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[174714_at] NH(4+) transporter

Description CEK011B5R_rc /REP_DB=TREMBL Accession /GB=D27508 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk11b5 : 3prime end, single read.
Cluster 6grp_total > 29      4grp_total > 14      6grp_cgc > 03      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 53.4
(1.2)
A 		7.9
(-2.7)
A 		4.8
(-3)
A 		74.7
(3)
A 		70
B 47.9
(1.2)
A 		11.1
(-3)
A 		21.1
(-1.9)
A 		63.8
(3)
A 		53
C 52
(0.8)
A 		5.8
(-3)
A 		8.4
(-2.8)
A 		78.1
(3)
A 		72
avr 51.1
(1) 		8.3
(-3) 		11.4
(-2.7) 		72.2
(3) 		64

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 36.1
(0.3)
A 		60.4
(3)
A 		6.4
(-3)
A 		27.6
(-0.6)
A 		17.2
(-1.8)
A 		46.6
(1.5)
A 		54
B 55.3
(3)
A 		24.5
(-1.1)
A 		27.3
(-0.7)
A 		10
(-3)
A 		49.2
(2.2)
A 		26.1
(-0.9)
A 		45
C 78.9
(3)
A 		60.6
(1.5)
M 		22
(-1.7)
A 		54.7
(1)
A 		61
(1.5)
A 		6.7
(-3)
A 		72
avr 56.8
(3) 		48.5
(1.7) 		18.6
(-3) 		30.8
(-1.1) 		42.5
(0.8) 		26.5
(-1.8) 		38
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 19.4
(3)
A 		1.7
(-2.9)
A 		1.3
(-3)
A 		10.9
(0.2)
A 		18
B 15.3
(3)
A 		2.8
(-3)
A 		4.9
(-2)
A 		13.6
(2.2)
A 		13
C 17.2
(3)
A 		1.7
(-3)
A 		2.9
(-2.5)
A 		13.2
(1.5)
A 		16
avr 17.3
(3) 		2.1
(-3) 		3
(-2.6) 		12.6
(1.1) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28
1 2 3 4 5 6 range
A 6.7
(-1.4)
A 		21.5
(3)
A 		1.4
(-3)
A 		7
(-1.3)
A 		5.2
(-1.9)
A 		11.3
(-0)
A 		20
B 19.3
(2.8)
A 		8.2
(-1.1)
A 		6.6
(-1.6)
A 		2.7
(-3)
A 		20
(3)
A 		9.7
(-0.6)
A 		17
C 29.3
(3)
A 		18.5
(0.6)
M 		5.6
(-2.2)
A 		11
(-1.1)
A 		19.7
(0.9)
A 		2.2
(-3)
A 		27
avr 18.4
(3) 		16.1
(2) 		4.5
(-3) 		6.9
(-2) 		15
(1.5) 		7.7
(-1.6) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174714_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20502
Sequence Type Exemplar sequence
Representative Public ID CEK011B5R NCBI
Target Description CEK011B5R_rc /REP_DB=TREMBL Accession /GB=D27508 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk11b5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_063360(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063360 NCBI Caenorhabditis elegans AMmonium Transporter homolog family member (amt-3) (amt-3) mRNA, complete cds. 11/11 A 
M195.3.2 ENSEMBL cdna:known chromosome:CEL140:II:8363082:8369005:-1 gene:M195.3 11/11 A 
M195.3.1 ENSEMBL cdna:known chromosome:CEL140:II:8363118:8369081:-1 gene:M195.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000004363 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:8363124-8363445(-) 100.0 100.0
Public Domain and Genome References
Gene Title NH(4+) transporter
Gene Symbol amt-3
Ensembl M195.3
Entrez Gene 174338 Entrez gene
SwissProt Q21565 EMBL-EBI
WormBase CE32912 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:20369_S_AT ammonium transporter 1, member 1 (AMT1.1) at
ATH1-121501:254723_AT ammonium transporter 1, member 1 (AMT1.1) at
DROSOPHILA_2:1633393_AT dm
DROSGENOME1:149943_AT dm
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 CAA91293 Hypothetical protein M195.3 [Caenorhabditis elegans] ref|NP_495761.2| AMmonium Transporter homolog family member (amt-3) [Caenorhabditis elegans] sp|Q21565|AMT3_CAEEL Putative ammonium transporter 0.0
blast CAE57701 Hypothetical protein CBG00705 [Caenorhabditis briggsae] 0.0
blast CAA94345 Hypothetical protein F49E11.3 [Caenorhabditis elegans] ref|NP_502496.1| AMmonium Transporter homolog family member (amt-2) [Caenorhabditis elegans] sp|Q20605|AMT2_CAEEL Putative ammonium transporter 3.0E-99
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_495761.2 11 42-64,77-99,133-155,162-181,196-217,238-260,270-292,299-318,322-344,351-373,399-421
M195.3.2 11 42-64,77-99,133-155,162-181,196-217,238-260,270-292,299-318,322-344,351-373,399-421
M195.3.1 11 42-64,77-99,133-155,162-181,196-217,238-260,270-292,299-318,322-344,351-373,399-421
Sequence
Target Sequence 
>C. ELEGANS:174714_AT
tctagcaaaaattcgacggttggcaaatttgttaaagcaccagctccaagagccttatca
ccgccggataataatccacctgtttgaaaaatttgcattttttgctattaaaatctccaa
tcaacaccgggtgtttccttgttagttttattatttttaaatttgtaacgtttctggctt
caatttcgggttttctttttctcgttcacaaaattttttgaatagtatctattcaaaacc
tttcagtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTAGCAAAAATTCGACGGTTGGCA 666 607 37 Antisense
GCAAATTTGTTAAAGCACCAGCTCC 640 317 59 Antisense
CCAGCTCCAAGAGCCTTATCACCGC 482 273 76 Antisense
TCACCGCCGGATAATAATCCACCTG 503 617 94 Antisense
AATCCACCTGTTTGAAAAATTTGCA 210 165 109 Antisense
TTTGCTATTAAAATCTCCAATCAAC 367 667 137 Antisense
AATCTCCAATCAACACCGGGTGTTT 126 167 148 Antisense
TCAACACCGGGTGTTTCCTTGTTAG 672 627 157 Antisense
TAAATTTGTAACGTTTCTGGCTTCA 96 641 194 Antisense
TAACGTTTCTGGCTTCAATTTCGGG 138 627 202 Antisense
AGTATCTATTCAAAACCTTTCAGTT 277 63 260 Antisense
Sequence Source Affymetrix Proprietary Database