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[190885_at] Nitrogen fixation (NIFS)

Description F13H8.9 /REP_DB=WormBase Gene ID /WP=CE02643 /TR=Q19434 /GB=AAK31490.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Nitrogen fixation (NIFS)
Cluster 6grp_highest_10_10 > 13      6grp_high1_10_10 > 30      4grp_high_8_8 > 33      6grp_highest_nonorm > 90      6grp_total > 33      4grp_total > 47      6grp_high1_sub > 03      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 176.4
(3)
P 		71
(-3)
P 		81.9
(-2.4)
P 		107.2
(-0.9)
A 		105
B 158.1
(3)
P 		112.2
(-0.4)
P 		79.6
(-2.7)
P 		76.1
(-3)
P 		82
C 198.5
(3)
P 		102.7
(-1.4)
P 		68.7
(-3)
P 		92.4
(-1.9)
A 		130
avr 177.7
(3) 		95.3
(-1.9) 		76.7
(-3) 		91.9
(-2.1) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 127
1 2 3 4 5 6 range
A 187.2
(1.8)
P 		154.7
(-0.1)
P 		208.3
(3)
P 		141
(-0.9)
P 		109.7
(-2.7)
P 		103.8
(-3)
P 		105
B 212.7
(2.3)
P 		152.1
(-0.5)
P 		226.9
(3)
P 		109
(-2.6)
P 		100.4
(-3)
P 		102.6
(-2.9)
P 		127
C 152.3
(1)
P 		177.3
(3)
P 		157.9
(1.5)
P 		162
(1.8)
P 		102.1
(-3)
P 		136.7
(-0.2)
P 		75
avr 184.1
(2.1) 		161.4
(0.7) 		197.7
(3) 		137.3
(-0.9) 		104.1
(-3) 		114.4
(-2.3) 		94
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 50
1 2 3 4 range
A 64.2
(3)
P 		15.4
(-3)
P 		21.4
(-2.3)
P 		15.7
(-3)
A 		49
B 50.4
(3)
P 		27.7
(-1)
P 		18.4
(-2.6)
P 		16.2
(-3)
P 		34
C 65.7
(3)
P 		29.5
(-1.3)
P 		23.9
(-2)
P 		15.6
(-3)
A 		50
avr 60.1
(3) 		24.2
(-1.9) 		21.2
(-2.3) 		15.8
(-3) 		44

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 49
1 2 3 4 5 6 range
A 34.5
(-1.1)
P 		55
(3)
P 		45.4
(1.1)
P 		35.8
(-0.9)
P 		33.1
(-1.4)
P 		25.3
(-3)
P 		30
B 74
(3)
P 		50.6
(-0.1)
P 		55.1
(0.5)
P 		28.9
(-3)
P 		40.8
(-1.4)
P 		38.3
(-1.7)
P 		45
C 56.4
(3)
P 		54.1
(2.4)
P 		40.2
(-1.1)
P 		32.6
(-3)
P 		33
(-2.9)
P 		45.8
(0.3)
P 		24
avr 55
(3) 		53.2
(2.5) 		46.9
(0.8) 		32.4
(-3) 		35.6
(-2.2) 		36.5
(-1.9) 		23
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190885_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5024
Sequence Type Exemplar sequence
Representative Public ID F13H8.9 NCBI
Target Description F13H8.9 /REP_DB=WormBase Gene ID /WP=CE02643 /TR=Q19434 /GB=AAK31490.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Nitrogen fixation (NIFS)
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_062857(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062857 NCBI Caenorhabditis elegans F13H8.9 (F13H8.9) mRNA, complete cds. 11/11 None
SNAP00000031308 ENSEMBL cdna:SNAP chromosome:CEL140:II:6279684:6281029:-1 11/11 None
GENEFINDER00000031313 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6279684:6281029:-1 11/11 None
F13H8.9 ENSEMBL cdna:known chromosome:CEL140:II:6279684:6281050:-1 gene:F13H8.9 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
chrII:6279680-6280849(-) 100.0 100.0
Public Domain and Genome References
Gene Title Nitrogen fixation (NIFS)
Ensembl F13H8.9
Entrez Gene 184440 Entrez gene
SwissProt Q19434 EMBL-EBI
WormBase CE02643 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1587162_AT similar to selenocysteine lyase cfa
CANINE_2:CFA.7874.1.A1_AT similar to selenocysteine lyase cfa
CANINE_2:CFAAFFX.19207.1.S1_AT similar to selenocysteine lyase cfa
CHICKEN:GGA.19649.1.S1_S_AT selenocysteine lyase gga
CHICKEN:GGAAFFX.12063.1.A1_S_AT selenocysteine lyase gga
HG-FOCUS:59705_AT selenocysteine lyase hs
HG-U133A_2:59705_AT selenocysteine lyase hs
HG-U133_PLUS_2:59705_AT selenocysteine lyase hs
HG-U133A:59705_AT selenocysteine lyase hs
HG-U95B:59705_AT selenocysteine lyase hs
HG-U133_PLUS_2:219808_AT selenocysteine lyase hs
HG-U133A:219808_AT selenocysteine lyase hs
HG-U133A_2:219808_AT selenocysteine lyase hs
HG-U133_PLUS_2:221575_AT selenocysteine lyase hs
HG-U133A_2:221575_AT selenocysteine lyase hs
HG-U133A:221575_AT selenocysteine lyase hs
HU35KSUBB:RC_Z39043_AT selenocysteine lyase hs
HU35KSUBB:RC_R40043_AT selenocysteine lyase hs
U133_X3P:G7706696_3P_AT selenocysteine lyase hs
U133_X3P:G12653616_3P_AT selenocysteine lyase hs
U133_X3P:HS.289051.0.A3_3P_AT selenocysteine lyase hs
U133_X3P:4855230_3P_S_AT selenocysteine lyase hs
HG-U133_PLUS_2:225791_AT selenocysteine lyase hs
HG-U133B:225791_AT selenocysteine lyase hs
HG-U95B:50845_AT selenocysteine lyase hs
HG-U95B:59707_G_AT selenocysteine lyase hs
HG-U95E:90949_AT selenocysteine lyase hs
HG-U95D:67203_AT Selenocysteine lyase hs
MG-U74BV2:112914_AT selenocysteine lyase mm
MOE430A:1417671_AT selenocysteine lyase mm
MOUSE430A_2:1417671_AT selenocysteine lyase mm
MOUSE430_2:1417671_AT selenocysteine lyase mm
MOE430B:1441192_AT selenocysteine lyase mm
MOUSE430_2:1441192_AT selenocysteine lyase mm
MU19KSUBA:TC16898_AT Selenocysteine lyase, mRNA (cDNA clone MGC:29386 IMAGE:5054691) mm
MU19KSUBA:TC19817_AT Selenocysteine lyase, mRNA (cDNA clone MGC:29386 IMAGE:5054691) mm
RG-U34A:RC_AA893080_AT selenocysteine lyase rn
RAE230A:1374524_AT selenocysteine lyase rn
RAT230_2:1374524_AT selenocysteine lyase rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8152 metabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8483 transaminase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK31490 Hypothetical protein F13H8.9 [Caenorhabditis elegans] ref|NP_495258.1| F13H8.9 [Caenorhabditis elegans] 0.0
blast CAE59281 Hypothetical protein CBG02613 [Caenorhabditis briggsae] 0.0
blast CAE59281 Hypothetical protein CBG02613 [Caenorhabditis briggsae] 1.0E-154
blast AAH79358 Selenocysteine lyase [Rattus norvegicus] ref|NP_001007756.1| selenocysteine lyase [Rattus norvegicus] 2.0E-78
Protein Domains
Database ID Description E-Value
Pfam IPR000192 EMBL-EBI Aminotransferase, class V 1.0E-32
Pfam IPR000192 EMBL-EBI Aminotransferase, class V 7.1E-36
Sequence
Target Sequence 
>C. ELEGANS:190885_AT
cccatttctccattctgatgttgcacaagctgcaggaaagatcccagttaatgttcgatc
gttgagtgccgatgcggttactgtagttggtcacaagttttatggaccgagaagtggagc
gctgatttttaatccgaaatctaaaaggattcctccaatgttattaggtggaaaccaaga
atctggatggagaagcggaactgaaaatactccgatgattgttggattgggagaagctgc
aaaagtttacaatgaaggatttttgaatattgagagtattctacgtcagaatagagatta
ttttgaagaacttttactgaaacgacttcgaaactcgcacataattcattttattggatc
ccagagacttccaaatacatcaagtgtggcttttctggattatccatcccatggctgtga
tctgctggaaaaatgtcaaacattcaacgcttcaactggtgcagcttgtcacaaaaacga
gtgtagtccaattctcaaagcttgtggaattccgtttgcagttgcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCCATTTCTCCATTCTGATGTTGCA 536 259 378 Antisense
GTTCGATCGTTGAGTGCCGATGCGG 289 443 430 Antisense
GGACCGAGAAGTGGAGCGCTGATTT 491 523 481 Antisense
GAAACGACTTCGAAACTCGCACATA 672 357 696 Antisense
ATCCCAGAGACTTCCAAATACATCA 67 39 735 Antisense
GTGTGGCTTTTCTGGATTATCCATC 80 489 761 Antisense
CATCCCATGGCTGTGATCTGCTGGA 542 211 782 Antisense
ATGTCAAACATTCAACGCTTCAACT 400 47 810 Antisense
GCTTCAACTGGTGCAGCTTGTCACA 555 305 826 Antisense
GTGTAGTCCAATTCTCAAAGCTTGT 530 477 858 Antisense
GTGGAATTCCGTTTGCAGTTGCGTC 279 489 881 Antisense
Sequence Source Affymetrix Proprietary Database