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[174710_s_at] neurotransmitter transporter

Description CEK066B4R_rc /REP_DB=TREMBL Accession /GB=D65688 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk66b4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 06      4grp_highest_8_8 > 49      4grp_high_8_8 > 42      6grp_highest_nonorm > 31      6grp_total > 07      4grp_total > 54      6grp_highest_sub > De      6grp_cgc > 11      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 746
1 2 3 4 range
A 1226.8
(3)
P 		991.2
(0.6)
P 		792.3
(-1.4)
P 		638.4
(-3)
P 		588
B 1191.2
(3)
P 		952.8
(0.5)
P 		887.9
(-0.2)
P 		624.8
(-3)
P 		566
C 1371.1
(3)
P 		972.4
(-0.6)
P 		849.5
(-1.7)
P 		706.8
(-3)
P 		664
avr 1263
(3) 		972.1
(0.1) 		843.2
(-1.2) 		656.7
(-3) 		606

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 630
1 2 3 4 5 6 range
A 1313.2
(3)
P 		1015.8
(0.1)
P 		810.5
(-1.9)
P 		699.5
(-3)
P 		870
(-1.3)
P 		784.5
(-2.2)
P 		614
B 1120.6
(3)
P 		918.9
(0)
P 		1055.8
(2)
P 		934.7
(0.2)
P 		716.7
(-3)
P 		733.4
(-2.8)
P 		404
C 1185.7
(3)
P 		786.8
(-1.8)
P 		872.6
(-0.7)
P 		811
(-1.5)
P 		821
(-1.4)
P 		682.8
(-3)
P 		503
avr 1206.5
(3) 		907.2
(-0.8) 		913
(-0.7) 		815.1
(-2) 		802.6
(-2.1) 		733.6
(-3) 		473
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 361
1 2 3 4 range
A 446.7
(3)
P 		215.2
(-0.9)
P 		207.1
(-1.1)
P 		93.4
(-3)
P 		353
B 379.9
(3)
P 		235.3
(-0.5)
P 		205.7
(-1.2)
P 		133.1
(-3)
P 		247
C 453.9
(3)
P 		279.6
(-0.1)
P 		296.1
(0.2)
P 		119.2
(-3)
P 		335
avr 426.8
(3) 		243.4
(-0.5) 		236.3
(-0.7) 		115.2
(-3) 		312

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 276
1 2 3 4 5 6 range
A 242.1
(-0.9)
P 		361.3
(3)
P 		176.5
(-3)
P 		177.4
(-3)
P 		262.5
(-0.2)
P 		191
(-2.5)
P 		185
B 389.9
(3)
P 		305.9
(-0.5)
P 		256.4
(-2.6)
P 		247.6
(-3)
P 		291.2
(-1.2)
P 		273.5
(-1.9)
P 		142
C 439.5
(3)
P 		240.1
(-1.3)
P 		222.1
(-1.7)
P 		163.1
(-3)
P 		265.7
(-0.8)
P 		228.6
(-1.6)
P 		276
avr 357.2
(3) 		302.4
(1) 		218.3
(-2.2) 		196
(-3) 		273.1
(-0.1) 		231
(-1.7) 		161
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174710_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20319
Sequence Type Exemplar sequence
Representative Public ID CEK066B4R NCBI
Target Description CEK066B4R_rc /REP_DB=TREMBL Accession /GB=D65688 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk66b4 : 3prime 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 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:4983561-4983936(+) 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
blast XP_394655 PREDICTED: similar to CG5549-PA [Apis mellifera] 6.0E-41
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
Sequence
Target Sequence 
>C. ELEGANS:174710_S_AT
atttccaatcgatctcgctgcgaacactgacagtcaattattttttcaatctaccacctc
ttctattttatacaacgaactactccactagctgctagaaatttgaatcttgtgcatatc
cactcggtttgccgccttttctctttcctgttaatccgaacttgtttcatttcttttctg
tttcgtttgtatcttcgtatccttctgctctttcctgccttatgtccctgtctgtcatca
taatcttgaatatgtttgcttgaatcaaactatttaccatcattcttcctaattatgtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTCCAATCGATCTCGCTGCGAAC 288 17 23 Antisense
ATCTCGCTGCGAACACTGACAGTCA 38 33 34 Antisense
ATTATTTTTTCAATCTACCACCTCT 588 13 59 Antisense
TACAACGAACTACTCCACTAGCTGC 609 639 93 Antisense
GAACTACTCCACTAGCTGCTAGAAA 282 349 99 Antisense
GAATCTTGTGCATATCCACTCGGTT 447 327 127 Antisense
TTTCTTTTCTGTTTCGTTTGTATCT 93 673 192 Antisense
TTCGTTTGTATCTTCGTATCCTTCT 41 697 204 Antisense
TATGTCCCTGTCTGTCATCATAATC 610 655 243 Antisense
ATCAAACTATTTACCATCATTCTTC 552 27 286 Antisense
TACCATCATTCTTCCTAATTATGTG 32 649 297 Antisense
Sequence Source Affymetrix Proprietary Database