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[175960_s_at]

Description R13A5.9 /REP_DB=WormBase Gene ID /WP=CE01381 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 50      4grp_high_8_8 > 33      6grp_highest_nonorm > 60      6grp_total > 15      4grp_total > 46      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 636
1 2 3 4 range
A 890.3
(3)
P 		548.2
(-0.2)
P 		283.6
(-2.7)
P 		256.8
(-3)
P 		634
B 893.1
(3)
P 		497.8
(-1.2)
P 		339.3
(-2.9)
P 		327.5
(-3)
P 		566
C 868.3
(3)
P 		340
(-2.6)
P 		384.3
(-2.1)
P 		301.9
(-3)
P 		566
avr 883.9
(3) 		462
(-1.3) 		335.7
(-2.6) 		295.4
(-3) 		589

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 548
1 2 3 4 5 6 range
A 728.8
(3)
P 		650.4
(2)
P 		268
(-2.6)
P 		338.2
(-1.8)
P 		237.4
(-3)
P 		305.7
(-2.2)
P 		491
B 777.4
(3)
P 		639.2
(1.5)
P 		408.5
(-1)
P 		260.9
(-2.7)
P 		236.8
(-2.9)
P 		229.6
(-3)
P 		548
C 742.9
(3)
P 		549.7
(0.7)
P 		364.8
(-1.5)
P 		327.2
(-1.9)
P 		235.4
(-3)
P 		280.1
(-2.5)
P 		508
avr 749.7
(3) 		613.1
(1.4) 		347.1
(-1.7) 		308.8
(-2.2) 		236.5
(-3) 		271.8
(-2.6) 		513
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 287
1 2 3 4 range
A 324.1
(3)
P 		119
(-1.3)
P 		74.1
(-2.2)
P 		37.6
(-3)
P 		287
B 284.8
(3)
P 		122.9
(-1.5)
P 		78.6
(-2.8)
P 		69.8
(-3)
P 		215
C 287.4
(3)
P 		97.7
(-1.8)
P 		133.9
(-0.9)
P 		50.9
(-3)
P 		237
avr 298.8
(3) 		113.2
(-1.5) 		95.5
(-2) 		52.8
(-3) 		246

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 217
1 2 3 4 5 6 range
A 134.4
(-0.4)
P 		231.3
(3)
P 		58.4
(-3)
P 		85.8
(-2)
P 		71.6
(-2.5)
P 		74.4
(-2.4)
P 		173
B 270.5
(3)
P 		212.8
(1.3)
P 		99.2
(-2.1)
P 		69.1
(-3)
P 		96.2
(-2.2)
P 		85.6
(-2.5)
P 		201
C 275.4
(3)
P 		167.7
(-0.1)
P 		92.8
(-2.2)
P 		65.8
(-3)
P 		76.2
(-2.7)
P 		93.8
(-2.2)
P 		210
avr 226.8
(3) 		203.9
(2.1) 		83.5
(-2.6) 		73.6
(-3) 		81.3
(-2.7) 		84.6
(-2.6) 		153
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175960_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7104
Sequence Type Exemplar sequence
Representative Public ID R13A5.9 NCBI
Target Description R13A5.9 /REP_DB=WormBase Gene ID /WP=CE01381 /SUBMIT=ST.LOUIS /CHR=3 /FEA=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_066261(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066261 NCBI Caenorhabditis elegans R13A5.9 (R13A5.9) mRNA, complete cds. 11/11 None
SNAP00000038249 ENSEMBL cdna:SNAP chromosome:CEL140:III:7575382:7579327:-1 11/11 None
GENEFINDER00000038255 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7575382:7579327:-1 11/11 None
R13A5.9 ENSEMBL cdna:known chromosome:CEL140:III:7575196:7579329:-1 gene:R13A5.9 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:7575379-7579325(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl R13A5.9
Entrez Gene 176073 Entrez gene
SwissProt Q95Y88 EMBL-EBI
WormBase CE01381 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604985_AT similar to CG12858-PA cfa
CANINE_2:CFAAFFX.14924.1.S1_AT similar to CG12858-PA cfa
DROSOPHILA_2:1635705_AT dm
DROSGENOME1:147219_AT dm
CHICKEN:GGA.16264.1.S1_AT similar to FLJ20160 protein gga
CHICKEN:GGAAFFX.1525.1.S1_AT similar to FLJ20160 protein gga
HG-U133A:219858_S_AT FLJ20160 protein hs
HG-U133_PLUS_2:219858_S_AT FLJ20160 protein hs
HG-U133A_2:219858_S_AT FLJ20160 protein hs
HU35KSUBA:RC_AA348014_AT FLJ20160 protein hs
U133_X3P:G8923159_3P_A_AT FLJ20160 protein hs
U133_X3P:HS.23412.1.S1_3P_AT FLJ20160 protein hs
HG-U133_PLUS_2:225325_AT FLJ20160 protein hs
HG-U133B:225325_AT FLJ20160 protein hs
HG-U95B:44047_AT FLJ20160 protein hs
HG-U95E:87389_AT FLJ20160 protein hs
HG-U95C:54580_AT FLJ20160 protein hs
HG-U95D:70456_R_AT FLJ20160 protein hs
MOUSE430_2:1419124_AT RIKEN cDNA 2210010L05 gene mm
MOE430A:1419124_AT RIKEN cDNA 2210010L05 gene mm
MOUSE430A_2:1419124_AT RIKEN cDNA 2210010L05 gene mm
MG-U74BV2:116891_AT RIKEN cDNA 2210010L05 gene mm
MG-U74BV2:110754_AT RIKEN cDNA 2210010L05 gene mm
MOE430A:1424463_AT RIKEN cDNA 2210010L05 gene mm
MOUSE430A_2:1424463_AT RIKEN cDNA 2210010L05 gene mm
MOUSE430_2:1424463_AT RIKEN cDNA 2210010L05 gene mm
MOE430A:1424464_S_AT RIKEN cDNA 2210010L05 gene mm
MOUSE430A_2:1424464_S_AT RIKEN cDNA 2210010L05 gene mm
MOUSE430_2:1424464_S_AT RIKEN cDNA 2210010L05 gene mm
MG-U74BV2:105696_AT RIKEN cDNA 2210010L05 gene, mRNA (cDNA clone IMAGE:3595801) mm
MU19KSUBC:TC37200_AT RIKEN cDNA 2210010L05 gene, mRNA (cDNA clone IMAGE:3595801) mm
Protein Similarities
Method ID Description E-Value
blast AAK84470 Hypothetical protein R13A5.9 [Caenorhabditis elegans] ref|NP_498662.1| R13A5.9 [Caenorhabditis elegans] 0.0
blast CAE64444 Hypothetical protein CBG09151 [Caenorhabditis briggsae] 0.0
blast AAF58217 CG12858-PA [Drosophila melanogaster] ref|NP_610983.1| CG12858-PA [Drosophila melanogaster] 3.0E-76
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498662.1 12 21-43,53-75,87-109,223-245,265-282,302-321,385-407,417-439,446-468,478-500,513-535,540-562
R13A5.9 12 21-43,53-75,87-109,223-245,265-282,302-321,385-407,417-439,446-468,478-500,513-535,540-562
SNAP00000038249 12 21-43,53-75,87-109,223-245,265-282,302-321,385-407,417-439,446-468,478-500,513-535,540-562
GENEFINDER00000038255 12 21-43,53-75,87-109,223-245,265-282,302-321,385-407,417-439,446-468,478-500,513-535,540-562
Sequence
Target Sequence 
>C. ELEGANS:175960_S_AT
atctgtggtcaatcacgcatccgagattatcacatatttctatgttttcaaactgattaa
taagtatggacatgtccgcgtcatgtacctgtgtctggctgtcaatttcttccgtttcat
ggcactctcaattcttgataatccatggatggtccttccacttcagatcttgcagggagc
ttgcctcgccactgtctggtcttgcgcatcatcgtatatttcgcttgttgctccaccaca
cgccaaacaacatgctcaatatgctcttcaagtagggtatcacggaattggaaaaggtct
cggatcaataattggtggatccgtgatctcgatcattggaacacgaacaacttttgtgat
ttatggattgatttgtcttgcgacatgtgctggaagttttggtctgaataagctgttcaa
gtatgaaggaatcaagtatggagctgggaatttcgaagaagaagatatggatattatggc
accacaaggagtcccgatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCTGTGGTCAATCACGCATCCGAG 380 33 1281 Antisense
ATGGACATGTCCGCGTCATGTACCT 12 53 1346 Antisense
CTGTCAATTTCTTCCGTTTCATGGC 571 239 1379 Antisense
GTTTCATGGCACTCTCAATTCTTGA 698 449 1394 Antisense
TAATCCATGGATGGTCCTTCCACTT 315 635 1419 Antisense
TCCTTCCACTTCAGATCTTGCAGGG 486 591 1433 Antisense
CTGGTCTTGCGCATCATCGTATATT 492 239 1476 Antisense
ATCGTATATTTCGCTTGTTGCTCCA 674 35 1491 Antisense
CACACGCCAAACAACATGCTCAATA 579 195 1517 Antisense
TGGTGGATCCGTGATCTCGATCATT 493 553 1593 Antisense
TATGGCACCACAAGGAGTCCCGATG 389 655 1755 Antisense
Sequence Source Affymetrix Proprietary Database