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[193450_at] Sodium:neurotransmitter symporter

Description ZK1010.9 /REP_DB=WormBase Gene ID /WP=CE23490 /GEN=snf-7 /TR=O18288 /GB=CAB04115.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Sodium:neurotransmitter symporter
Cluster 6grp_total > 55      4grp_total > 26      6grp_cgc > 46      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 69
1 2 3 4 range
A 7.2
(-3)
A 		27.7
(3)
A 		14.6
(-0.8)
A 		19.1
(0.5)
A 		21
B 42.9
(2.3)
A 		11.3
(-3)
A 		47.2
(3)
A 		23.4
(-1)
A 		36
C 4.6
(-3)
A 		63.6
(2.1)
A 		11
(-2.4)
A 		73.9
(3)
A 		69
avr 18.2
(-3) 		34.2
(1.7) 		24.3
(-1.2) 		38.8
(3) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 56
1 2 3 4 5 6 range
A 31.9
(-0.3)
A 		27.3
(-0.7)
A 		54.3
(2.1)
A 		6.2
(-3)
A 		41.8
(0.8)
A 		62.4
(3)
A 		56
B 37.3
(1.2)
A 		44.1
(2.2)
A 		39.2
(1.5)
A 		7.4
(-3)
A 		50.1
(3)
A 		33.5
(0.7)
A 		43
C 28
(-0.5)
A 		26.6
(-0.7)
A 		39.2
(1.3)
A 		50.6
(3)
A 		11.4
(-3)
A 		36.6
(0.9)
A 		39
avr 32.4
(-0.1) 		32.7
(-0) 		44.2
(3) 		21.4
(-3) 		34.4
(0.4) 		44.2
(3) 		23
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17
1 2 3 4 range
A 2.6
(-3)
A 		6
(3)
A 		3.8
(-0.9)
A 		2.8
(-2.6)
A 		3
B 13.7
(3)
A 		2.8
(-3)
A 		10.9
(1.5)
A 		5
(-1.8)
A 		11
C 1.5
(-3)
A 		18.3
(3)
A 		3.8
(-2.2)
A 		12.5
(0.9)
A 		17
avr 5.9
(-3) 		9
(3) 		6.2
(-2.4) 		6.8
(-1.3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19
1 2 3 4 5 6 range
A 5.9
(-1.1)
A 		9.7
(0.6)
A 		11.8
(1.5)
A 		1.6
(-3)
A 		12.6
(1.9)
A 		15.2
(3)
A 		14
B 13
(0.6)
A 		14.7
(1.2)
A 		9.5
(-0.5)
A 		2
(-3)
A 		20.3
(3)
A 		12.5
(0.4)
A 		18
C 10.4
(1.7)
A 		8.1
(0.1)
A 		10
(1.4)
A 		10.2
(1.5)
A 		3.7
(-3)
A 		12.3
(3)
A 		9
avr 9.8
(0.6) 		10.8
(1.3) 		10.4
(1) 		4.6
(-3) 		12.2
(2.2) 		13.3
(3) 		9
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193450_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7351
Sequence Type Exemplar sequence
Representative Public ID ZK1010.9 NCBI
Target Description ZK1010.9 /REP_DB=WormBase Gene ID /WP=CE23490 /GEN=snf-7 /TR=O18288 /GB=CAB04115.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Sodium:neurotransmitter symporter
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_067301(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067301 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-7) (snf-7) mRNA, complete cds. 11/11 None
SNAP00000000289 ENSEMBL cdna:SNAP chromosome:CEL140:III:13009033:13013338:1 11/11 None
GENEFINDER00000000299 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13009066:13010646:1 11/11 None
ZK1010.9 ENSEMBL cdna:known chromosome:CEL140:III:13005000:13010646:1 gene:ZK1010.9 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
chrIII:13005063-13010642(+) 100.0 100.0
Public Domain and Genome References
Gene Title Sodium:neurotransmitter symporter
Gene Symbol snf-7
Ensembl ZK1010.9
Entrez Gene 176723 Entrez gene
SwissProt O18288 EMBL-EBI
WormBase CE23490 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 CAB04975 Hypothetical protein ZK1010.9 [Caenorhabditis elegans] emb|CAB04115.1| Hypothetical protein ZK1010.9 [Caenorhabditis elegans] ref|NP_499702.1| Sodium:Neurotransmitter symporter Family family member (snf-7) [Caenorhabditis elegans] 0.0
blast CAB03142 Hypothetical protein F55H12.1 [Caenorhabditis elegans] ref|NP_492396.1| Sodium:Neurotransmitter symporter Family family member (snf-2) [Caenorhabditis elegans] 1.0E-155
blast CAB04975 Hypothetical protein ZK1010.9 [Caenorhabditis elegans] emb|CAB04115.1| Hypothetical protein ZK1010.9 [Caenorhabditis elegans] ref|NP_499702.1| Sodium:Neurotransmitter symporter Family family member (snf-7) [Caenorhabditis elegans] 1.0E-150
blast CAE69565 Hypothetical protein CBG15777 [Caenorhabditis briggsae] 1.0E-149
blast CAB04975 Hypothetical protein ZK1010.9 [Caenorhabditis elegans] emb|CAB04115.1| Hypothetical protein ZK1010.9 [Caenorhabditis elegans] ref|NP_499702.1| Sodium:Neurotransmitter symporter Family family member (snf-7) [Caenorhabditis elegans] 1.0E-148
blast CAB03142 Hypothetical protein F55H12.1 [Caenorhabditis elegans] ref|NP_492396.1| Sodium:Neurotransmitter symporter Family family member (snf-2) [Caenorhabditis elegans] 1.0E-107
blast CAB03142 Hypothetical protein F55H12.1 [Caenorhabditis elegans] ref|NP_492396.1| Sodium:Neurotransmitter symporter Family family member (snf-2) [Caenorhabditis elegans] 1.0E-106
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.8E-22
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 8.8E-73
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 4.5E-33
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 2.3E-38
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499702.1 12 99-121,136-153,158-180,200-222,229-251,283-305,318-340,383-405,425-447,457-479,506-528,548-570
ZK1010.9 12 99-121,136-153,158-180,200-222,229-251,283-305,318-340,383-405,425-447,457-479,506-528,548-570
SNAP00000000289 6 5-27,69-91,103-121,136-158,185-207,227-249
GENEFINDER00000000299 5 56-78,98-120,130-152,179-201,221-243
Sequence
Target Sequence 
>C. ELEGANS:193450_AT
atgacgtctgatgctggcttctattggttcgacctctacgacgagtatagtgcaggagtc
tcagcgaccattggaactgcaatcatgtgcctcacagtttgctggtgctatgggcttgat
aattttcgagcagatatccgagaaatgtgggaagaaccggaaagccggctcgataagtac
ttgggaccgggcgcctatgtttggactattgtctggagatttgttactccgatctgttgt
ttggttataatgttcgcttggatatgggataaaaagtacccattcaaaggagacagcaag
aagtaccctccagtgtttgatgcttttggctggtttgtagcagcgctcccatttttcgtt
gttccagtgtttgcaggttttgcaatcaaaaggttcaaggatctgaatattccaatccgt
ggagtttttatggttcaaaaacaacaccccgcttacgatcgaatcagtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGACGTCTGATGCTGGCTTCTATT 292 45 1333 Antisense
TCTATTGGTTCGACCTCTACGACGA 626 613 1352 Antisense
TGCAGGAGTCTCAGCGACCATTGGA 217 579 1383 Antisense
GGAACTGCAATCATGTGCCTCACAG 668 529 1405 Antisense
TGCCTCACAGTTTGCTGGTGCTATG 26 585 1420 Antisense
GCCGGCTCGATAAGTACTTGGGACC 385 283 1496 Antisense
GGCGCCTATGTTTGGACTATTGTCT 511 539 1522 Antisense
GTTACTCCGATCTGTTGTTTGGTTA 166 447 1555 Antisense
AAGAAGTACCCTCCAGTGTTTGATG 420 151 1630 Antisense
CATTTTTCGTTGTTCCAGTGTTTGC 665 213 1682 Antisense
CACCCCGCTTACGATCGAATCAGTG 616 199 1777 Antisense
Sequence Source Affymetrix Proprietary Database