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[172208_x_at]

Description C28D4.8 /REP_DB=WormBase Gene ID /WP=CE25790 /TR=Q9NAR1 /GB=CAB97265.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 99      4grp_total > 33      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 45
1 2 3 4 range
A 17.6
(-3)
A 		39
(1.3)
A 		31.6
(-0.2)
A 		47.4
(3)
A 		30
B 4.8
(-2.1)
A 		7.3
(-1.1)
A 		2.6
(-3)
A 		17.3
(3)
A 		15
C 8.5
(-1.7)
A 		15.4
(1.1)
A 		20.1
(3)
A 		5.4
(-3)
A 		15
avr 10.3
(-3) 		20.6
(1.7) 		18.1
(0.6) 		23.4
(3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 47.6
(0.9)
A 		17.1
(-1.8)
A 		36.5
(-0.1)
A 		3.2
(-3)
A 		66.7
(2.5)
A 		72.1
(3)
A 		69
B 6.1
(-3)
A 		22.1
(0.5)
A 		21.6
(0.4)
A 		30.2
(2.3)
A 		32.5
(2.8)
A 		33.2
(3)
A 		27
C 2.8
(-3)
A 		10.2
(-2.4)
A 		5
(-2.8)
A 		36.9
(-0.2)
A 		76.3
(3)
A 		23.3
(-1.3)
A 		74
avr 18.8
(-2.7) 		16.5
(-3) 		21
(-2.4) 		23.4
(-2) 		58.5
(3) 		42.9
(0.8) 		42
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8
1 2 3 4 range
A 6.4
(-3)
A 		8.5
(3)
A 		8.3
(2.4)
A 		6.9
(-1.6)
A 		2
B 1.5
(-1.3)
A 		1.8
(-0.7)
A 		0.6
(-3)
A 		3.7
(3)
A 		3
C 2.8
(-1.1)
A 		4.4
(0.4)
A 		7
(3)
A 		0.9
(-3)
A 		6
avr 3.6
(-3) 		4.9
(1.6) 		5.3
(3) 		3.8
(-2.3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 8.8
(-0.5)
A 		6.1
(-1.4)
A 		7.9
(-0.8)
A 		0.8
(-3)
A 		20.1
(3)
A 		17.6
(2.2)
A 		19
B 2.1
(-3)
A 		7.4
(-0.1)
A 		5.3
(-1.3)
A 		8
(0.2)
A 		13.2
(3)
A 		12.4
(2.6)
A 		11
C 1
(-3)
A 		3.1
(-2.5)
A 		1.3
(-2.9)
A 		7.4
(-1.4)
A 		24.7
(3)
A 		7.8
(-1.3)
A 		24
avr 4
(-3) 		5.5
(-2.4) 		4.8
(-2.7) 		5.4
(-2.5) 		19.3
(3) 		12.6
(0.4) 		15
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172208_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9130
Sequence Type Exemplar sequence
Representative Public ID C28D4.8 NCBI
Target Description C28D4.8 /REP_DB=WormBase Gene ID /WP=CE25790 /TR=Q9NAR1 /GB=CAB97265.1 /SUBMIT=HINXTON /CHR=4 /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_069336(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069336 NCBI Caenorhabditis elegans C28D4.8 (C28D4.8) mRNA, complete cds. 11/11 None
SNAP00000030232 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9747203:9748397:-1 11/11 None
GENEFINDER00000030234 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9747203:9751561:-1 11/11 None
C28D4.8 ENSEMBL cdna:known chromosome:CEL140:IV:9747203:9748397:-1 gene:C28D4.8 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_069334 2/11 Cross Hyb Matching Probes A 
NM_069333 2/11 Cross Hyb Matching Probes A 
NM_069335 3/11 Cross Hyb Matching Probes A 
SNAP00000030229 2/11 Cross Hyb Matching Probes None
SNAP00000030230 2/11 Cross Hyb Matching Probes None
SNAP00000030231 3/11 Cross Hyb Matching Probes None
GENEFINDER00000030235 3/11 Cross Hyb Matching Probes None
GENEFINDER00000030237 2/11 Cross Hyb Matching Probes None
C28D4.7 2/11 Cross Hyb Matching Probes A 
C28D4.4 2/11 Cross Hyb Matching Probes A 
C28D4.5 3/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:9747208-9748403(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl C28D4.8
Entrez Gene 182983 Entrez gene
SwissProt Q9NAR1 EMBL-EBI
WormBase CE25790 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB97265 Hypothetical protein C28D4.8 [Caenorhabditis elegans] ref|NP_501737.1| C28D4.8 [Caenorhabditis elegans] 0.0
blast CAB05125 Hypothetical protein C28D4.5 [Caenorhabditis elegans] ref|NP_501736.1| C28D4.5 [Caenorhabditis elegans] 0.0
blast CAB05128 Hypothetical protein C28D4.4 [Caenorhabditis elegans] ref|NP_501735.1| C28D4.4 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR009658 EMBL-EBI Protein of unknown function DUF1248 1.4E-116
Pfam IPR009658 EMBL-EBI Protein of unknown function DUF1248 1.4E-116
Sequence
Target Sequence 
>C. ELEGANS:172208_X_AT
aggtctcggaatcaagcggaaaatgatcttggcacatatctgcctcatgcggcgaacatg
atcaagagaatatatggaactaatgattaccagcatatcatgtacgtttcatattaccag
ccagatgagatgcaggtacctgatgatttgaatcttgatggaatattctttaaaaatgca
acggaggtaccagatatggatattgtgaaatatgataacactgtgtttccatatgaaaga
tccaagtacatgttaaatcttcttagagatcctgaaggttttggaaaggtagcatacgac
aataatggaaaagtgattggatttggaaatgtgatcatctatccatctggtgaatgtgta
ttgactccactatatgctgatgatagtaaagtggctcaggcaatattcaaaagcatttta
aaagaaattccactcaatgacaagaagcttttgagattccaaataagatcaatcgatcga
tgtgaaaatgcatttgaatggattcaacccttcgttaaaaatccaataagaaaagaaatc
atgggatatatggctggttcttctcatcctccaaccgtcaattacaaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGTCTCGGAATCAAGCGGAAAATG 499 49 445 Antisense
GATCTTGGCACATATCTGCCTCATG 553 419 469 Antisense
CATATCTGCCTCATGCGGCGAACAT 73 215 479 Antisense
TGTACGTTTCATATTACCAGCCAGA 580 559 545 Antisense
CCAGCCAGATGAGATGCAGGTACCT 109 273 561 Antisense
GCAGGTACCTGATGATTTGAATCTT 493 309 576 Antisense
AATGTGATCATCTATCCATCTGGTG 226 163 772 Antisense
GTGTATTGACTCCACTATATGCTGA 122 487 800 Antisense
TGAATGGATTCAACCCTTCGTTAAA 46 575 939 Antisense
GATATATGGCTGGTTCTTCTCATCC 180 427 989 Antisense
CATCCTCCAACCGTCAATTACAAGA 390 211 1009 Antisense
Sequence Source Affymetrix Proprietary Database