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[190898_at]

Description K08A2.5 /REP_DB=WormBase Gene ID /WP=CE21034 /TR=Q9N5J5 /GB=AAF39914.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_total > 18      4grp_total > 01      6grp_cgc > 06      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 486
1 2 3 4 range
A 163.5
(-1.6)
A 		75.3
(-3)
A 		230.3
(-0.6)
A 		461.4
(3)
P 		386
B 196.1
(-2.5)
A 		165.8
(-3)
A 		247.4
(-1.8)
A 		561.6
(3)
P 		396
C 202.9
(-2.9)
A 		293.2
(-0.9)
A 		200.5
(-3)
A 		463.6
(3)
P 		263
avr 187.5
(-2.8) 		178.1
(-3) 		226.1
(-2.1) 		495.5
(3) 		317

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 148
1 2 3 4 5 6 range
A 202.3
(3)
A 		81.9
(-1.9)
A 		53.9
(-3)
A 		73
(-2.2)
A 		81.3
(-1.9)
A 		145.8
(0.7)
A 		148
B 190.2
(3)
A 		128.9
(-1.1)
A 		136.4
(-0.6)
A 		143.2
(-0.1)
A 		99.5
(-3)
A 		114.6
(-2)
A 		91
C 196.6
(3)
A 		112.1
(-1)
A 		167.9
(1.6)
A 		71.2
(-3)
A 		123.4
(-0.5)
A 		101.5
(-1.6)
A 		125
avr 196.4
(3) 		107.6
(-2.3) 		119.4
(-1.6) 		95.8
(-3) 		101.4
(-2.7) 		120.6
(-1.5) 		101
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 103
1 2 3 4 range
A 59.5
(2.1)
A 		16.3
(-3)
A 		60.2
(2.1)
A 		67.5
(3)
P 		51
B 62.5
(-1.4)
A 		40.9
(-3)
A 		57.3
(-1.8)
A 		119.7
(3)
P 		79
C 67.2
(-3)
A 		84.3
(3)
A 		69.9
(-2.1)
A 		78.2
(0.9)
P 		17
avr 63.1
(-0.7) 		47.2
(-3) 		62.5
(-0.8) 		88.5
(3) 		41

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 61
1 2 3 4 5 6 range
A 37.3
(3)
A 		29.1
(1.1)
A 		11.7
(-3)
A 		18.5
(-1.4)
A 		24.5
(0)
A 		35.5
(2.6)
A 		26
B 66.2
(3)
A 		42.9
(-1.2)
A 		33.1
(-3)
A 		37.9
(-2.1)
A 		40.4
(-1.7)
A 		42.7
(-1.3)
A 		33
C 72.9
(3)
A 		34.2
(-1)
A 		42.7
(-0.1)
A 		14.3
(-3)
A 		39.9
(-0.4)
A 		34
(-1)
A 		59
avr 58.8
(3) 		35.4
(-1) 		29.2
(-2) 		23.6
(-3) 		34.9
(-1.1) 		37.4
(-0.6) 		35
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190898_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5970
Sequence Type Exemplar sequence
Representative Public ID K08A2.5 NCBI
Target Description K08A2.5 /REP_DB=WormBase Gene ID /WP=CE21034 /TR=Q9N5J5 /GB=AAF39914.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster Evidence This cluster is supported by a 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_001027064(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027064 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-88) (nhr-88) mRNA, complete cds. 11/11 None
SNAP00000036642 ENSEMBL cdna:SNAP chromosome:CEL140:II:2980998:2985921:1 11/11 None
GENEFINDER00000036649 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:2982758:2985921:1 11/11 None
K08A2.5a.4 ENSEMBL cdna:known chromosome:CEL140:II:2976634:2986976:1 gene:K08A2.5 11/11 None
K08A2.5a.3 ENSEMBL cdna:known chromosome:CEL140:II:2978404:2986976:1 gene:K08A2.5 11/11 None
K08A2.5a.2 ENSEMBL cdna:known chromosome:CEL140:II:2978404:2986976:1 gene:K08A2.5 11/11 A 
K08A2.5a.1 ENSEMBL cdna:known chromosome:CEL140:II:2978411:2986976:1 gene:K08A2.5 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
173641 3 1 NM_001027064 190898_at (11)
NM_001027065 172773_x_at (9), 173008_s_at (11), 189548_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:2983139-2985920(+) 100.0 100.0
Public Domain and Genome References
Ensembl K08A2.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAF39914 Nuclear hormone receptor family protein 88, isoform a [Caenorhabditis elegans] ref|NP_001022235.1| Nuclear Hormone Receptor family member (nhr-88) [Caenorhabditis elegans] 0.0
blast AAG15179 nuclear receptor NHR-88 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 3.99999999927983E-23
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.8E-27
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 9.3E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.8E-27
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 8.8E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.4E-16
Sequence
Target Sequence 
>C. ELEGANS:190898_AT
tgttcgggatcccaattgactccctgctcgtcgagctctacgtcgacgcagattctccgg
agctgatctcccaaggatcccacgctcgggaacgatccgacgtctccacacagacagcgt
ccctagagggcgccagcgcctccatgacaccagacgttacctcctcggaatttgtgaaaa
tggagcaaaacgagagcccgtcaagctcagaggagccaatgtgcatcggagcacctgcca
cgtcatccgccaacgcagtcgccacgaaccttgccgctgatcttttggggcttctgccca
actttgacgcgacgggtcttgacctggcaagcgctgcggcggcagctgcgacatccgtca
actacagtcatttttatggattcgggaacctcggcggctcactggacgactcatcctcat
cggggacgggctcggtgggcagtttcgcaccccactcggcaccgccaatctcgaataatg
tgaacccgttcgccgtccatggattctttgaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTTCGGGATCCCAATTGACTCCCT 474 561 668 Antisense
TGCTCGTCGAGCTCTACGTCGACGC 190 561 692 Antisense
TCTCCGGAGCTGATCTCCCAAGGAT 583 609 721 Antisense
GAGCCCGTCAAGCTCAGAGGAGCCA 606 385 861 Antisense
CAATGTGCATCGGAGCACCTGCCAC 462 183 884 Antisense
TGATCTTTTGGGGCTTCTGCCCAAC 280 565 945 Antisense
CGACGGGTCTTGACCTGGCAAGCGC 310 251 977 Antisense
CTGCGACATCCGTCAACTACAGTCA 201 237 1013 Antisense
GGCACCGCCAATCTCGAATAATGTG 668 535 1125 Antisense
GAATAATGTGAACCCGTTCGCCGTC 360 325 1140 Antisense
TTCGCCGTCCATGGATTCTTTGACA 580 697 1156 Antisense
Sequence Source Affymetrix Proprietary Database