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[175408_at]

Description AU112975_rc /REP_DB=TREMBL Accession /GB=AU112975 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk701b4 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 87      6grp_total > 86      4grp_total > 05      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 63
1 2 3 4 range
A 66.3
(2.3)
A 		37.7
(-3)
A 		39.2
(-2.7)
A 		70
(3)
A 		32
B 62.4
(-1.9)
P 		53.6
(-3)
A 		77.7
(0.1)
P 		100.3
(3)
P 		47
C 54.4
(-3)
P 		64.3
(3)
A 		60.1
(0.5)
P 		61.4
(1.2)
A 		10
avr 61
(-0.8) 		51.9
(-3) 		59
(-1.3) 		77.2
(3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 94
1 2 3 4 5 6 range
A 38.7
(-3)
A 		71.9
(-0.8)
P 		71.8
(-0.8)
P 		84.6
(0.1)
P 		74.5
(-0.6)
P 		128.9
(3)
P 		90
B 76.7
(-0.6)
P 		53.6
(-3)
P 		77.5
(-0.5)
P 		86.3
(0.5)
P 		110.4
(3)
P 		105.2
(2.5)
P 		57
C 41.3
(-3)
A 		57.7
(-1.9)
P 		79.5
(-0.5)
P 		65.5
(-1.4)
P 		77.8
(-0.6)
P 		132.8
(3)
P 		92
avr 52.2
(-3) 		61.1
(-2.2) 		76.3
(-0.9) 		78.8
(-0.7) 		87.6
(0) 		122.3
(3) 		70
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 24.1
(3)
A 		8.2
(-3)
A 		10.2
(-2.2)
A 		10.3
(-2.2)
A 		16
B 19.9
(1.9)
P 		13.2
(-3)
A 		18
(0.5)
P 		21.4
(3)
P 		8
C 18
(1.3)
P 		18.5
(1.6)
A 		21
(3)
P 		10.4
(-3)
A 		11
avr 20.7
(3) 		13.3
(-3) 		16.4
(-0.5) 		14
(-2.4) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 7.1
(-3)
A 		25.6
(1.6)
P 		15.6
(-0.9)
P 		21.5
(0.6)
P 		22.5
(0.8)
P 		31.4
(3)
P 		24
B 26.7
(-1)
P 		17.9
(-3)
P 		18.8
(-2.8)
P 		22.8
(-1.9)
P 		44.9
(3)
P 		39.2
(1.7)
P 		27
C 15.3
(-2.6)
A 		17.6
(-2.2)
P 		20.2
(-1.7)
P 		13.2
(-3)
P 		25.2
(-0.7)
P 		44.5
(3)
P 		31
avr 16.4
(-3) 		20.4
(-1.9) 		18.2
(-2.5) 		19.2
(-2.2) 		30.9
(1) 		38.4
(3) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175408_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21103
Sequence Type Exemplar sequence
Representative Public ID AU112975 NCBI
Target Description AU112975_rc /REP_DB=TREMBL Accession /GB=AU112975 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk701b4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_066941(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066941 NCBI Caenorhabditis elegans Homolog of S.Pombe Rad family member (hpr-9) (hpr-9) mRNA, complete cds. 11/11 None
Y39A1A.23.1 ENSEMBL cdna:known chromosome:CEL140:III:10621418:10626260:1 gene:Y39A1A.23 11/11 None
Y39A1A.23.2 ENSEMBL cdna:known chromosome:CEL140:III:10621462:10626260:1 gene:Y39A1A.23 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000012909 8/11 Cross Hyb Matching Probes None
GENEFINDER00000012939 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10625353-10626170(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol hpr-9
Ensembl Y39A1A.23
Entrez Gene 176483 Entrez gene
SwissProt Q95Q27 EMBL-EBI
WormBase CE33217 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
74 regulation of progression through cell cycle inferred from electronic annotation QuickGO AmiGO
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAC42372 Hypothetical protein Y39A1A.23 [Caenorhabditis elegans] ref|NP_499342.2| Homolog of S.Pombe Rad family member (hpr-9) [Caenorhabditis elegans] 0.0
blast AAF66431 cell cycle checkpoint protein Rad9 [Caenorhabditis elegans] 1.0E-168
blast CAE71436 Hypothetical protein CBG18347 [Caenorhabditis briggsae] 1.0E-150
Protein Domains
Database ID Description E-Value
Pfam IPR007268 EMBL-EBI Rad9 2.6E-72
Pfam IPR007268 EMBL-EBI Rad9 7.5E-109
Sequence
Target Sequence 
>C. ELEGANS:175408_AT
gaaatgctagaagaacctgaacaagaagatcaagaaatattcaaaattccccagccgaaa
agaagaaaaaccgccgaagatgacagaaatagaaagattcgtcgaattctaatgggaact
gaaacgacgtctaaaatgagaatgagccaacaattcgacaagcggcttggtccattggtt
tcggatactcaatatgaatcgagatgaccgttgcgatgacgtttggcacctgcaaggat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAATGCTAGAAGAACCTGAACAAG 36 363 23 Antisense
TATTCAAAATTCCCCAGCCGAAAAG 546 659 60 Antisense
AAAAACCGCCGAAGATGACAGAAAT 483 127 88 Antisense
GATTCGTCGAATTCTAATGGGAACT 500 431 118 Antisense
TAATGGGAACTGAAACGACGTCTAA 163 635 132 Antisense
CAACAATTCGACAAGCGGCTTGGTC 297 189 170 Antisense
CAAGCGGCTTGGTCCATTGGTTTCG 563 185 181 Antisense
GGTCCATTGGTTTCGGATACTCAAT 203 503 191 Antisense
AATATGAATCGAGATGACCGTTGCG 39 171 213 Antisense
GACCGTTGCGATGACGTTTGGCACC 320 381 228 Antisense
GATGACGTTTGGCACCTGCAAGGAT 391 411 237 Antisense
Sequence Source Affymetrix Proprietary Database