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[193774_s_at] Na(+)/Cl(-)-dependent betain transporter

Description F55H12.1 /REP_DB=WormBase Gene ID /WP=CE11206 /GEN=snf-2 /TR=P90890 /GB=CAB03142.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Na(+)-Cl(-)-dependent betain transporter
Cluster 6grp_total > 78      4grp_total > 24      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 70
1 2 3 4 range
A 4.6
(-3)
A 		17
(-1.8)
A 		65
(3)
A 		59.8
(2.5)
M 		60
B 45.2
(-1.2)
P 		66.1
(3)
M 		36.2
(-3)
A 		49
(-0.4)
A 		30
C 29.6
(-0.7)
A 		3
(-3)
A 		44.9
(0.6)
A 		72.8
(3)
P 		70
avr 26.5
(-3) 		28.7
(-2.6) 		48.7
(0.9) 		60.5
(3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 45.9
(-0.7)
A 		6
(-3)
A 		31.6
(-1.5)
A 		10.8
(-2.7)
A 		71.6
(0.8)
A 		110.6
(3)
P 		105
B 4.4
(-3)
A 		16.8
(-2.2)
A 		33.9
(-1.2)
A 		8.3
(-2.8)
A 		37.4
(-1)
A 		101.3
(3)
P 		97
C 39
(0.5)
A 		27.9
(-0.6)
A 		3.1
(-3)
A 		19.6
(-1.4)
A 		60.5
(2.5)
P 		65.3
(3)
P 		62
avr 29.8
(-1.7) 		16.9
(-2.7) 		22.9
(-2.2) 		12.9
(-3) 		56.5
(0.3) 		92.4
(3) 		80
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 1.7
(-3)
A 		3.7
(-2.2)
A 		17
(3)
A 		8.8
(-0.2)
M 		15
B 14.4
(1.6)
P 		16.3
(3)
M 		8.4
(-3)
A 		10.4
(-1.5)
A 		8
C 9.8
(0.6)
A 		0.8
(-3)
A 		15.6
(3)
A 		12.3
(1.7)
P 		15
avr 8.6
(-1.5) 		6.9
(-3) 		13.7
(3) 		10.5
(0.2) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 37
1 2 3 4 5 6 range
A 8.5
(-1.5)
A 		2.1
(-3)
A 		6.9
(-1.8)
A 		2.7
(-2.9)
A 		21.6
(1.7)
A 		26.9
(3)
P 		25
B 1.5
(-3)
A 		5.6
(-2.3)
A 		8.2
(-1.9)
A 		2.2
(-2.9)
A 		15.2
(-0.7)
A 		37.8
(3)
P 		36
C 14.4
(0.9)
A 		8.5
(-0.8)
A 		0.8
(-3)
A 		3.9
(-2.1)
A 		19.6
(2.3)
P 		21.9
(3)
P 		21
avr 8.1
(-1.8) 		5.4
(-2.4) 		5.3
(-2.4) 		2.9
(-3) 		18.8
(0.7) 		28.9
(3) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193774_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2509
Sequence Type Exemplar sequence
Representative Public ID F55H12.1 NCBI
Target Description F55H12.1 /REP_DB=WormBase Gene ID /WP=CE11206 /GEN=snf-2 /TR=P90890 /GB=CAB03142.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Na(+)-Cl(-)-dependent betain 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_059995(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059995 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-2) (snf-2) mRNA, complete cds. 11/11 A 
SNAP00000036152 ENSEMBL cdna:SNAP chromosome:CEL140:I:8880075:8883358:1 11/11 None
GENEFINDER00000036160 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8880075:8901126:1 11/11 None
F55H12.1 ENSEMBL cdna:known chromosome:CEL140:I:8879963:8883485:1 gene:F55H12.1 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
chrI:8880005-8883416(+) 93.37 100.0
Public Domain and Genome References
Gene Title Na(+)/Cl(-)-dependent betain transporter
Gene Symbol snf-2
Ensembl F55H12.1
Entrez Gene 172701 Entrez gene
SwissProt P90890 EMBL-EBI
WormBase CE11206 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 CAB03142 Hypothetical protein F55H12.1 [Caenorhabditis elegans] ref|NP_492396.1| Sodium:Neurotransmitter symporter Family family member (snf-2) [Caenorhabditis elegans] 0.0
blast CAE69565 Hypothetical protein CBG15777 [Caenorhabditis briggsae] 0.0
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 CAB03143 Hypothetical protein F55H12.3 [Caenorhabditis elegans] ref|NP_492397.1| F55H12.3 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.8E-22
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 8.6E-65
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.5E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.5E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 9.8E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.2E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-5
Pfam IPR003410 EMBL-EBI Hyalin 1.8E-32
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 5.0E-6
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.5E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492396.1 10 142-164,200-222,314-336,346-368,428-450,493-515,535-557,567-589,616-638,658-680
F55H12.1 10 142-164,200-222,314-336,346-368,428-450,493-515,535-557,567-589,616-638,658-680
SNAP00000036152 10 142-164,200-222,314-336,346-368,428-450,493-515,535-557,567-589,616-638,658-680
GENEFINDER00000036160 10 142-164,200-222,314-336,346-368,428-450,493-515,535-557,616-638,658-680,3483-3505
Sequence
Target Sequence 
>C. ELEGANS:193774_S_AT
ggtaaaatctatccgccagtgtttgatgcacttggatggttcattgcagtcgttccgttt
ttggtgatccctggattcgccattgctgctgtgatcaatacccgaagaatgaatattccg
atccgtggagcattcatgttgcagaaacaacacccatcctatgatagaatcagtgagcaa
tggccagaatggaagaaagcaattggtgataaactgccggagcaagagcctggagat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTAAAATCTATCCGCCAGTGTTTG 623 503 1957 Antisense
TCCGCCAGTGTTTGATGCACTTGGA 493 595 1968 Antisense
GCACTTGGATGGTTCATTGCAGTCG 647 315 1984 Antisense
TCATTGCAGTCGTTCCGTTTTTGGT 656 617 1997 Antisense
TTTGGTGATCCCTGGATTCGCCATT 517 651 2016 Antisense
TGCTGCTGTGATCAATACCCGAAGA 193 583 2040 Antisense
ATATTCCGATCCGTGGAGCATTCAT 180 19 2069 Antisense
GTTGCAGAAACAACACCCATCCTAT 56 439 2094 Antisense
GAATCAGTGAGCAATGGCCAGAATG 544 327 2123 Antisense
CAATTGGTGATAAACTGCCGGAGCA 601 179 2156 Antisense
ACTGCCGGAGCAAGAGCCTGGAGAT 353 97 2169 Antisense
Sequence Source Affymetrix Proprietary Database