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[190400_at] 4-coumarate-CoA ligase

Description F11A3.1 /REP_DB=WormBase Gene ID /WP=CE05585 /TR=Q19339 /GB=CAA94751.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=4-coumarate-CoA ligase
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 57      4grp_highest_8_8 > 21      4grp_high_8_8 > 15      6grp_highest_nonorm > 69      6grp_total > 57      4grp_total > 08      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3849
1 2 3 4 range
A 2620.6
(-2)
P 		2102.6
(-3)
P 		3205.6
(-0.9)
P 		5221.1
(3)
P 		3119
B 2558.4
(-3)
P 		2563.4
(-3)
P 		3662.7
(-1)
P 		5951.3
(3)
P 		3393
C 2848.8
(-2.2)
P 		2418.1
(-3)
P 		3437
(-1.1)
P 		5617
(3)
P 		3199
avr 2675.9
(-2.4) 		2361.4
(-3) 		3435.1
(-1) 		5596.5
(3) 		3235

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3287
1 2 3 4 5 6 range
A 2618.9
(-0.3)
P 		1842.6
(-1.8)
P 		2071.9
(-1.4)
P 		1542.1
(-2.4)
P 		1255
(-3)
P 		4235.9
(3)
P 		2981
B 2747.1
(0.2)
P 		1890.7
(-1.9)
P 		1950.7
(-1.7)
P 		1429.9
(-3)
P 		1455
(-2.9)
P 		3918.4
(3)
P 		2489
C 2915.9
(-0.2)
P 		1802.7
(-2.5)
P 		1930.1
(-2.2)
P 		1933.6
(-2.2)
P 		1537.3
(-3)
P 		4542.3
(3)
P 		3005
avr 2760.6
(-0.1) 		1845.3
(-2.1) 		1984.2
(-1.8) 		1635.2
(-2.5) 		1415.8
(-3) 		4232.2
(3) 		2816
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 812
1 2 3 4 range
A 954.2
(3)
P 		456.4
(-3)
P 		838
(1.6)
P 		764.3
(0.7)
P 		498
B 815.8
(-1.3)
P 		633.1
(-3)
P 		848.7
(-1)
P 		1268.2
(3)
P 		635
C 943
(-0)
P 		695.2
(-3)
P 		1197.9
(3)
P 		947.1
(0)
P 		503
avr 904.3
(1.7) 		594.9
(-3) 		961.5
(2.5) 		993.2
(3) 		398

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1142
1 2 3 4 5 6 range
A 482.8
(-2)
P 		655.3
(-0.5)
P 		451.2
(-2.3)
P 		391.1
(-2.9)
P 		378.7
(-3)
P 		1031.3
(3)
P 		653
B 955.9
(0.2)
P 		629.3
(-1.6)
P 		473.7
(-2.5)
P 		378.7
(-3)
P 		591.2
(-1.8)
P 		1461.1
(3)
P 		1082
C 1080.8
(0.7)
P 		550.1
(-2.1)
P 		491.2
(-2.5)
P 		388.8
(-3)
P 		497.5
(-2.4)
P 		1520.6
(3)
P 		1132
avr 839.8
(-0.1) 		611.6
(-1.6) 		472
(-2.5) 		386.2
(-3) 		489.1
(-2.4) 		1337.7
(3) 		952
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190400_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12059
Sequence Type Exemplar sequence
Representative Public ID F11A3.1 NCBI
Target Description F11A3.1 /REP_DB=WormBase Gene ID /WP=CE05585 /TR=Q19339 /GB=CAA94751.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=4-coumarate-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_073050(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073050 NCBI Caenorhabditis elegans F11A3.1 (F11A3.1) mRNA, complete cds. 11/11 None
SNAP00000010082 ENSEMBL cdna:SNAP chromosome:CEL140:V:9510718:9512923:1 11/11 None
GENEFINDER00000010087 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9510718:9512923:1 11/11 None
F11A3.1.2 ENSEMBL cdna:known chromosome:CEL140:V:9510684:9512982:1 gene:F11A3.1 11/11 None
F11A3.1.1 ENSEMBL cdna:known chromosome:CEL140:V:9510716:9512982:1 gene:F11A3.1 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
chrV:9510717-9512923(+) 100.0 100.0
Public Domain and Genome References
Gene Title 4-coumarate-CoA ligase
Ensembl F11A3.1
Entrez Gene 179330 Entrez gene
SwissProt Q19339 EMBL-EBI
WormBase CE05585 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247380_AT 4-coumarate--CoA ligase family protein / 4-coumaroyl-CoA synthase family protein at
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 CAA94751 Hypothetical protein F11A3.1 [Caenorhabditis elegans] ref|NP_505451.1| F11A3.1 [Caenorhabditis elegans] 0.0
blast CAE72182 Hypothetical protein CBG19289 [Caenorhabditis briggsae] 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-156
Protein Domains
Database ID Description E-Value
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 9.2E-105
Sequence
Target Sequence 
>C. ELEGANS:190400_AT
gttcaatggctagtcatcttcctgatttaagaaatgatcaaccatatggatccgttggaa
aacttgcttcaaatttggttatgaagattgtggaaccaggaaccgacagagagcaaccgg
ttaaccaacgaggagaaatttgtgttcgtggtccaacaattatgcttgggtatctcggaa
gaccagaagcaacagccagcactgtcatcgatggatggcttcacactggagacattggtt
atctcaatgaggatggaaatttgtttattgttgatcgacttaaagagctaatcaaggtca
aagggcttcaagtaccaccagctgaacttgaagatcttcttctatctcatccaaagatta
gagattgtgcagttattggaatcccagatgctaaagctggagaattacctaaagcatttg
ttgtaagagctgataacactctcactgaacaagaagttaaggactttgttaaaccaaaag
tgtctccttacaaacaactcgaaggtggtgtcgaatttattgaagaaattccaaagtccg
cagctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCAATGGCTAGTCATCTTCCTGA 410 445 1052 Antisense
GAGAGCAACCGGTTAACCAACGAGG 465 389 1160 Antisense
GAGAAATTTGTGTTCGTGGTCCAAC 527 389 1184 Antisense
AGCAACAGCCAGCACTGTCATCGAT 209 77 1239 Antisense
ATCGATGGATGGCTTCACACTGGAG 264 35 1258 Antisense
GTCAAAGGGCTTCAAGTACCACCAG 529 461 1348 Antisense
GTACCACCAGCTGAACTTGAAGATC 513 457 1363 Antisense
TGAAGATCTTCTTCTATCTCATCCA 507 575 1380 Antisense
GAGCTGATAACACTCTCACTGAACA 277 387 1478 Antisense
AAGTGTCTCCTTACAAACAACTCGA 644 157 1529 Antisense
GAAGAAATTCCAAAGTCCGCAGCTG 515 339 1573 Antisense
Sequence Source Affymetrix Proprietary Database