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[189901_at] amino acid permease

Description F28F9.4 /REP_DB=WormBase Gene ID /WP=CE17028 /TR=Q94197 /GB=AAB09125.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=amino acid permease
Cluster 6grp_total > 99      4grp_total > 05      6grp_cgc > 89      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 259
1 2 3 4 range
A 116.8
(-0.5)
A 		65
(-2.2)
A 		39.6
(-3)
A 		226.8
(3)
M 		187
B 118.3
(1.9)
A 		45
(-3)
A 		101.6
(0.8)
A 		135.3
(3)
P 		90
C 138.7
(0)
A 		9.2
(-3)
A 		56.4
(-1.9)
A 		268
(3)
A 		259
avr 124.6
(-0) 		39.7
(-3) 		65.9
(-2.1) 		210
(3) 		170

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 121
1 2 3 4 5 6 range
A 52.9
(0.7)
A 		29.4
(-1.5)
A 		28.3
(-1.6)
A 		14
(-3)
A 		76.9
(3)
A 		50.3
(0.5)
A 		63
B 93.2
(1.1)
A 		16.5
(-3)
A 		36.5
(-1.9)
A 		76.5
(0.2)
A 		129
(3)
A 		92.7
(1.1)
A 		113
C 61.6
(0.9)
A 		62.6
(1)
A 		8.1
(-3)
A 		71.7
(1.6)
A 		90.6
(3)
A 		86.3
(2.7)
A 		83
avr 69.2
(0.6) 		36.2
(-2) 		24.3
(-3) 		54.1
(-0.6) 		98.8
(3) 		76.4
(1.2) 		75
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 42.5
(3)
A 		14.1
(-2.3)
A 		10.4
(-3)
A 		33.2
(1.3)
M 		32
B 37.7
(3)
A 		11.1
(-3)
A 		23.5
(-0.2)
A 		28.8
(1)
P 		27
C 45.9
(3)
A 		2.6
(-3)
A 		19.7
(-0.6)
A 		45.2
(2.9)
A 		43
avr 42
(3) 		9.3
(-3) 		17.9
(-1.4) 		35.7
(1.8) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 50
1 2 3 4 5 6 range
A 9.7
(-1.1)
A 		10.4
(-0.9)
A 		6.2
(-2.2)
A 		3.5
(-3)
A 		23.2
(3)
A 		12.2
(-0.4)
A 		20
B 32.4
(0.4)
A 		5.5
(-3)
A 		8.9
(-2.6)
A 		20.3
(-1.1)
A 		52.4
(3)
A 		34.6
(0.7)
A 		47
C 22.8
(1.6)
A 		19.1
(0.8)
A 		2
(-3)
A 		14.4
(-0.3)
A 		29.3
(3)
A 		28.9
(2.9)
A 		27
avr 21.6
(0.3) 		11.7
(-1.8) 		5.7
(-3) 		12.7
(-1.6) 		35
(3) 		25.2
(1) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189901_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11155
Sequence Type Exemplar sequence
Representative Public ID F28F9.4 NCBI
Target Description F28F9.4 /REP_DB=WormBase Gene ID /WP=CE17028 /TR=Q94197 /GB=AAB09125.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=amino acid permease
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_068024(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068024 NCBI Caenorhabditis elegans Amino Acid Transporter family member (aat-8) (aat-8) mRNA, complete cds. 11/11 None
F28F9.4 ENSEMBL cdna:known chromosome:CEL140:IV:3862123:3865024:-1 gene:F28F9.4 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
chrIV:3862128-3865030(-) 100.0 100.0
Public Domain and Genome References
Gene Title amino acid permease
Gene Symbol aat-8
Ensembl F28F9.4
Entrez Gene 185079 Entrez gene
SwissProt Q94197 EMBL-EBI
WormBase CE34547 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB09125 Amino acid transporter protein 8 [Caenorhabditis elegans] ref|NP_500425.2| Amino Acid Transporter family member (aat-8) [Caenorhabditis elegans] 0.0
blast CAE65671 Hypothetical protein CBG10737 [Caenorhabditis briggsae] 0.0
blast CAE60537 Hypothetical protein CBG04164 [Caenorhabditis briggsae] 3.0E-71
Protein Domains
Database ID Description E-Value
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 4.0E-9
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.2E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500425.2 11 9-31,41-63,76-98,136-153,166-188,203-225,245-267,292-314,364-386,401-418,425-444
F28F9.4 11 9-31,41-63,76-98,136-153,166-188,203-225,245-267,292-314,364-386,401-418,425-444
Sequence
Target Sequence 
>C. ELEGANS:189901_AT
gggaaatggtccagcttttgccgtacctgctgtggtgggctttttgcttgttggtacgct
taatggagacgttcccataaaaaatttcaaaaccctgacaagcgacatgacccaattttg
caggtatatggtcgccggatcacgtcggaagatgatgcccacctgcttcagtttgataca
tgttgacaacgacagtccgcgggtttctgtcttttttcatacccttacctcaataatctt
tgcatttatgggagacaccgatcaactagtggattatctcaccgtaacaggaatgctcac
aacaattttcgcacttttggtcttggttatcataaaatggaagaaaatgccaattgcatc
ggatcctgtgaaatatagcattttttggccaattttaaatttggtaattatgatcgctct
actggtaatacctattcaacaagaccccctgtcatcaattattggattttccatgttttt
aggcggtgttgttgtctacttcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGGAAATGGTCCAGCTTTTGCCGTA 673 493 951 Antisense
GGCTTTTTGCTTGTTGGTACGCTTA 613 535 988 Antisense
TATATGGTCGCCGGATCACGTCGGA 215 661 1075 Antisense
CACGTCGGAAGATGATGCCCACCTG 144 177 1091 Antisense
TGCCCACCTGCTTCAGTTTGATACA 228 585 1106 Antisense
TTGACAACGACAGTCCGCGGGTTTC 447 635 1133 Antisense
TTTTCATACCCTTACCTCAATAATC 708 675 1164 Antisense
TTCGCACTTTTGGTCTTGGTTATCA 231 695 1258 Antisense
ATGCCAATTGCATCGGATCCTGTGA 335 41 1297 Antisense
AACAAGACCCCCTGTCATCAATTAT 576 133 1388 Antisense
TAGGCGGTGTTGTTGTCTACTTCAT 302 653 1430 Antisense
Sequence Source Affymetrix Proprietary Database