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[173302_at]

Description CEK027H1R_rc /REP_DB=TREMBL Accession /GB=D33221 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk27h1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 77      4grp_highest_8_8 > 25      4grp_high_8_8 > 59      6grp_highest_nonorm > 93      6grp_total > 67      4grp_total > 60      6grp_highest_sub > Da      6grp_cgc > 48      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 257
1 2 3 4 range
A 284.4
(2)
P 		245.3
(0.8)
P 		316
(3)
P 		125.9
(-3)
P 		190
B 295.4
(2)
P 		329.7
(3)
P 		301.9
(2.2)
P 		132.2
(-3)
P 		198
C 364.1
(2.5)
P 		274.5
(0.1)
P 		382.6
(3)
P 		159.3
(-3)
P 		223
avr 314.6
(2.4) 		283.2
(1.4) 		333.5
(3) 		139.1
(-3) 		194

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 853
1 2 3 4 5 6 range
A 289
(-2.8)
P 		309.5
(-2.5)
P 		302.1
(-2.6)
P 		265.8
(-3)
P 		382.2
(-1.8)
P 		838.4
(3)
P 		573
B 289.7
(-2.8)
P 		323.7
(-2.5)
P 		260.9
(-3)
P 		340.9
(-2.3)
P 		285
(-2.8)
P 		959.4
(3)
P 		699
C 244.4
(-3)
P 		306.4
(-2.6)
P 		278.2
(-2.8)
P 		303.2
(-2.6)
P 		285.1
(-2.7)
P 		1097.3
(3)
P 		853
avr 274.4
(-3) 		313.2
(-2.7) 		280.4
(-2.9) 		303.3
(-2.7) 		317.4
(-2.6) 		965
(3) 		691
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 103.5
(3)
P 		53.3
(-0.5)
P 		82.6
(1.5)
P 		18.4
(-3)
P 		85
B 94.2
(3)
P 		81.4
(1.8)
P 		70
(0.8)
P 		28.2
(-3)
P 		66
C 120.5
(2.3)
P 		78.9
(-0.1)
P 		133.4
(3)
P 		26.9
(-3)
P 		107
avr 106.1
(3) 		71.2
(0.4) 		95.3
(2.2) 		24.5
(-3) 		82

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 314
1 2 3 4 5 6 range
A 53.3
(-3)
P 		110.1
(-0.7)
P 		65.8
(-2.5)
P 		67.4
(-2.4)
P 		115.3
(-0.5)
P 		204.1
(3)
P 		151
B 100.8
(-2.2)
P 		107.7
(-2.1)
P 		63.4
(-3)
P 		90.3
(-2.5)
P 		115.8
(-1.9)
P 		357.8
(3)
P 		294
C 90.6
(-2.4)
P 		93.5
(-2.4)
P 		70.8
(-2.8)
P 		61
(-3)
P 		92.3
(-2.4)
P 		367.3
(3)
P 		306
avr 81.6
(-2.6) 		103.8
(-2.1) 		66.7
(-3) 		72.9
(-2.8) 		107.8
(-2) 		309.7
(3) 		243
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173302_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27877
Sequence Type Exemplar sequence
Representative Public ID CEK027H1R NCBI
Target Description CEK027H1R_rc /REP_DB=TREMBL Accession /GB=D33221 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk27h1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_068799
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000005187 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7478437:7485311:1 None
SNAP00000005170 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7478437:7485311:1 None
NM_068799 NCBI Caenorhabditis elegans ROD (Drosophila RoughDeal) homolog family member (rod-1) (rod-1) mRNA, complete cds. A 
F55G1.4 ENSEMBL cdna:known chromosome:CEL140:IV:7478436:7485493:1 gene:F55G1.4 A 
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
chrIV:7485241-7485493(+) 52.3 52.3
Public Domain and Genome References
Gene Title
Gene Symbol rod-1
Ensembl F55G1.4
Entrez Gene 177520 Entrez gene
SwissProt Q20849 EMBL-EBI
WormBase CE07281 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB00646 Rod (drosophila roughdeal) homolog protein 1 [Caenorhabditis elegans] ref|NP_501200.1| ROD (Drosophila RoughDeal) homolog family member (rod-1) [Caenorhabditis elegans] 0.0
blast CAE70091 Hypothetical protein CBG16533 [Caenorhabditis briggsae] 0.0
blast AAY54263 putative RoughDeal [Caenorhabditis remanei] 2.0E-81
Sequence
Target Sequence 
>C. ELEGANS:173302_AT
ggatccatggcgaatccagattggaattacgaacaatgcgttatgcttcgaaaatggact
ttgtgggcaatgagcagcaatgtcgaaggaggacgtcaaccaaatattgctcgnnnnctc
cgtgaaatcaattgtcccatcagtgcctcgattatttctgtcctttctaactggactatt
gataaaatggacgacgttgactcttccaagttggatccgaaacgtgacatttcacttgga
tgggatgtaggatgcgttcctgttagcgcaaactcttccaactcttaaataaattcgnnn
nnnnnnnnnnnnnnnnnnnnnnnnnctagcatagatctcaataaaggggactattatttt
nnnnnnnnnnnnnnnnnnnnnnnnnnnntctattacatctttctaccaaatta

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATCCATGGCGAATCCAGATTGGA 377 513 23 Antisense
CAATGCGTTATGCTTCGAAAATGGA 382 167 56 Antisense
TGGACTTTGTGGGCAATGAGCAGCA 523 547 77 Antisense
GAGGACGTCAACCAAATATTGCTCG 650 403 111 Antisense
CTCCGTGAAATCAATTGTCCCATCA 290 233 140 Antisense
TCCCATCAGTGCCTCGATTATTTCT 201 599 157 Antisense
CAGTGCCTCGATTATTTCTGTCCTT 125 209 163 Antisense
ATTTCTGTCCTTTCTAACTGGACTA 165 15 176 Antisense
AATGGACGACGTTGACTCTTCCAAG 267 161 208 Antisense
GACGTTGACTCTTCCAAGTTGGATC 300 375 215 Antisense
TCTATTACATCTTTCTACCAAATTA 297 615 411 Antisense
Sequence Source Affymetrix Proprietary Database