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[190301_s_at] ammonium transporter

Description C05E11.5 /REP_DB=WormBase Gene ID /WP=CE27655 /TR=Q17663 /GB=AAA96190.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ammonium transporter
Cluster 6grp_highest_10_10 > 24      6grp_high1_10_10 > 31      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 62      6grp_total > 42      4grp_total > 58      6grp_cgc > 81      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1017
1 2 3 4 range
A 775.3
(-0.7)
P 		1403.2
(3)
P 		1166.5
(1.6)
P 		386
(-3)
P 		1017
B 896
(-0.3)
P 		1289.5
(2.5)
P 		1358
(3)
P 		515.9
(-3)
P 		842
C 965.5
(0.6)
P 		1143.5
(2.2)
P 		1229.9
(3)
P 		561.5
(-3)
P 		668
avr 878.9
(-0) 		1278.7
(3) 		1251.5
(2.8) 		487.8
(-3) 		791

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 538
1 2 3 4 5 6 range
A 489.6
(0.4)
P 		646.2
(2.8)
P 		660.3
(3)
P 		529
(1)
P 		352.6
(-1.6)
P 		261.6
(-3)
P 		399
B 426.2
(-1.2)
P 		513.2
(-0.2)
P 		793.6
(3)
P 		483.1
(-0.6)
P 		438.6
(-1.1)
P 		271.2
(-3)
P 		522
C 548.4
(0.9)
P 		484.3
(0)
P 		709.8
(3)
P 		379.2
(-1.4)
P 		442
(-0.5)
P 		255.5
(-3)
P 		454
avr 488.1
(-0.1) 		547.9
(0.7) 		721.2
(3) 		463.8
(-0.4) 		411.1
(-1.1) 		262.8
(-3) 		458
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 372
1 2 3 4 range
A 282.3
(2.5)
P 		304.6
(3)
P 		304.9
(3)
P 		56.5
(-3)
P 		248
B 285.7
(2.1)
P 		318.5
(3)
P 		314.7
(2.9)
P 		109.9
(-3)
P 		209
C 319.6
(1)
P 		328.8
(1.2)
P 		428.7
(3)
P 		94.7
(-3)
P 		334
avr 295.9
(1.8) 		317.3
(2.3) 		349.4
(3) 		87
(-3) 		262

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 166
1 2 3 4 5 6 range
A 90.3
(-2)
P 		229.8
(3)
P 		143.8
(-0.1)
P 		134.2
(-0.5)
P 		106.4
(-1.5)
P 		63.7
(-3)
P 		166
B 148.3
(0.1)
P 		170.8
(1.6)
P 		192.7
(3)
P 		128
(-1.2)
P 		178.2
(2.1)
P 		101.1
(-3)
P 		92
C 203.3
(3)
P 		147.8
(0.4)
P 		180.7
(1.9)
P 		76.3
(-3)
P 		143
(0.2)
P 		85.5
(-2.6)
P 		127
avr 147.3
(0.9) 		182.8
(3) 		172.4
(2.4) 		112.8
(-1.2) 		142.5
(0.6) 		83.4
(-3) 		99
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190301_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17068
Sequence Type Exemplar sequence
Representative Public ID C05E11.5 NCBI
Target Description C05E11.5 /REP_DB=WormBase Gene ID /WP=CE27655 /TR=Q17663 /GB=AAA96190.2 /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_076382(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076382 NCBI Caenorhabditis elegans AMmonium Transporter homolog family member (amt-4) (amt-4) mRNA, complete cds. 11/11 None
SNAP00000025326 ENSEMBL cdna:SNAP chromosome:CEL140:X:4565000:4569222:1 11/11 None
GENEFINDER00000025333 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4565337:4569222:1 11/11 None
C05E11.5 ENSEMBL cdna:known chromosome:CEL140:X:4565274:4569531:1 gene:C05E11.5 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:4565337-4569223(+) 100.0 100.0
Public Domain and Genome References
Gene Title ammonium transporter
Gene Symbol amt-4
Ensembl C05E11.5
Entrez Gene 180728 Entrez gene
SwissProt Q17663 EMBL-EBI
WormBase CE27655 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:262883_AT ammonium transporter 1, member 2 (AMT1.2) at
ATGENOME1:17572_S_AT ammonium transporter 1, member 2 (AMT1.2) 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 AAA96190 Ammonium transporter homolog protein 4 [Caenorhabditis elegans] ref|NP_508783.1| AMmonium Transporter homolog family member (amt-4) [Caenorhabditis elegans] 0.0
blast CAE68613 Hypothetical protein CBG14494 [Caenorhabditis briggsae] emb|CAE68611.1| Hypothetical protein CBG14492 [Caenorhabditis briggsae] 0.0
blast CAE68614 Hypothetical protein CBG14495 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR010256 EMBL-EBI Rh-like protein/ammonium transporter 1.0E-126
Pfam IPR010256 EMBL-EBI Rh-like protein/ammonium transporter 1.0E-126
Pfam IPR010256 EMBL-EBI Rh-like protein/ammonium transporter 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508783.1 10 10-32,45-67,96-115,122-144,169-191,204-226,241-263,298-320,335-357,377-399
C05E11.5 10 10-32,45-67,96-115,122-144,169-191,204-226,241-263,298-320,335-357,377-399
SNAP00000025326 9 48-70,85-104,111-133,159-181,194-216,231-253,288-310,325-347,367-389
GENEFINDER00000025333 10 10-32,45-67,101-123,130-152,177-199,212-234,249-271,306-328,343-365,385-407
Sequence
Target Sequence 
>C. ELEGANS:190301_S_AT
gacggtgtagtttattcgattggtaacactattggtggagctacaaatggaggtgatcaa
attgctcaggcatttgctcaacttggatggcaatgggtgtgcgcactcgcaatcgtcaca
tggtcaattctctggatgtggcctatttttgcactgttgaggaaaataggaaaacttaga
gtgtccgctgaggtggagattaatggattggatatctacaaacatggagagtcggcctac
ccgctacacgcctacggacacgggtggcacgatttcgaagctgctccagacagcaaaatc
aatcatagtaaacatcttccagttggaagaaagaacagaataatgagtgttcatccagaa
atgtccttggaacaacttgcgtcagtatacgacaggactggaagtgttggagagtctgat
caaccaaagaggctatttatgaatcaaactgagaggagaaaatccagaatgattgaagca
aatgcacttcatgcattgtacttagatgataatgaggttcctgaaaggaaaaacacaaat
ccaaagactgtcagcttacaagtccccacaacaattattgaggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGGTGTAGTTTATTCGATTGGTA 520 377 1162 Antisense
GGATGGCAATGGGTGTGCGCACTCG 208 515 1246 Antisense
CACTCGCAATCGTCACATGGTCAAT 586 197 1265 Antisense
ATGGTCAATTCTCTGGATGTGGCCT 293 51 1281 Antisense
GATGTGGCCTATTTTTGCACTGTTG 238 409 1296 Antisense
AAAACTTAGAGTGTCCGCTGAGGTG 425 129 1332 Antisense
CAAACATGGAGAGTCGGCCTACCCG 351 191 1380 Antisense
ACGGACACGGGTGGCACGATTTCGA 399 95 1415 Antisense
GTCCTTGGAACAACTTGCGTCAGTA 495 477 1524 Antisense
AAGACTGTCAGCTTACAAGTCCCCA 112 153 1705 Antisense
AAGTCCCCACAACAATTATTGAGGC 582 149 1721 Antisense
Sequence Source Affymetrix Proprietary Database