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[193712_s_at] DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene)

Description C14F11.6 /REP_DB=WormBase Gene ID /WP=CE02482 /TR=Q17993 /GB=AAA80364.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene)
Cluster 6grp_highest_10_10 > 28      6grp_high1_10_10 > 71      4grp_highest_8_8 > 02      4grp_high_8_8 > 54      6grp_highest_nonorm > 25      6grp_total > 71      4grp_total > 57      6grp_highest_sub > 04      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3754
1 2 3 4 range
A 66.4
(-3)
P 		2484.2
(1.7)
P 		3147.3
(3)
P 		158.3
(-2.8)
P 		3081
B 95
(-3)
P 		3248.7
(2.1)
P 		3819.9
(3)
P 		200.7
(-2.8)
P 		3725
C 89.3
(-3)
P 		3238.2
(2.2)
P 		3740.9
(3)
P 		190.5
(-2.8)
P 		3652
avr 83.6
(-3) 		2990.4
(2) 		3569.4
(3) 		183.2
(-2.8) 		3486

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8737
1 2 3 4 5 6 range
A 1357.8
(-2.8)
P 		2659.5
(-1.9)
P 		6422.9
(0.7)
P 		9808.8
(3)
P 		4701.8
(-0.5)
P 		1071.6
(-3)
P 		8737
B 1181.2
(-3)
P 		2396.3
(-2.1)
P 		5400.6
(0.3)
P 		8949.3
(3)
P 		5101.4
(0)
P 		1209.5
(-3)
P 		7768
C 1142.6
(-3)
P 		2606.4
(-1.8)
P 		5623.3
(0.7)
P 		8435.1
(3)
P 		4247.8
(-0.4)
P 		1449.7
(-2.7)
P 		7293
avr 1227.2
(-3) 		2554.1
(-2) 		5815.6
(0.5) 		9064.4
(3) 		4683.7
(-0.4) 		1243.6
(-3) 		7837
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1281
1 2 3 4 range
A 24.2
(-3)
P 		539.2
(0.9)
P 		822.8
(3)
P 		23.2
(-3)
P 		800
B 30.3
(-3)
P 		802.4
(2.4)
P 		885.2
(3)
P 		42.8
(-2.9)
P 		855
C 29.6
(-3)
P 		931
(1.2)
P 		1303.8
(3)
P 		32.1
(-3)
P 		1274
avr 28
(-3) 		757.5
(1.5) 		1003.9
(3) 		32.7
(-3) 		976

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2237
1 2 3 4 5 6 range
A 250.3
(-3)
P 		945.8
(-1.1)
P 		1398.8
(0.1)
P 		2487.7
(3)
P 		1418.8
(0.1)
P 		260.9
(-3)
P 		2237
B 411
(-3)
P 		797.6
(-1.8)
P 		1311.4
(-0.2)
P 		2370.4
(3)
P 		2072.7
(2.1)
P 		451
(-2.9)
P 		1959
C 423.5
(-3)
P 		795.3
(-1.2)
P 		1431.2
(1.8)
P 		1696.3
(3)
P 		1374.5
(1.5)
P 		485.3
(-2.7)
P 		1273
avr 361.6
(-3) 		846.2
(-1.4) 		1380.5
(0.4) 		2184.8
(3) 		1622
(1.1) 		399.1
(-2.9) 		1823
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193712_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17082
Sequence Type Exemplar sequence
Representative Public ID C14F11.6 NCBI
Target Description C14F11.6 /REP_DB=WormBase Gene ID /WP=CE02482 /TR=Q17993 /GB=AAA80364.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene)
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_076645(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076645 NCBI Caenorhabditis elegans C14F11.6 (C14F11.6) mRNA, complete cds. 11/11 None
SNAP00000008176 ENSEMBL cdna:SNAP chromosome:CEL140:X:6238188:6239015:-1 11/11 None
GENEFINDER00000008183 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6238188:6239015:-1 11/11 None
C14F11.6 ENSEMBL cdna:known chromosome:CEL140:X:6238084:6239044:-1 gene:C14F11.6 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
chrX:6238187-6239015(-) 100.0 100.0
Public Domain and Genome References
Gene Title DTDP-4-dehydrorhamnose 3,5-epimerase (RFBC gene)
Ensembl C14F11.6
Entrez Gene 180896 Entrez gene
SwissProt Q17993 EMBL-EBI
WormBase CE02482 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
9103 lipopolysaccharide biosynthesis inferred from electronic annotation QuickGO AmiGO
9273 cell wall biosynthesis (sensu Bacteria) inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3824 catalytic activity inferred from electronic annotation QuickGO AmiGO
8830 dTDP-4-dehydrorhamnose 3,5-epimerase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA80364 Hypothetical protein C14F11.6 [Caenorhabditis elegans] ref|NP_509046.1| C14F11.6 [Caenorhabditis elegans] 1.0E-110
blast CAE61216 Hypothetical protein CBG05010 [Caenorhabditis briggsae] 1.0E-107
blast AAZ66345 RmlC [Listonella anguillarum] 4.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR000888 EMBL-EBI dTDP-4-dehydrorhamnose 3,5-epimerase related 5.9E-111
Sequence
Target Sequence 
>C. ELEGANS:193712_S_AT
atgtcgcatcctactccaggaaaacgtttccaactcgagaaagaagtcatcgaggctatc
ccggaccttcttgtcattaagccaaaggtgttcccagacgagcgtggtttcttttccgag
agttacaacaaaactgaatgggcagagaaaatcggctacactgaggatcttcaacaggat
aaccactcgttctcccattatggcgttctccgtggtcttcatacccaaccacacatggga
aaattagttactgtggttagcggcgagatcttcgatgtggctgttgacattcgcaaggac
agtccaacgtacggaaaatggcatggagtggttctcaacggagataataagcacgcattc
tggattccagccgggttccttcacggattccaagttctcagcaaagaaggagctcatgtc
acttataagtgctccgctgtttacgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTCGCATCCTACTCCAGGAAAAC 65 49 13 Antisense
AAAGAAGTCATCGAGGCTATCCCGG 648 121 52 Antisense
TCCCGGACCTTCTTGTCATTAAGCC 15 597 71 Antisense
AAGCCAAAGGTGTTCCCAGACGAGC 199 147 91 Antisense
AAATCGGCTACACTGAGGATCTTCA 662 117 161 Antisense
CAACAGGATAACCACTCGTTCTCCC 299 189 184 Antisense
GCGGCGAGATCTTCGATGTGGCTGT 74 295 272 Antisense
GTGGCTGTTGACATTCGCAAGGACA 245 491 289 Antisense
TAAGCACGCATTCTGGATTCCAGCC 477 637 360 Antisense
GTTCCTTCACGGATTCCAAGTTCTC 292 395 387 Antisense
TTATAAGTGCTCCGCTGTTTACGAT 367 659 435 Antisense
Sequence Source Affymetrix Proprietary Database