avr 5.1
(-3) 		4.1
(-3) 		4.1
(-3) 		6.5
(-2.9) 		140.2
(2.9) 		142.5
(3) 		138
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4
1 2 3 4 range
A 1.3
(0.8)
A 		1.6
(3)
A 		0.8
(-3)
A 		0.8
(-3)
A 		1
B 1.5
(3)
A 		0.6
(-1.9)
A 		1.1
(0.8)
A 		0.4
(-3)
A 		1
C 1.6
(-1.6)
A 		2.4
(0)
A 		0.9
(-3)
A 		3.9
(3)
A 		3
avr 1.5
(1.5) 		1.5
(1.5) 		0.9
(-3) 		1.7
(3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 63
1 2 3 4 5 6 range
A 1.4
(-2.9)
A 		1.3
(-2.9)
A 		0.6
(-3)
A 		1.3
(-2.9)
A 		39.3
(3)
P 		38.9
(2.9)
P 		39
B 1.4
(-2.9)
A 		0.7
(-3)
A 		1.2
(-3)
A 		1.2
(-3)
A 		63.9
(3)
P 		50.3
(1.7)
P 		63
C 1.3
(-3)
A 		2
(-2.9)
A 		1.2
(-3)
A 		2
(-2.9)
A 		43.1
(2.8)
P 		44.5
(3)
P 		43
avr 1.4
(-2.9) 		1.3
(-3) 		1
(-3) 		1.5
(-2.9) 		48.8
(3) 		44.6
(2.5) 		48
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193953_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9906
Sequence Type Exemplar sequence
Representative Public ID C49C3.1 NCBI
Target Description C49C3.1 /REP_DB=WormBase Gene ID /WP=CE18554 /GEN=snf-9 /TR=Q9XUG5 /GB=CAB05153.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Sodium:neurotransmitter symporter family (2 domains)
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_070676(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070676 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-9) (snf-9) mRNA, complete cds. 11/11 A 
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
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:17312405-17315390(+) 100.0 100.0
Public Domain and Genome References
Gene Title Sodium:neurotransmitter symporter family (2 domains)
Gene Symbol snf-9
Ensembl C49C3.1
Entrez Gene 178512 Entrez gene
SwissProt Q9XUG5 EMBL-EBI
WormBase CE18554 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 5.7E-40
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.8E-71
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:193953_S_AT
gtacgctgctggagtatcatcttgctgtgcagttaccgctgaagttctcattgttgcata
cgtctatggtcgtcgaaatcaacttgctgatatgaaggagatgtttggagagtcaaagaa
caaatgcactagctggattgggcaacactccccctactttgggttcaactggatgtttgt
cacaccggttcttggatcgatcctaatcgttttggctagcattcgtcagtatccctacca
gactgatgaaaataaaccaaatatgtacccattggcttttgatattgtcggttgggcggt
ttgtcttctaccaatggcattggttcctatatttgcattctgtgcatttgtggagttcaa
aaggaagggtcatgatctgagagctctgtttatgaaacaacgacaactcaaatcgtttgg
aagaatttatcaaacgatggcatcgaaggatcgcgctaaacagaaaattctacctgatcg
ggagccatgggatgacgctccaactggtcatcagtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTACGCTGCTGGAGTATCATCTTGC 253 459 1506 Antisense
TCATCTTGCTGTGCAGTTACCGCTG 452 621 1522 Antisense
GAAGTTCTCATTGTTGCATACGTCT 443 337 1546 Antisense
ATGGTCGTCGAAATCAACTTGCTGA 407 51 1571 Antisense
CTAGCTGGATTGGGCAACACTCCCC 361 225 1634 Antisense
AACTGGATGTTTGTCACACCGGTTC 530 139 1672 Antisense
CTAATCGTTTTGGCTAGCATTCGTC 292 225 1708 Antisense
TTCGTCAGTATCCCTACCAGACTGA 15 697 1727 Antisense
TGGTTCCTATATTTGCATTCTGTGC 354 551 1826 Antisense
AATTCTACCTGATCGGGAGCCATGG 349 173 1971 Antisense
ATGACGCTCCAACTGGTCATCAGTT 607 45 1997 Antisense
Sequence Source Affymetrix Proprietary Database