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[192253_s_at] long-chain-fatty-acid-CoA ligase

Description R09E10.3 /REP_DB=WormBase Gene ID /WP=CE23909 /TR=Q21872 /GB=CAA94298.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=long-chain-fatty-acid-CoA ligase
Cluster 6grp_total > 87      4grp_total > 03      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 39.6
(0.9)
A 		50.4
(3)
A 		31.1
(-0.8)
A 		19.7
(-3)
A 		31
B 15.5
(-0.7)
A 		11.8
(-1.7)
A 		6.9
(-3)
A 		29.7
(3)
A 		23
C 27.4
(-1.2)
A 		12.9
(-3)
A 		39.2
(0.2)
A 		62.6
(3)
A 		50
avr 27.5
(-1.8) 		25
(-3) 		25.7
(-2.7) 		37.3
(3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 11.5
(-3)
A 		34.3
(-2.2)
A 		29.9
(-2.3)
A 		64.8
(-1)
A 		110.3
(0.6)
A 		175.1
(3)
P 		164
B 18.1
(-2.7)
A 		39.9
(-2.1)
A 		8.3
(-3)
A 		60.7
(-1.4)
A 		85.9
(-0.7)
A 		208.3
(3)
P 		200
C 32.4
(-2.5)
A 		19.3
(-3)
A 		34
(-2.4)
A 		23.8
(-2.8)
A 		82
(-0.6)
A 		174.4
(3)
P 		155
avr 20.7
(-3) 		31.2
(-2.6) 		24.1
(-2.9) 		49.8
(-1.9) 		92.7
(-0.4) 		185.9
(3) 		165
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 14.4
(3)
A 		10.9
(1.2)
A 		8.1
(-0.3)
A 		2.9
(-3)
A 		12
B 4.9
(1.2)
A 		2.9
(-1.3)
A 		1.6
(-3)
A 		6.3
(3)
A 		5
C 9.1
(0.2)
A 		3.7
(-3)
A 		13.7
(3)
A 		10.6
(1.1)
A 		10
avr 9.5
(3) 		5.8
(-3) 		7.8
(0.2) 		6.6
(-1.7) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 76
1 2 3 4 5 6 range
A 2.1
(-3)
A 		12.2
(-1.5)
A 		6.5
(-2.3)
A 		16.4
(-0.9)
A 		33.3
(1.6)
A 		42.6
(3)
P 		41
B 6.3
(-2.7)
A 		13.3
(-2.1)
A 		2
(-3)
A 		16.1
(-1.9)
A 		34.9
(-0.4)
A 		77.7
(3)
P 		76
C 12
(-2.2)
A 		5.9
(-2.9)
A 		8.6
(-2.6)
A 		4.8
(-3)
A 		26.5
(-0.6)
A 		58.4
(3)
P 		54
avr 6.8
(-2.9) 		10.5
(-2.5) 		5.7
(-3) 		12.4
(-2.3) 		31.6
(-0.1) 		59.6
(3) 		54
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192253_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10220
Sequence Type Exemplar sequence
Representative Public ID R09E10.3 NCBI
Target Description R09E10.3 /REP_DB=WormBase Gene ID /WP=CE23909 /TR=Q21872 /GB=CAA94298.2 /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_069492(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069492 NCBI Caenorhabditis elegans R09E10.3 (R09E10.3) mRNA, complete cds. 11/11 None
SNAP00000005973 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10310769:10315827:-1 10/11 None
GENEFINDER00000005981 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10306116:10313577:-1 9/11 None
R09E10.3 ENSEMBL cdna:known chromosome:CEL140:IV:10310769:10313595:-1 gene:R09E10.3 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:10310774-10313583(-) 100.0 100.0
Public Domain and Genome References
Gene Title long-chain-fatty-acid-CoA ligase
Ensembl R09E10.3
Entrez Gene 177918 Entrez gene
SwissProt Q21872 EMBL-EBI
WormBase CE23909 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 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] 0.0
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) 1.0E-108
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 5.7E-35
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 3.3E-40
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 IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 6.4E-24
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 3.6E-24
Sequence
Target Sequence 
>C. ELEGANS:192253_S_AT
gaagcaactgcatcatctttcactgaagatggatacatgaaaactggagatattggaaga
ttcactgctgaaggatctcttcaaattattgatcgacgcaaaaacgttttcaaaatgcca
caaggaaagtttgtggctccagatctcacagaatccctctacacttcttcgagttttgtc
caacagatttacgttcatggcgatatggaaaaaccgtggcttgtagcaatcgttgtccca
gatccagagtatcttgcttcatatgcgctaaccaaacacaacatcaatgggaaaacctat
gaacaattgtgcaacattccgattctcgcagatgatgtgctgcgacaatttgtagaactc
acagaagaagataaaaggccaagatatgaaggggtgtacggcgttcacttgacgccagtt
gctttttcggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGCAACTGCATCATCTTTCACTG 459 341 1558 Antisense
AGATTCACTGCTGAAGGATCTCTTC 706 65 1615 Antisense
GAAAGTTTGTGGCTCCAGATCTCAC 171 361 1682 Antisense
TCCCTCTACACTTCTTCGAGTTTTG 270 597 1711 Antisense
TGTCCAACAGATTTACGTTCATGGC 1 557 1734 Antisense
CGTGGCTTGTAGCAATCGTTGTCCC 114 243 1772 Antisense
ATCGTTGTCCCAGATCCAGAGTATC 332 35 1786 Antisense
GTATCTTGCTTCATATGCGCTAACC 606 453 1806 Antisense
TGTGCAACATTCCGATTCTCGCAGA 429 555 1865 Antisense
GGGTGTACGGCGTTCACTTGACGCC 84 497 1949 Antisense
ACTTGACGCCAGTTGCTTTTTCGGC 387 101 1964 Antisense
Sequence Source Affymetrix Proprietary Database