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[190834_at] ammonium transporter

Description C05E11.4 /REP_DB=WormBase Gene ID /WP=CE06770 /TR=SW:P54145 /GB=AAA96191.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ammonium transporter
Cluster 6grp_total > 77      4grp_total > 33      6grp_cgc > 48      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 62
1 2 3 4 range
A 16
(-3)
A 		77.5
(3)
A 		59.8
(1.3)
A 		73.6
(2.6)
M 		62
B 24.8
(-3)
A 		54.2
(2.1)
A 		59.3
(3)
A 		56.8
(2.6)
A 		35
C 42.4
(-2.8)
A 		68.8
(1.5)
P 		41.3
(-3)
A 		77.8
(3)
P 		37
avr 27.7
(-3) 		66.8
(2.6) 		53.5
(0.7) 		69.4
(3) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 781
1 2 3 4 5 6 range
A 15.7
(-3)
A 		29.8
(-2.9)
A 		51.6
(-2.7)
P 		94.1
(-2.4)
P 		205.2
(-1.4)
P 		746.1
(3)
P 		730
B 43.7
(-2.9)
A 		28.4
(-3)
A 		69.7
(-2.7)
P 		65.5
(-2.7)
P 		171.9
(-1.8)
P 		753.8
(3)
P 		725
C 50.2
(-3)
P 		44.5
(-3)
A 		108.7
(-2.5)
P 		91.3
(-2.6)
P 		233.7
(-1.5)
P 		796.7
(3)
P 		752
avr 36.5
(-3) 		34.2
(-3) 		76.7
(-2.7) 		83.6
(-2.6) 		203.6
(-1.6) 		765.5
(3) 		731
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 5.8
(-3)
A 		16.8
(3)
A 		15.6
(2.3)
A 		10.8
(-0.3)
M 		11
B 7.9
(-3)
A 		13.4
(2.7)
A 		13.7
(3)
A 		12.1
(1.3)
A 		6
C 14
(-2.2)
A 		19.8
(3)
P 		14.4
(-1.8)
A 		13.1
(-3)
P 		7
avr 9.2
(-3) 		16.7
(3) 		14.6
(1.3) 		12
(-0.8) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 278
1 2 3 4 5 6 range
A 2.9
(-3)
A 		10.6
(-2.7)
A 		11.2
(-2.7)
P 		23.9
(-2.3)
P 		61.9
(-1)
P 		181.6
(3)
P 		179
B 15.2
(-2.9)
A 		9.5
(-3)
A 		16.9
(-2.8)
P 		17.3
(-2.8)
P 		69.8
(-1.7)
P 		281.1
(3)
P 		272
C 18.6
(-2.9)
P 		13.6
(-3)
A 		27.7
(-2.7)
P 		18.4
(-2.9)
P 		75.6
(-1.5)
P 		266.7
(3)
P 		253
avr 12.2
(-3) 		11.2
(-3) 		18.6
(-2.8) 		19.9
(-2.8) 		69.1
(-1.5) 		243.1
(3) 		232
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190834_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17198
Sequence Type Exemplar sequence
Representative Public ID C05E11.4 NCBI
Target Description C05E11.4 /REP_DB=WormBase Gene ID /WP=CE06770 /TR=SW:P54145 /GB=AAA96191.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ammonium 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_076383(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076383 NCBI Caenorhabditis elegans AMmonium Transporter homolog family member (amt-1) (amt-1) mRNA, complete cds. 11/11 None
SNAP00000025327 ENSEMBL cdna:SNAP chromosome:CEL140:X:4571439:4573782:1 11/11 None
GENEFINDER00000025337 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4571439:4573782:1 11/11 None
C05E11.4 ENSEMBL cdna:known chromosome:CEL140:X:4571419:4573865:1 gene:C05E11.4 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
chrX:4571439-4573783(+) 100.0 100.0
Public Domain and Genome References
Gene Title ammonium transporter
Gene Symbol amt-1
Ensembl C05E11.4
Entrez Gene 180729 Entrez gene
SwissProt P54145 EMBL-EBI
WormBase CE06770 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257162_S_AT ammonium transporter, putative at
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
GO Molecular Function (view graph)
ID Description Evidence Links
8519 ammonium transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA96191 Ammonium transporter homolog protein 1 [Caenorhabditis elegans] ref|NP_508784.1| AMmonium Transporter homolog family member (amt-1) [Caenorhabditis elegans] sp|P54145|AMT1_CAEEL Putative ammonium transporter 0.0
blast CAE68614 Hypothetical protein CBG14495 [Caenorhabditis briggsae] 0.0
blast CAE68613 Hypothetical protein CBG14494 [Caenorhabditis briggsae] emb|CAE68611.1| Hypothetical protein CBG14492 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR010256 EMBL-EBI Rh-like protein/ammonium transporter 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508784.1 11 29-51,64-86,115-134,139-161,188-210,223-245,260-282,291-310,314-333,354-376,396-418
C05E11.4 11 29-51,64-86,115-134,139-161,188-210,223-245,260-282,291-310,314-333,354-376,396-418
SNAP00000025327 11 29-51,64-86,115-134,139-161,188-210,223-245,260-282,291-310,314-333,354-376,396-418
GENEFINDER00000025337 11 29-51,64-86,115-134,139-161,188-210,223-245,260-282,291-310,314-333,354-376,396-418
Sequence
Target Sequence 
>C. ELEGANS:190834_AT
tcatctaccttgcgttctcaaaacttatgataaggctgaaaatcgacgatcctcttgacg
ctttcgccgtgcacgctggtggtggcttctggggattaatgtcatcgtcaattatttctc
acggaggagttgcgtacgctttggctgatgcagtttctggtgcaaaaaattcgggtgatc
atctcacacaagctttcgcgcaacttggatggcaaatgatctgcgcgctggcaatcatag
cttggtcacttggagtcatgttaccaatattctggattctcaaaaaaactggaaagcttc
gcgtctcagaagaagtggagatcaatgggctggatgtatttaagcatggagagatggcat
acccactccgagcatatggtcatggatggcacgactttgaacgggcgaataagatccaag
catttagcgcaaaaattacagtaggagagggaaaaaatacgaggatcatgaagattcatc
ctgaaatgtccattgaacaattggcgtcagtgtacgatagaagtggaaacatcataccta
tgcccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCATCTACCTTGCGTTCTCAAAACT 339 619 995 Antisense
AGTTGCGTACGCTTTGGCTGATGCA 37 65 1122 Antisense
GTGATCATCTCACACAAGCTTTCGC 40 485 1169 Antisense
AGCTTTCGCGCAACTTGGATGGCAA 341 79 1185 Antisense
GATGGCAAATGATCTGCGCGCTGGC 426 407 1202 Antisense
GCGCGCTGGCAATCATAGCTTGGTC 594 287 1217 Antisense
GCTTGGTCACTTGGAGTCATGTTAC 223 307 1234 Antisense
AAACTGGAAAGCTTCGCGTCTCAGA 586 125 1280 Antisense
ATACCCACTCCGAGCATATGGTCAT 430 23 1353 Antisense
GGATGGCACGACTTTGAACGGGCGA 14 515 1378 Antisense
GTGGAAACATCATACCTATGCCCAA 438 491 1517 Antisense
Sequence Source Affymetrix Proprietary Database