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[173012_at] glutamate synthase

Description CEK002H9R_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=D27720 /DEF=C.elegans cDNA clone yk2h9 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 58      4grp_high_8_8 > 21      6grp_total > 58      4grp_total > 18      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 112.9
(-3)
P 		158
(0)
P 		137.8
(-1.3)
P 		203.1
(3)
A 		90
B 108.3
(-3)
P 		162.1
(1.1)
P 		156.7
(0.6)
P 		187.9
(3)
P 		80
C 162.2
(2.4)
P 		146.4
(1.1)
P 		97.1
(-3)
P 		169.2
(3)
A 		72
avr 127.8
(-3) 		155.5
(-0.2) 		130.5
(-2.7) 		186.7
(3) 		59

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 177
1 2 3 4 5 6 range
A 214.6
(3)
P 		147
(-0.5)
P 		104.6
(-2.7)
P 		99
(-3)
P 		176.9
(1)
P 		170.9
(0.7)
P 		116
B 140.4
(1.7)
P 		114.7
(0.5)
P 		160.7
(2.6)
P 		169.2
(3)
P 		37.7
(-3)
P 		169.9
(3)
P 		132
C 109.1
(-1.6)
P 		110.3
(-1.6)
A 		163.4
(1)
P 		81.1
(-3)
P 		204.1
(3)
P 		150.3
(0.4)
P 		123
avr 154.7
(1.9) 		124
(-2) 		142.9
(0.4) 		116.4
(-3) 		139.6
(-0.1) 		163.7
(3) 		47
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 41.1
(3)
P 		34.3
(-0.6)
P 		36
(0.3)
P 		29.7
(-3)
A 		11
B 34.5
(-3)
P 		40
(2.9)
P 		36.3
(-1.1)
P 		40.1
(3)
P 		6
C 53.7
(3)
P 		42.1
(0.2)
P 		33.8
(-1.7)
P 		28.5
(-3)
A 		25
avr 43.1
(3) 		38.8
(0.5) 		35.4
(-1.5) 		32.8
(-3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 39.6
(0.3)
P 		52.3
(2.8)
P 		22.8
(-3)
P 		25.1
(-2.5)
P 		53.4
(3)
P 		41.6
(0.7)
P 		31
B 48.9
(1.2)
P 		38.2
(-0.1)
P 		39
(-0)
P 		44.8
(0.7)
P 		15.3
(-3)
P 		63.4
(3)
P 		48
C 40.4
(-0.1)
P 		33.6
(-0.9)
A 		41.6
(0)
P 		16.3
(-3)
P 		66.1
(3)
P 		50.3
(1.1)
P 		50
avr 43
(0.7) 		41.4
(0.3) 		34.5
(-1.5) 		28.7
(-3) 		44.9
(1.2) 		51.8
(3) 		23
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173012_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27319
Sequence Type Exemplar sequence
Representative Public ID CEK002H9R NCBI
Target Description CEK002H9R_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=D27720 /DEF=C.elegans cDNA clone yk2h9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_077292
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
W07E11.1 ENSEMBL cdna:known chromosome:CEL140:X:10083935:10103992:1 gene:W07E11.1 A 
GENEFINDER00000021217 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:10095484:10103823:1 None
SNAP00000021206 ENSEMBL cdna:SNAP chromosome:CEL140:X:10098798:10103823:1 None
NM_077292 NCBI Caenorhabditis elegans W07E11.1 (W07E11.1) mRNA, complete cds. A 
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:10103512-10103975(+) 87.22 87.22
Public Domain and Genome References
Gene Title glutamate synthase
Ensembl W07E11.1
Entrez Gene 181223 Entrez gene
SwissProt Q22275 EMBL-EBI
WormBase CE02372 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:248267_AT glutamate synthase (NADH), chloroplast, putative at
DROSOPHILA_2:1629048_S_AT dm
DROSGENOME1:153030_AT dm
YEAST_2:1776998_AT NAD(+)-dependent glutamate synthase (GOGAT), synthesizes glutamate from glutamine and alpha-ketoglutarate; with Gln1p, forms the secondary pathway for glutamate biosynthesis from ammonia; expression regulated by nitrogen source Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
6537 glutamate biosynthesis inferred from electronic annotation QuickGO AmiGO
6807 nitrogen compound metabolism inferred from electronic annotation QuickGO AmiGO
8152 metabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
15036 disulfide oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
15930 glutamate synthase activity inferred from electronic annotation QuickGO AmiGO
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
16639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90070 Hypothetical protein W07E11.1 [Caenorhabditis elegans] emb|CAA90032.1| Hypothetical protein W07E11.1 [Caenorhabditis elegans] ref|NP_509693.1| W07E11.1 [Caenorhabditis elegans] 0.0
blast CAE58778 Hypothetical protein CBG01975 [Caenorhabditis briggsae] 0.0
blast EAA10819 ENSANGP00000013025 [Anopheles gambiae str. PEST] ref|XP_316385.2| ENSANGP00000013025 [Anopheles gambiae str. PEST] 0.0
Protein Domains
Database ID Description E-Value
scop a.1.2.Dihydropyrimidine dehydrogenase, N-terminal domain All alpha proteins; Globin-like; alpha-helical ferredoxin; Dihydropyrimidine dehydrogenase, N-terminal domain 0.0160000007599592
scop a.1.2.Dihydropyrimidine dehydrogenase, N-terminal domain All alpha proteins; Globin-like; alpha-helical ferredoxin; Dihydropyrimidine dehydrogenase, N-terminal domain 0.0140000004321337
Pfam IPR006981 EMBL-EBI Glutamate synthase amidotransferase domain 1.0E-126
Pfam IPR002489 EMBL-EBI Protein of unknown function DUF14 4.9E-80
Pfam IPR006982 EMBL-EBI Glutamate synthase central domain 1.0E-126
Pfam IPR002932 EMBL-EBI Ferredoxin-dependent glutamate synthase 1.0E-126
Pfam IPR006981 EMBL-EBI Glutamate synthase amidotransferase domain 6.5E-14
Pfam IPR002489 EMBL-EBI Protein of unknown function DUF14 4.9E-80
Pfam IPR006982 EMBL-EBI Glutamate synthase central domain 1.0E-126
Pfam IPR002932 EMBL-EBI Ferredoxin-dependent glutamate synthase 1.0E-126
Pfam IPR002489 EMBL-EBI Protein of unknown function DUF14 4.9E-80
Pfam IPR002932 EMBL-EBI Ferredoxin-dependent glutamate synthase 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:173012_AT
ctgatgtggcacaaggttgttcgctnctggagaatgtcgtcgtggacagtcactcgtggt
gtgggccattcacgaagggcgtcaagctgcccgacaagttgtcgagtatctaatgggcaa
gacaacattgtcagggccgggaggaattgtgaccgctacaagtcaactgnagaatgccan
ttaaatattttcactgttgatttccattttttgctctcgcattttgtttttcattagttg
ataatagcttatagtaagcaagtantatttcccctcacccgttctaattanccccatgtt
gatgtatttcgtcccagcatcaatc

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGATGTGGCACAAGGTTGTTCGCT 289 239 95 Antisense
GGCAAGACAACATTGTCAGGGCCGG 670 533 210 Antisense
GACAACATTGTCAGGGCCGGGAGGA 457 335 215 Antisense
ATTGTCAGGGCCGGGAGGAATTGTG 366 3 221 Antisense
TCACTGTTGATTTCCATTTTTTGCT 59 627 285 Antisense
TTTGCTCTCGCATTTTGTTTTTCAT 31 669 304 Antisense
GCTCTCGCATTTTGTTTTTCATTAG 492 299 307 Antisense
GTTTTTCATTAGTTGATAATAGCTT 521 449 320 Antisense
CCCATGTTGATGTATTTCGTCCCAG 296 257 387 Antisense
ATGTTGATGTATTTCGTCCCAGCAT 516 47 390 Antisense
GATGTATTTCGTCCCAGCATCAATC 372 409 395 Antisense
Sequence Source Affymetrix Proprietary Database