[Home] | [Total List]

[188178_s_at]

Description Y46G5A.25 /REP_DB=WormBase Gene ID /WP=CE24297 /GEN=snf-4 /TR=Q9U2E3 /GB=CAB60368.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_total > 85      4grp_total > 09      6grp_cgc > 77      6grp_cgc_sub > 04_05_06      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 94
1 2 3 4 range
A 10.4
(-2.7)
A 		31.9
(-1.3)
A 		6.7
(-3)
A 		95.4
(3)
A 		89
B 40.5
(3)
A 		39.5
(2.2)
A 		33.3
(-3)
A 		34.9
(-1.7)
A 		7
C 1.9
(-3)
A 		4.7
(-2.6)
A 		28.8
(0.7)
A 		45.4
(3)
A 		44
avr 17.6
(-3) 		25.4
(-1.9) 		22.9
(-2.2) 		58.6
(3) 		41

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 43
1 2 3 4 5 6 range
A 6.2
(-3)
A 		16.3
(-1.4)
A 		34.4
(1.4)
A 		34.3
(1.4)
A 		45
(3)
A 		5.9
(-3)
A 		39
B 25.4
(1.9)
A 		17.1
(-3)
A 		22
(-0.1)
A 		24.4
(1.3)
A 		21.2
(-0.6)
A 		27.2
(3)
A 		10
C 16.1
(-1)
A 		15.1
(-1.1)
A 		2.2
(-3)
A 		12.9
(-1.5)
A 		7.6
(-2.2)
A 		43.9
(3)
A 		42
avr 15.9
(-3) 		16.2
(-2.8) 		19.5
(-0.8) 		23.9
(1.9) 		24.6
(2.3) 		25.7
(3) 		10
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 3.8
(-2)
A 		6.9
(-0.5)
A 		1.7
(-3)
A 		14
(3)
A 		12
B 12.9
(3)
A 		9.7
(-0.5)
A 		7.7
(-2.7)
A 		7.4
(-3)
A 		6
C 0.6
(-3)
A 		1.4
(-2.5)
A 		10
(3)
A 		7.7
(1.5)
A 		9
avr 5.8
(-3) 		6
(-2.7) 		6.5
(-1.9) 		9.7
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 1.1
(-3)
A 		5.8
(-0.7)
A 		7.5
(0.1)
A 		8.7
(0.6)
A 		13.6
(3)
A 		1.4
(-2.9)
A 		13
B 8.9
(1.5)
A 		5.7
(-2.5)
A 		5.3
(-3)
A 		6.5
(-1.5)
A 		8.6
(1.1)
A 		10.1
(3)
A 		5
C 6
(-0.7)
A 		4.6
(-1.3)
A 		0.6
(-3)
A 		2.6
(-2.1)
A 		2.5
(-2.2)
A 		14.7
(3)
A 		14
avr 5.3
(-1.9) 		5.4
(-1.7) 		4.5
(-3) 		5.9
(-1) 		8.2
(2.3) 		8.7
(3) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188178_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3750
Sequence Type Exemplar sequence
Representative Public ID Y46G5A.25 NCBI
Target Description Y46G5A.25 /REP_DB=WormBase Gene ID /WP=CE24297 /GEN=snf-4 /TR=Q9U2E3 /GB=CAB60368.1 /SUBMIT=HINXTON /CHR=2 /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_064329(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064329 NCBI Caenorhabditis elegans Sodium:Neurotransmitter symporter Family family member (snf-4) (snf-4) mRNA, complete cds. 11/11 None
SNAP00000039005 ENSEMBL cdna:SNAP chromosome:CEL140:II:12832812:12833639:-1 11/11 None
GENEFINDER00000039016 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12832812:12841972:-1 11/11 None
Y46G5A.25 ENSEMBL cdna:known chromosome:CEL140:II:12832772:12835756:-1 gene:Y46G5A.25 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
chrII:12832808-12835718(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol snf-4
Ensembl Y46G5A.25
Entrez Gene 174919 Entrez gene
SwissProt Q9U2E3 EMBL-EBI
WormBase CE36672 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 CAB60368 Hypothetical protein Y46G5A.25 [Caenorhabditis elegans] ref|NP_496730.2| Sodium:Neurotransmitter symporter Family family member (snf-4) [Caenorhabditis elegans] 0.0
blast CAB60369 Hypothetical protein Y46G5A.26a [Caenorhabditis elegans] ref|NP_001022438.1| Y46G5A.26a [Caenorhabditis elegans] 0.0
blast CAE71492 Hypothetical protein CBG18417 [Caenorhabditis briggsae] 1.0E-149
blast CAB60368 Hypothetical protein Y46G5A.25 [Caenorhabditis elegans] ref|NP_496730.2| Sodium:Neurotransmitter symporter Family family member (snf-4) [Caenorhabditis elegans] 1.0E-130
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-114
blast CAE57482 Hypothetical protein CBG00451 [Caenorhabditis briggsae] 1.0E-95
Protein Domains
Database ID Description E-Value
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 8.5E-17
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.2E-76
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 7.2E-20
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 8.1E-9
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 2.6E-22
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.2E-76
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.8E-59
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496730.2 9 131-153,214-236,263-285,297-319,355-377,397-419,429-451,477-499,514-536
Y46G5A.25 9 131-153,214-236,263-285,297-319,355-377,397-419,429-451,477-499,514-536
SNAP00000039005 4 17-39,49-71,98-120,135-157
GENEFINDER00000039016 15 490-512,525-547,552-571,584-606,673-695,927-949,964-986,1031-1053,1080-1102,1114-1136,1172-1194,1214-1236,1246-1268,1294-1316,1331-1353
Sequence
Target Sequence 
>C. ELEGANS:188178_S_AT
gattggagtctgtttccttcttttcttgtgtggtgtcatcctgacaactgacgctggaat
ctactggttcgcgctctttgacgagtatggctcaggattcggagcgttgatatcggctac
ctctatgtgcattatcatttcctacatctatggaatgcgaaacttccgggcggatatcgc
gtcaatgttgggtcgtggaacgcgaatttcaaacattttcggccacaacagcccgtatta
tggattcaattggatgttcattatgccgatttttggatgtgtattgatctttttgacggc
taaccgaggctatccgttcaaaggagaatcagctgtttatccagttgtttttgatatcgt
cggatggcttttggcagtgtttccgtttatgatggtcccggtaattgcgttgtgcactta
tatggatttcaaaaagcgtggaattccgattcgcgggatgttcttgctccaaaagagcca
tccatcctacccaagaatctcgaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATTGGAGTCTGTTTCCTTCTTTTC 566 435 1251 Antisense
TTTTCTTGTGTGGTGTCATCCTGAC 459 675 1271 Antisense
GTTCGCGCTCTTTGACGAGTATGGC 132 443 1317 Antisense
TATCGGCTACCTCTATGTGCATTAT 324 655 1361 Antisense
GTGCATTATCATTTCCTACATCTAT 631 479 1377 Antisense
ACTTCCGGGCGGATATCGCGTCAAT 188 99 1412 Antisense
CGGCCACAACAGCCCGTATTATGGA 563 239 1470 Antisense
GACGGCTAACCGAGGCTATCCGTTC 462 261 1545 Antisense
ATGGCTTTTGGCAGTGTTTCCGTTT 252 53 1614 Antisense
TGGTCCCGGTAATTGCGTTGTGCAC 580 549 1643 Antisense
TCCATCCTACCCAAGAATCTCGAGA 333 591 1731 Antisense
Sequence Source Affymetrix Proprietary Database