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[192340_at] long-chain-fatty-acid-CoA ligase

Description R09E10.4 /REP_DB=WormBase Gene ID /WP=CE06286 /TR=Q21873 /GB=CAA94299.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=long-chain-fatty-acid-CoA ligase
Cluster 6grp_total > 99      4grp_total > 18      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 3.4
(-2.7)
A 		7.6
(3)
A 		3.2
(-3)
A 		4.4
(-1.4)
A 		4
B 4.9
(1.8)
A 		4.8
(1.6)
A 		2.4
(-3)
A 		5.5
(3)
A 		3
C 2
(-3)
A 		6.9
(-1.6)
A 		2.3
(-2.9)
A 		23.1
(3)
A 		21
avr 3.4
(-2.4) 		6.4
(-0.3) 		2.6
(-3) 		11
(3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 4.7
(1)
A 		3.8
(-1)
A 		5.1
(1.9)
A 		3.8
(-1)
A 		5.6
(3)
A 		2.9
(-3)
A 		3
B 3.1
(-2.9)
A 		2.8
(-3)
A 		5.5
(-1.8)
A 		3.5
(-2.7)
A 		16
(3)
A 		3.6
(-2.6)
A 		13
C 4.3
(-1.7)
A 		4.4
(-1.7)
A 		2.3
(-2.7)
A 		4
(-1.9)
A 		1.6
(-3)
A 		14.2
(3)
A 		13
avr 4
(-2.6) 		3.7
(-3) 		4.3
(-2.1) 		3.8
(-2.9) 		7.7
(3) 		6.9
(1.8) 		4
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3
1 2 3 4 range
A 1.2
(0.6)
A 		1.6
(3)
A 		0.8
(-1.8)
A 		0.6
(-3)
A 		1
B 1.6
(3)
A 		1.2
(0.8)
A 		0.5
(-3)
A 		1.2
(0.8)
A 		1
C 0.7
(-3)
A 		2
(-0.6)
A 		0.8
(-2.8)
A 		3.9
(3)
A 		3
avr 1.2
(-0.5) 		1.6
(1.5) 		0.7
(-3) 		1.9
(3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6
1 2 3 4 5 6 range
A 0.9
(-1.8)
A 		1.4
(1.2)
A 		1.1
(-0.6)
A 		1
(-1.2)
A 		1.7
(3)
A 		0.7
(-3)
A 		1
B 1.1
(-2.8)
A 		0.9
(-3)
A 		1.3
(-2.6)
A 		0.9
(-3)
A 		6.5
(3)
A 		1.3
(-2.6)
A 		6
C 1.6
(-1.5)
A 		1.4
(-1.7)
A 		0.6
(-2.9)
A 		0.8
(-2.6)
A 		0.5
(-3)
A 		4.8
(3)
A 		4
avr 1.2
(-2.1) 		1.2
(-2.1) 		1
(-2.7) 		0.9
(-3) 		2.9
(3) 		2.3
(1.2) 		2
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192340_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9830
Sequence Type Exemplar sequence
Representative Public ID R09E10.4 NCBI
Target Description R09E10.4 /REP_DB=WormBase Gene ID /WP=CE06286 /TR=Q21873 /GB=CAA94299.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=long-chain-fatty-acid-CoA ligase
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_069490(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069490 NCBI Caenorhabditis elegans R09E10.4 (R09E10.4) mRNA, complete cds. 11/11 None
SNAP00000005971 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10306116:10307851:-1 10/11 None
GENEFINDER00000005981 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10306116:10313577:-1 10/11 None
R09E10.4 ENSEMBL cdna:known chromosome:CEL140:IV:10306145:10307851:-1 gene:R09E10.4 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
chrIV:10306121-10307857(-) 100.0 100.0
Public Domain and Genome References
Gene Title long-chain-fatty-acid-CoA ligase
Ensembl R09E10.4
Entrez Gene 187742 Entrez gene
SwissProt Q21873 EMBL-EBI
WormBase CE36448 Wormbase
Functional Annotations
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
3824 catalytic activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA94299 Hypothetical protein R09E10.4 [Caenorhabditis elegans] ref|NP_501891.2| R09E10.4 [Caenorhabditis elegans] 0.0
blast AAB66234 Hypothetical protein R07C3.4 [Caenorhabditis elegans] ref|NP_493856.1| R07C3.4 [Caenorhabditis elegans] 0.0
blast CAA94298 Hypothetical protein R09E10.3 [Caenorhabditis elegans] ref|NP_501893.1| R09E10.3 [Caenorhabditis elegans] 0.0
blast CAE60718 Hypothetical protein CBG04390 [Caenorhabditis briggsae] 0.0
blast AAB66234 Hypothetical protein R07C3.4 [Caenorhabditis elegans] ref|NP_493856.1| R07C3.4 [Caenorhabditis elegans] 1.0E-157
Protein Families
Method ID Description E-Value
ec 4CL1_ARATH (Q42524) 4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1) 5.0E-65
ec 4CL1_ARATH (Q42524) 4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1) 1.0E-111
Protein Domains
Database ID Description E-Value
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 5.0E-32
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 7.7E-32
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 5.7E-35
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 3.3E-40
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 3.6E-24
Sequence
Target Sequence 
>C. ELEGANS:192340_AT
gctgacccatttaaacttgtgctccacaacaatggcatttgaagaattcgagcatgtcga
aggagaacaggattcgtatctatcttatcttccgttggctcatatgtacgaaagacactg
tactctagagcacactttaaaatcggatcgtaagattattttctcgaaaattgggttttc
tcgaggtgatccagatcttttagtggaagacattcaggcactgggtccacgtacatttgc
taccgttccccgcgttttagacaagatttataagtctgtaatgaagcaaatacaaaataa
acctgtgaaaaagatgattctaaactctgccattgcatacaaattgtatcattacaaaat
aaccggaaaagctactcgggatactttggtggacaagtatattctgcacaagattcaaat
gatgctcggtcctaacatcaagcaatttctgatagcggctgcaaaaacagataaatcatt
gttgaaatttgctcgtggagcttttgggattgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTGACCCATTTAAACTTGTGCTCC 117 297 885 Antisense
CTTGTGCTCCACAACAATGGCATTT 176 219 900 Antisense
CGTATCTATCTTATCTTCCGTTGGC 430 247 959 Antisense
GACACTGTACTCTAGAGCACACTTT 389 367 998 Antisense
GGGTTTTCTCGAGGTGATCCAGATC 564 495 1057 Antisense
TCCCCGCGTTTTAGACAAGATTTAT 418 597 1131 Antisense
GATTCTAAACTCTGCCATTGCATAC 7 431 1200 Antisense
GATTCAAATGATGCTCGGTCCTAAC 278 431 1296 Antisense
TCGGTCCTAACATCAAGCAATTTCT 12 605 1310 Antisense
AGCAATTTCTGATAGCGGCTGCAAA 44 77 1325 Antisense
TGCTCGTGGAGCTTTTGGGATTGAA 386 581 1374 Antisense
Sequence Source Affymetrix Proprietary Database