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[190053_at] amino acid permease

Description F52H2.2 /REP_DB=WormBase Gene ID /WP=CE28440 /TR=O17395 /GB=AAB71312.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=amino acid permease
Cluster 6grp_highest_10_10 > 72      6grp_high1_10_10 > 27      4grp_high_8_8 > 34      6grp_highest_nonorm > 60      6grp_total > 17      4grp_total > 45      6grp_highest_sub > Cu      6grp_cgc > 15      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 353
1 2 3 4 range
A 484.6
(3)
P 		336.3
(0.5)
P 		220.4
(-1.5)
P 		132
(-3)
A 		353
B 253.4
(0.7)
P 		302.5
(3)
P 		196.6
(-2)
P 		174.8
(-3)
P 		128
C 404.2
(3)
P 		266
(-1.5)
P 		218.6
(-3)
P 		257.7
(-1.7)
P 		186
avr 380.7
(3) 		301.6
(0.5) 		211.9
(-2.3) 		188.2
(-3) 		193

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 520
1 2 3 4 5 6 range
A 717
(3)
P 		323.6
(-2.1)
P 		250.8
(-3)
P 		252
(-3)
P 		288.4
(-2.5)
P 		349.4
(-1.7)
P 		466
B 492.3
(3)
P 		436.6
(1.9)
P 		417.1
(1.5)
P 		298.4
(-0.9)
P 		196.7
(-3)
P 		368.6
(0.5)
P 		296
C 587.2
(3)
P 		437.3
(0.6)
P 		268
(-2.2)
P 		318.5
(-1.4)
P 		217
(-3)
P 		328.5
(-1.2)
P 		370
avr 598.8
(3) 		399.2
(-0.3) 		312
(-1.7) 		289.6
(-2.1) 		234
(-3) 		348.8
(-1.1) 		365
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 157
1 2 3 4 range
A 176.5
(3)
P 		73
(-1)
P 		57.6
(-1.5)
P 		19.3
(-3)
A 		157
B 80.8
(3)
P 		74.7
(2.2)
P 		45.6
(-1.9)
P 		37.3
(-3)
P 		44
C 133.8
(3)
P 		76.5
(-0.8)
P 		76.2
(-0.8)
P 		43.4
(-3)
P 		90
avr 130.4
(3) 		74.7
(-0.4) 		59.8
(-1.4) 		33.3
(-3) 		97

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 132.2
(3)
P 		115.1
(1.7)
P 		54.6
(-3)
P 		63.9
(-2.3)
P 		87
(-0.5)
P 		85.1
(-0.6)
P 		78
B 171.3
(3)
P 		145.3
(1.3)
P 		101.3
(-1.6)
P 		79
(-3)
P 		79.9
(-2.9)
P 		137.4
(0.8)
P 		92
C 217.7
(3)
P 		133.4
(-0.3)
P 		68.2
(-2.8)
P 		64
(-3)
P 		70.2
(-2.8)
P 		110
(-1.2)
P 		154
avr 173.7
(3) 		131.3
(0.6) 		74.7
(-2.7) 		69
(-3) 		79
(-2.4) 		110.8
(-0.6) 		105
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190053_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18509
Sequence Type Exemplar sequence
Representative Public ID F52H2.2 NCBI
Target Description F52H2.2 /REP_DB=WormBase Gene ID /WP=CE28440 /TR=O17395 /GB=AAB71312.1 /SUBMIT=ST.LOUIS /CHR=X /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_076060(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076060 NCBI Caenorhabditis elegans Amino Acid Transporter family member (aat-3) (aat-3) mRNA, complete cds. 9/11 None
SNAP00000036205 ENSEMBL cdna:SNAP chromosome:CEL140:X:2554232:2557469:1 9/11 None
GENEFINDER00000036218 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:2554232:2557469:1 9/11 None
F52H2.2 ENSEMBL cdna:known chromosome:CEL140:X:2554225:2557708:1 gene:F52H2.2 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:2554231-2557469(+) 92.14 100.0
Public Domain and Genome References
Gene Title amino acid permease
Gene Symbol aat-3
Ensembl F52H2.2
Entrez Gene 180557 Entrez gene
SwissProt O17395 EMBL-EBI
WormBase CE28440 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.31112.1.S1_AT similar to solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 cfa
DROSOPHILA_2:1626581_S_AT dm
DROSGENOME1:151567_AT dm
DROSGENOME1:142423_AT dm
CHICKEN:GGA.9956.1.S1_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 gga
CHICKEN:GGAAFFX.11823.1.S1_S_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 gga
MU11KSUBA:C79507_RC_F_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MU11KSUBA:AA592030_G_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MU11KSUBA:AA592030_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MG-U74AV2:99863_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MG-U74AV2:100417_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MG-U74BV2:165240_I_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MG-U74CV2:171354_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOE430A:1433467_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOUSE430A_2:1433467_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOUSE430_2:1433467_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOE430A:1460541_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOUSE430A_2:1460541_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MOUSE430_2:1460541_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 mm
MU19KSUBC:TC41650_AT Expressed sequence AI643885, mRNA (cDNA clone MGC:37035 IMAGE:4949962) mm
RG-U34C:RC_AI072213_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 (predicted) rn
RAE230A:1373629_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 (predicted) rn
RAT230_2:1373629_AT solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 (predicted) rn
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 AAB71312 Amino acid transporter protein 3 [Caenorhabditis elegans] ref|NP_508461.1| Amino Acid Transporter family member (aat-3) [Caenorhabditis elegans] 0.0
blast CAE58861 Hypothetical protein CBG02089 [Caenorhabditis briggsae] 0.0
blast CAE72788 Hypothetical protein CBG20050 [Caenorhabditis briggsae] 1.0E-171
Protein Domains
Database ID Description E-Value
Pfam IPR004841 EMBL-EBI Amino acid permease-associated region 1.5E-20
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508461.1 12 35-57,67-89,120-139,154-176,181-203,223-245,257-279,304-326,356-373,383-402,415-437,442-461
F52H2.2 12 35-57,67-89,120-139,154-176,181-203,223-245,257-279,304-326,356-373,383-402,415-437,442-461
SNAP00000036205 12 35-57,67-89,120-139,154-176,181-203,223-245,257-279,304-326,356-373,383-402,415-437,442-461
GENEFINDER00000036218 12 35-57,67-89,120-139,154-176,181-203,223-245,257-279,304-326,356-373,383-402,415-437,442-461
Sequence
Target Sequence 
>C. ELEGANS:190053_AT
ggcaattgccgaatttgacgagccaaaaaatttttggaaaccggcaattgcctttttttg
aaaatttttttgttgaaattatatttttgagcgctttggaaaaaagtatggtcgtttttt
tcttttacagtgaaacattattctactgcggagctcgtgaaggacaaatgccaaatgtat
taaccatggtgaacaaaaccacaaaaactccaatcccagccgtaattctcactggacttc
tttccttgctctaccttcttctctccaacaacatttactctctcatcaactacattcaag
tcagctactggattgctattggaggagccatccttgcgctcttctactttagaaaaacaa
tgccagatgctccaagagctgtgaaagcgccgatagttttcccaatcatattcttcattg
ggtgcgtgcttcttgtgttggtcccagttcttggaaacccgaaggatactgcaattggaa
tccttattatgctgtctggtgtccctgtataccttattttcattgcatggaaaggaaaac
caaagtgcattgactcgctcacagattccgtcacgatcttcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCAATTGCCGAATTTGACGAGCCA 123 533 1079 Antisense
AACATTATTCTACTGCGGAGCTCGT 501 137 1212 Antisense
CAATCCCAGCCGTAATTCTCACTGG 229 181 1289 Antisense
TAATTCTCACTGGACTTCTTTCCTT 95 635 1301 Antisense
TCCTTGCGCTCTTCTACTTTAGAAA 60 593 1409 Antisense
GAAAGCGCCGATAGTTTTCCCAATC 489 359 1461 Antisense
ATATTCTTCATTGGGTGCGTGCTTC 446 19 1486 Antisense
CCTTATTATGCTGTCTGGTGTCCCT 390 267 1560 Antisense
GGTGTCCCTGTATACCTTATTTTCA 280 499 1576 Antisense
AAGTGCATTGACTCGCTCACAGATT 128 159 1621 Antisense
TCACAGATTCCGTCACGATCTTCAC 95 629 1637 Antisense
Sequence Source Affymetrix Proprietary Database