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[193297_at]

Description F56A8.2 /REP_DB=WormBase Gene ID /WP=CE16122 /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains) (HINXTON) TR:O45573 protein_id:CAB05742.1
Cluster 6grp_high1_10_10 > 21      6grp_total > 32      4grp_total > 58      6grp_high1_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 427
1 2 3 4 range
A 300
(-2)
P 		521
(3)
P 		500.8
(2.5)
P 		257.4
(-3)
M 		264
B 338.3
(-1)
P 		524.4
(1.9)
P 		592.6
(3)
P 		208.1
(-3)
A 		385
C 460.3
(0.1)
P 		635.3
(3)
P 		505
(0.9)
P 		270.4
(-3)
A 		365
avr 366.2
(-0.7) 		560.2
(3) 		532.8
(2.5) 		245.3
(-3) 		315

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 223
1 2 3 4 5 6 range
A 337
(2.7)
A 		343.5
(3)
P 		286.3
(0.1)
P 		253.8
(-1.6)
P 		257
(-1.5)
A 		227
(-3)
P 		117
B 285.5
(-0.1)
P 		233.6
(-1.5)
P 		400.5
(3)
P 		321.2
(0.9)
A 		226
(-1.7)
P 		177.6
(-3)
P 		223
C 348.5
(1.8)
P 		263
(-0.7)
P 		301
(0.4)
P 		392
(3)
A 		283.6
(-0.1)
P 		183.2
(-3)
M 		209
avr 323.7
(2.7) 		280
(0.8) 		329.3
(3) 		322.3
(2.7) 		255.5
(-0.3) 		195.9
(-3) 		133
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 145
1 2 3 4 range
A 109.2
(1.6)
P 		113.1
(1.9)
P 		130.9
(3)
P 		37.7
(-3)
M 		93
B 107.9
(1.1)
P 		129.5
(2.5)
P 		137.3
(3)
P 		44.3
(-3)
A 		93
C 152.4
(1.7)
P 		182.6
(3)
P 		176
(2.7)
P 		45.6
(-3)
A 		137
avr 123.2
(1.6) 		141.7
(2.6) 		148.1
(3) 		42.5
(-3) 		106

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 62.1
(-2.4)
A 		122.2
(3)
P 		62.3
(-2.4)
P 		64.4
(-2.2)
P 		77.5
(-1)
A 		55.3
(-3)
P 		67
B 99.3
(3)
P 		77.7
(-0.9)
P 		97.2
(2.6)
P 		85.1
(0.4)
A 		91.8
(1.6)
P 		66.2
(-3)
P 		33
C 129.2
(3)
P 		80.3
(-1.3)
P 		76.6
(-1.6)
P 		78.8
(-1.5)
A 		91.8
(-0.3)
P 		61.3
(-3)
M 		68
avr 96.9
(3) 		93.4
(2.4) 		78.7
(-0) 		76.1
(-0.5) 		87
(1.4) 		60.9
(-3) 		36
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193297_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6266
Sequence Type Exemplar sequence
Representative Public ID F56A8.2 NCBI
Target Description F56A8.2 /REP_DB=WormBase Gene ID /WP=CE16122 /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains) (HINXTON) TR:O45573 protein_id:CAB05742.1
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_067329(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067329 NCBI Caenorhabditis elegans F56A8.3a (F56A8.3) mRNA, complete cds. 10/11 A 
SNAP00000043510 ENSEMBL cdna:SNAP chromosome:CEL140:III:13256420:13257173:1 10/11 None
GENEFINDER00000043517 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13256420:13262052:1 10/11 None
F56A8.3a.3 ENSEMBL cdna:known chromosome:CEL140:III:13256395:13262395:1 gene:F56A8.3 10/11 None
F56A8.3a.1 ENSEMBL cdna:known chromosome:CEL140:III:13256396:13262395:1 gene:F56A8.3 10/11 A 
F56A8.3a.2 ENSEMBL cdna:known chromosome:CEL140:III:13256396:13262399:1 gene:F56A8.3 10/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176740 2 1 NM_067329 193297_at (10)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:13256415-13257215(+) 92.21 100.0
Public Domain and Genome References
Ensembl F56A8.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAC42304 Hypothetical protein F56A8.3a [Caenorhabditis elegans] ref|NP_499730.1| F56A8.3a [Caenorhabditis elegans] 0.0
blast CAE60062 Hypothetical protein CBG03577 [Caenorhabditis briggsae] 1.0E-174
blast CAB05743 Hypothetical protein F56A8.3b [Caenorhabditis elegans] ref|NP_499731.1| F56A8.3b [Caenorhabditis elegans] 1.0E-146
blast CAC42304 Hypothetical protein F56A8.3a [Caenorhabditis elegans] ref|NP_499730.1| F56A8.3a [Caenorhabditis elegans] 1.0E-144
Protein Domains
Database ID Description E-Value
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 4.0E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.041
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 8.5E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499730.1 1 244-266
F56A8.3a.3 1 244-266
F56A8.3a.1 1 244-266
F56A8.3a.2 1 244-266
GENEFINDER00000043517 3 188-210,242-264,342-364
Sequence
Target Sequence 
>C. ELEGANS:193297_AT
tcaagaattccccaatgcaatcgtccaactgccacggttgacgaaattggatctgagctc
aaatgcaatcactttcttgccggaatctttctgcaagatgactaagcttattcggttaga
cttcggaagttgccagcttcatcatctccctgatggaatcgggctcttgacaagcttgca
gcacttgaacctttataacaatcaaatagaggacttgccgctctcgttcgccaacttaaa
atccttgaagtggctggatttgaagaaaaatccgctcaactcgaagctcgccgccatcgc
aggaaactgtgggactgatgccgagtgtaagcaggctgccaagcaagtcgtcgacgttta
tatgggcgagcagaagaaggccatcgatagcctgaaagcccaggaagctaagcataaggc
caaggtgcagaaggcccaggaagaggagagaatgaagaagaatcaggagaaaaaggagaa
ggcggcggctaaaaagggtacatttgcaggaaaaaaaactatagaaatattctggaattt
gagatatcagagcccgttttccattaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAAGAATTCCCCAATGCAATCGTC 5 633 93 Antisense
ATGCAATCACTTTCTTGCCGGAATC 697 43 155 Antisense
GACTTCGGAAGTTGCCAGCTTCATC 388 337 211 Antisense
GAATCGGGCTCTTGACAAGCTTGCA 269 327 248 Antisense
AAATAGAGGACTTGCCGCTCTCGTT 191 117 296 Antisense
GCTCTCGTTCGCCAACTTAAAATCC 98 299 312 Antisense
AAAAATCCGCTCAACTCGAAGCTCG 219 129 358 Antisense
CGCCGCCATCGCAGGAAACTGTGGG 157 257 381 Antisense
GATGCCGAGTGTAAGCAGGCTGCCA 441 415 409 Antisense
GGCCATCGATAGCCTGAAAGCCCAG 233 543 471 Antisense
ATATCAGAGCCCGTTTTCCATTAAT 429 19 636 Antisense
Sequence Source Affymetrix Proprietary Database