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[172228_x_at]

Description R11A5.5 /REP_DB=WormBase Gene ID /WP=CE12730 /TR=O45715 /GB=CAB05595.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 33      4grp_highest_8_8 > 30      4grp_high_8_8 > 05      6grp_highest_nonorm > 51      6grp_total > 11      4grp_total > 04      6grp_highest_sub > 02      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3432
1 2 3 4 range
A 618.5
(-2.5)
P 		349.3
(-3)
P 		416.7
(-2.9)
P 		3737.1
(3)
P 		3388
B 1037.3
(0.5)
P 		379.2
(-3)
P 		468.7
(-2.5)
P 		1519.8
(3)
P 		1141
C 808.6
(-2)
P 		305
(-3)
P 		398.8
(-2.8)
P 		3439.5
(3)
P 		3135
avr 821.5
(-1.9) 		344.5
(-3) 		428.1
(-2.8) 		2898.8
(3) 		2554

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1818
1 2 3 4 5 6 range
A 396.1
(-1.9)
P 		361.8
(-2)
P 		1370.1
(3)
P 		170.1
(-3)
P 		644.4
(-0.6)
P 		165.6
(-3)
P 		1205
B 636.2
(0.5)
P 		890.9
(3)
P 		652
(0.7)
P 		279.5
(-3)
P 		514.4
(-0.7)
P 		291.7
(-2.9)
P 		611
C 276.3
(-2.6)
P 		1960.5
(3)
P 		261
(-2.6)
P 		432.8
(-2)
P 		142.4
(-3)
P 		385.9
(-2.2)
P 		1818
avr 436.2
(-1.8) 		1071.1
(3) 		761
(0.6) 		294.1
(-2.9) 		433.7
(-1.8) 		281.1
(-3) 		790
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 504
1 2 3 4 range
A 225.2
(-1.1)
P 		75.8
(-3)
P 		108.9
(-2.6)
P 		547
(3)
P 		471
B 330.8
(3)
P 		93.6
(-3)
P 		108.6
(-2.6)
P 		323.9
(2.8)
P 		237
C 267.7
(-0.8)
P 		87.7
(-3)
P 		139
(-2.4)
P 		580
(3)
P 		492
avr 274.6
(-0.2) 		85.7
(-3) 		118.8
(-2.5) 		483.6
(3) 		398

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 558
1 2 3 4 5 6 range
A 73
(-2.2)
P 		128.7
(-0.9)
P 		298.4
(3)
P 		43.1
(-2.9)
P 		194.4
(0.6)
P 		40.3
(-3)
P 		258
B 221.4
(1)
P 		296.5
(3)
P 		158.3
(-0.7)
P 		74
(-3)
P 		209
(0.6)
P 		108.8
(-2.1)
P 		223
C 102.4
(-2.4)
P 		598.2
(3)
P 		66.4
(-2.8)
P 		87
(-2.6)
P 		46.1
(-3)
P 		129.2
(-2.1)
P 		552
avr 132.3
(-1.6) 		341.1
(3) 		174.4
(-0.7) 		68
(-3) 		149.8
(-1.2) 		92.8
(-2.5) 		273
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172228_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2519
Sequence Type Exemplar sequence
Representative Public ID R11A5.5 NCBI
Target Description R11A5.5 /REP_DB=WormBase Gene ID /WP=CE12730 /TR=O45715 /GB=CAB05595.1 /SUBMIT=HINXTON /CHR=1 /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_059775(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059775 NCBI Caenorhabditis elegans R11A5.5 (R11A5.5) mRNA, complete cds. 11/11 None
GENEFINDER00000037591 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7875673:7876681:-1 10/11 None
SNAP00000037587 ENSEMBL cdna:SNAP chromosome:CEL140:I:7876340:7883642:-1 11/11 None
R11A5.5 ENSEMBL cdna:known chromosome:CEL140:I:7876340:7876681:-1 gene:R11A5.5 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_077052 1/11 Cross Hyb Matching Probes A 
NM_065168 2/11 Cross Hyb Matching Probes A 
NM_071316 1/11 Cross Hyb Matching Probes A 
GENEFINDER00000002760 1/11 Cross Hyb Matching Probes None
GENEFINDER00000011306 6/11 Cross Hyb Matching Probes None
SNAP00000003365 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003374 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008828 2/11 Cross Hyb Matching Probes None
GENEFINDER00000021430 3/11 Cross Hyb Matching Probes None
SNAP00000021879 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043144 1/11 Cross Hyb Matching Probes None
SNAP00000039716 5/11 Cross Hyb Matching Probes None
GENEFINDER00000039724 5/11 Cross Hyb Matching Probes None
GENEFINDER00000025201 6/11 Cross Hyb Matching Probes None
SNAP00000031960 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031976 1/11 Cross Hyb Matching Probes None
SNAP00000004114 7/11 Cross Hyb Matching Probes None
GENEFINDER00000004194 7/11 Cross Hyb Matching Probes None
SNAP00000006182 2/11 Cross Hyb Matching Probes None
GENEFINDER00000011916 3/11 Cross Hyb Matching Probes None
GENEFINDER00000013167 2/11 Cross Hyb Matching Probes None
GENEFINDER00000017989 2/11 Cross Hyb Matching Probes None
SNAP00000019399 3/11 Cross Hyb Matching Probes None
GENEFINDER00000019412 1/11 Cross Hyb Matching Probes None
SNAP00000021391 3/11 Cross Hyb Matching Probes None
SNAP00000026162 6/11 Cross Hyb Matching Probes None
GENEFINDER00000026170 6/11 Cross Hyb Matching Probes None
GENEFINDER00000027324 2/11 Cross Hyb Matching Probes None
GENEFINDER00000030894 1/11 Cross Hyb Matching Probes None
SNAP00000031789 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031792 1/11 Cross Hyb Matching Probes None
SNAP00000007194 1/11 Cross Hyb Matching Probes None
SNAP00000019039 2/11 Cross Hyb Matching Probes None
GENEFINDER00000019053 2/11 Cross Hyb Matching Probes None
SNAP00000031107 2/11 Cross Hyb Matching Probes None
GENEFINDER00000031114 2/11 Cross Hyb Matching Probes None
SNAP00000035781 5/11 Cross Hyb Matching Probes None
GENEFINDER00000035787 5/11 Cross Hyb Matching Probes None
GENEFINDER00000035790 5/11 Cross Hyb Matching Probes None
GENEFINDER00000041706 4/11 Cross Hyb Matching Probes None
GENEFINDER00000041707 5/11 Cross Hyb Matching Probes None
GENEFINDER00000015658 3/11 Cross Hyb Matching Probes None
SNAP00000008036 1/11 Cross Hyb Matching Probes None
SNAP00000008037 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031395 1/11 Cross Hyb Matching Probes None
SNAP00000031393 1/11 Cross Hyb Matching Probes None
SNAP00000039243 1/11 Cross Hyb Matching Probes None
GENEFINDER00000017316 2/11 Cross Hyb Matching Probes None
SNAP00000039276 4/11 Cross Hyb Matching Probes None
GENEFINDER00000039281 4/11 Cross Hyb Matching Probes None
SNAP00000032586 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032588 1/11 Cross Hyb Matching Probes None
Y54F10AM.7 2/11 Cross Hyb Matching Probes A 
W02H5.5 1/11 Cross Hyb Matching Probes A 
F18E9.6 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Ensembl R11A5.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB05602 Hypothetical protein R11A5.7 [Caenorhabditis elegans] ref|NP_492177.2| R11A5.7 [Caenorhabditis elegans] 0.0
blast CAE63736 Hypothetical protein CBG08265 [Caenorhabditis briggsae] 0.0
blast CAE54930 Hypothetical protein ZC434.9b [Caenorhabditis elegans] ref|NP_001021852.1| ZC434.9b [Caenorhabditis elegans] 1.0E-106
blast CAB05596 Hypothetical protein R11A5.6 [Caenorhabditis elegans] ref|NP_492175.1| R11A5.6 [Caenorhabditis elegans] 2.0E-54
blast NP_492176 R11A5.5 [Caenorhabditis elegans] 1.0E-10
Protein Domains
Database ID Description E-Value
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 1.6E-9
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 3.5E-8
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 2.9E-10
Pfam IPR000834 EMBL-EBI Peptidase M14, carboxypeptidase A 6.4E-41
Pfam IPR000834 EMBL-EBI Peptidase M14, carboxypeptidase A 2.9E-30
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 7.8E-7
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 1.6E-9
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 3.5E-8
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 2.9E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492176.1 3 7-29,39-61,68-90
R11A5.5 3 7-29,39-61,68-90
GENEFINDER00000037591 3 7-29,39-61,68-90
SNAP00000037587 4 638-657,664-686,696-718,725-747
Sequence
Target Sequence 
>C. ELEGANS:172228_X_AT
gccacgatgggtttcaccacgatgggtcttaccacgatgggtctcaccacgacgggtctc
accacggtgggtctcaccacgatgggtctcaccacgatgggtctcgccacgacgggtctc
accacgatgggtctggccacgatgggtatcgccacgatgggtctcaccacgatgggtctc
accacgatgggtttcgccacgatgggtctcgccacgatgggtctcaccacgaaggatgac
agaccccgcccacaattctcagtgactttgggt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCACGATGGGTTTCACCACGATGG 619 279 52 Antisense
GTTTCACCACGATGGGTCTTACCAC 432 449 62 Antisense
CACCACGATGGGTCTTACCACGATG 513 95 66 Antisense
CGATGGGTCTTACCACGATGGGTCT 230 247 71 Antisense
GTCTGGCCACGATGGGTATCGCCAC 393 471 182 Antisense
GCCACGATGGGTATCGCCACGATGG 620 279 187 Antisense
CGATGGGTATCGCCACGATGGGTCT 698 247 191 Antisense
CACGATGGGTCTCACCACGAAGGAT 424 199 264 Antisense
CACCACGAAGGATGACAGACCCCGC 324 195 276 Antisense
CCGCCCACAATTCTCAGTGACTTTG 289 263 297 Antisense
CCCACAATTCTCAGTGACTTTGGGT 29 259 300 Antisense
Sequence Source Affymetrix Proprietary Database