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[181096_at]

Description F54D8.1 /REP_DB=WormBase Gene ID /WP=CE11066 /TR=Q20778 /GB=AAA20613.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 57      6grp_highest_nonorm > 99      6grp_total > 58      4grp_total > 09      6grp_highest_sub > Cu      6grp_cgc > 28      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 637
1 2 3 4 range
A 45.3
(-3)
A 		125.7
(-2.1)
M 		211.6
(-1.2)
P 		611.3
(3)
P 		566
B 54.3
(-3)
A 		156.8
(-2)
P 		120.2
(-2.4)
P 		681.9
(3)
P 		628
C 68.2
(-3)
M 		99
(-2.6)
P 		135.3
(-2.2)
P 		557.8
(3)
P 		490
avr 55.9
(-3) 		127.2
(-2.2) 		155.7
(-1.9) 		617
(3) 		561

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3035
1 2 3 4 5 6 range
A 1542.5
(-0.2)
P 		270.1
(-2.7)
P 		159.3
(-3)
P 		139.9
(-3)
P 		317.5
(-2.6)
P 		3174.5
(3)
P 		3035
B 1558.6
(-0)
P 		314.6
(-2.7)
P 		150.7
(-3)
P 		156.5
(-3)
P 		313
(-2.7)
P 		3014.1
(3)
P 		2863
C 1716.8
(1.4)
P 		310.3
(-2.5)
P 		148.2
(-3)
P 		193.6
(-2.9)
P 		301.9
(-2.6)
P 		2299.1
(3)
P 		2151
avr 1606
(0.3) 		298.3
(-2.7) 		152.7
(-3) 		163.3
(-3) 		310.8
(-2.6) 		2829.2
(3) 		2677
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 129
1 2 3 4 range
A 16.5
(-3)
A 		27.3
(-2.1)
M 		55.3
(0.2)
P 		89.5
(3)
P 		73
B 17.3
(-3)
A 		38.7
(-2)
P 		27.9
(-2.5)
P 		145.3
(3)
P 		128
C 22.6
(-3)
M 		28.5
(-2.5)
P 		47.1
(-0.9)
P 		94
(3)
P 		71
avr 18.8
(-3) 		31.5
(-2.2) 		43.4
(-1.4) 		109.6
(3) 		91

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1089
1 2 3 4 5 6 range
A 284.3
(-1)
P 		96.1
(-2.5)
P 		34.7
(-3)
P 		35.5
(-3)
P 		95.8
(-2.5)
P 		772.9
(3)
P 		738
B 542.3
(-0.2)
P 		104.7
(-2.6)
P 		36.6
(-3)
P 		41.5
(-3)
P 		127.2
(-2.5)
P 		1123.9
(3)
P 		1087
C 636.4
(1.9)
P 		94.7
(-2.5)
P 		37.7
(-3)
P 		38.9
(-3)
P 		97.7
(-2.5)
P 		769.7
(3)
P 		732
avr 487.7
(0.2) 		98.5
(-2.6) 		36.3
(-3) 		38.6
(-3) 		106.9
(-2.5) 		888.8
(3) 		853
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 181096_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6955
Sequence Type Exemplar sequence
Representative Public ID F54D8.1 NCBI
Target Description F54D8.1 /REP_DB=WormBase Gene ID /WP=CE11066 /TR=Q20778 /GB=AAA20613.1 /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_065685(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065685 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-17) (dpy-17) mRNA, complete cds. 11/11 None
SNAP00000022628 ENSEMBL cdna:SNAP chromosome:CEL140:III:5107290:5108400:1 11/11 None
GENEFINDER00000022631 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5107290:5108400:1 11/11 None
F54D8.1.1 ENSEMBL cdna:known chromosome:CEL140:III:5107285:5108637:1 gene:F54D8.1 11/11 None
F54D8.1.3 ENSEMBL cdna:known chromosome:CEL140:III:5107285:5108637:1 gene:F54D8.1 11/11 None
F54D8.1.2 ENSEMBL cdna:known chromosome:CEL140:III:5107287:5108637:1 gene:F54D8.1 11/11 None
F54D8.1.4 ENSEMBL cdna:known chromosome:CEL140:III:5107290:5108458:1 gene:F54D8.1 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:5107288-5108399(+) 96.88 100.0
Public Domain and Genome References
Gene Title
Gene Symbol dpy-17
Ensembl F54D8.1
Entrez Gene 175696 Entrez gene
SwissProt Q20778 EMBL-EBI
WormBase CE11066 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK84534 Dumpy : shorter than wild-type protein 17 [Caenorhabditis elegans] ref|NP_498086.1| DumPY : shorter than wild-type family member (dpy-17) [Caenorhabditis elegans] 1.0E-107
blast H88449 protein F54D8.1 [imported] - Caenorhabditis elegans 1.0E-107
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498086.1 1 3-25
F54D8.1.1 1 3-25
F54D8.1.3 1 3-25
F54D8.1.2 1 3-25
F54D8.1.4 1 3-25
SNAP00000022628 1 3-25
GENEFINDER00000022631 1 3-25
Sequence
Target Sequence 
>C. ELEGANS:181096_AT
tgcaacaccgaaaactcatgcccagctggaccagccggaccaaagggaactccaggacat
gatggaccagatggaattccaggagttccaggagttgacggagaagatgctgatgatgcc
aaggctcagactcaacaatacgatggatgcttcacttgcccagctggaccacaaggacca
ccaggatcccaaggaaagccaggagcccgtggaatgcgtggagcccgtggacaagccgct
atgccaggaagagacggatccccaggaatgcccggatctttgggaccaattggaccacca
ggagccgctggagaagaaggaccaactggagagccaggagccgatgttgaacaccaaatc
ggacttccag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCAACACCGAAAACTCATGCCCAG 249 577 451 Antisense
GACCAAAGGGAACTCCAGGACATGA 424 383 488 Antisense
AGGAGTTGACGGAGAAGATGCTGAT 229 57 540 Antisense
GCTGATGATGCCAAGGCTCAGACTC 586 295 559 Antisense
GCCAAGGCTCAGACTCAACAATACG 400 277 568 Antisense
ACAATACGATGGATGCTTCACTTGC 230 115 585 Antisense
CGTGGACAAGCCGCTATGCCAGGAA 651 243 676 Antisense
CAAGCCGCTATGCCAGGAAGAGACG 475 183 682 Antisense
CCCCAGGAATGCCCGGATCTTTGGG 115 261 710 Antisense
ATGCCCGGATCTTTGGGACCAATTG 519 39 718 Antisense
GTTGAACACCAAATCGGACTTCCAG 53 439 796 Antisense
Sequence Source Affymetrix Proprietary Database