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[193256_at] Leucine Rich Repeat (2 copies) (2 domains)

Description B0393.3 /REP_DB=WormBase Gene ID /WP=CE00856 /TR=Q17492 /GB=CAA86056.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains)
Cluster 6grp_total > 78      4grp_total > 56      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 221.4
(1)
A 		152.4
(-3)
P 		256.8
(3)
A 		174.7
(-1.7)
A 		104
B 192.9
(-0.1)
A 		231.8
(2.7)
A 		236.2
(3)
A 		153.5
(-3)
M 		83
C 182.8
(0.1)
A 		186.9
(0.3)
A 		240.8
(3)
P 		121
(-3)
P 		120
avr 199
(0.1) 		190.4
(-0.4) 		244.6
(3) 		149.7
(-3) 		95

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1081
1 2 3 4 5 6 range
A 284.8
(-2.2)
A 		238.3
(-2.4)
A 		147.6
(-3)
A 		260.4
(-2.3)
P 		536.3
(-0.6)
P 		1134.7
(3)
P 		987
B 209.8
(-2.7)
P 		203.5
(-2.7)
A 		156.4
(-3)
P 		271.5
(-2.3)
P 		458.4
(-1.1)
P 		1086.4
(3)
P 		930
C 237.8
(-2.9)
P 		240.9
(-2.9)
M 		218.5
(-3)
P 		281.1
(-2.6)
P 		465.4
(-1.5)
P 		1228.1
(3)
P 		1010
avr 244.1
(-2.6) 		227.6
(-2.7) 		174.2
(-3) 		271
(-2.4) 		486.7
(-1.1) 		1149.7
(3) 		976
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 80.6
(3)
A 		33.1
(-2.2)
P 		67.1
(1.5)
A 		25.6
(-3)
A 		55
B 61.5
(3)
A 		57.3
(2.1)
A 		54.7
(1.6)
A 		32.7
(-3)
M 		29
C 60.5
(0.8)
A 		53.7
(0.1)
A 		83.9
(3)
P 		20.4
(-3)
P 		64
avr 67.5
(2.8) 		48
(0.1) 		68.6
(3) 		26.2
(-3) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 379
1 2 3 4 5 6 range
A 52.5
(-2.5)
A 		84.7
(-1.7)
A 		32.1
(-3)
A 		66
(-2.2)
P 		161.8
(0.2)
P 		276.3
(3)
P 		244
B 73
(-2.4)
P 		67.8
(-2.5)
A 		38
(-3)
P 		71.9
(-2.4)
P 		186.2
(-0.6)
P 		405.1
(3)
P 		367
C 88.2
(-2.4)
P 		73.5
(-2.7)
M 		55.6
(-3)
P 		56.5
(-3)
P 		150.6
(-1.4)
P 		411.1
(3)
P 		356
avr 71.2
(-2.5) 		75.3
(-2.4) 		41.9
(-3) 		64.8
(-2.6) 		166.2
(-0.7) 		364.2
(3) 		322
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193256_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7517
Sequence Type Exemplar sequence
Representative Public ID B0393.3 NCBI
Target Description B0393.3 /REP_DB=WormBase Gene ID /WP=CE00856 /TR=Q17492 /GB=CAA86056.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains)
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_065579(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065579 NCBI Caenorhabditis elegans B0393.3 (B0393.3) mRNA, complete cds. 11/11 None
GENEFINDER00000037574 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4757264:4759506:1 11/11 None
SNAP00000037566 ENSEMBL cdna:SNAP chromosome:CEL140:III:4757267:4759506:1 11/11 None
B0393.3 ENSEMBL cdna:known chromosome:CEL140:III:4757210:4759666:1 gene:B0393.3 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
chrIII:4757266-4759506(+) 100.0 100.0
Public Domain and Genome References
Gene Title Leucine Rich Repeat (2 copies) (2 domains)
Ensembl B0393.3
Entrez Gene 175630 Entrez gene
SwissProt Q17492 EMBL-EBI
WormBase CE00856 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA86056 Hypothetical protein B0393.3 [Caenorhabditis elegans] ref|NP_497980.1| B0393.3 [Caenorhabditis elegans] 0.0
blast CAE71136 Hypothetical protein CBG17991 [Caenorhabditis briggsae] 0.0
blast XP_698524 PREDICTED: similar to F-box and leucine-rich repeat protein 13, partial [Danio rerio] 1.0E-9
Protein Domains
Database ID Description E-Value
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.013
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.83
Pfam IPR001810 EMBL-EBI Cyclin-like F-box 1.5E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.013
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.83
Pfam IPR001810 EMBL-EBI Cyclin-like F-box 1.5E-4
Sequence
Target Sequence 
>C. ELEGANS:193256_AT
tcaatgtggcgtcagttacctccattctcctatcaaagccgcgtcgaaatcgttaacatc
aatgatcgttacccggaagaatacgtagagtccttgtcagtgaatacagcgcaacagatt
cctcgtggacatttgataccagaccttcggcgaggaaatcgctataaaatgcttgacatt
gcgttgaacacttccggagagcagctagttgatccctccatcttcgagcaacacgaccag
gaaaatcaagctccatcattttctccccctggtcctctagctgtattgtctgaaaaagag
caagaagagctcgctcgcatgttaatggagattcagccacctttccaaaatgctgattgg
ttgaattatgacccatatggaatgtcaaatgtcttccaaccttcttataccgactttgaa
aatagcatcacagtcggatcagcaggagcaccaggaccaccaaaagaaaaaggatccgat
aaaattttgaagcattctcgtccgagccga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAATGTGGCGTCAGTTACCTCCAT 638 631 1252 Antisense
TCTCCTATCAAAGCCGCGTCGAAAT 478 595 1277 Antisense
TACAGCGCAACAGATTCCTCGTGGA 142 637 1356 Antisense
GGACATTTGATACCAGACCTTCGGC 285 521 1378 Antisense
GCGTTGAACACTTCCGGAGAGCAGC 171 291 1432 Antisense
GGAGAGCAGCTAGTTGATCCCTCCA 593 517 1447 Antisense
TGGTCCTCTAGCTGTATTGTCTGAA 129 553 1521 Antisense
AAGAGCTCGCTCGCATGTTAATGGA 41 151 1556 Antisense
GATTCAGCCACCTTTCCAAAATGCT 191 431 1581 Antisense
TCAAATGTCTTCCAACCTTCTTATA 295 629 1636 Antisense
TTTGAAGCATTCTCGTCCGAGCCGA 341 665 1737 Antisense
Sequence Source Affymetrix Proprietary Database