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[189858_at]

Description K08A2.7 /REP_DB=WormBase Gene ID /WP=CE23862 /TR=Q9N5J7 /GB=AAF39918.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 6grp_total > 26      4grp_total > 04      6grp_cgc > 14      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 813
1 2 3 4 range
A 190.9
(-1.8)
P 		34.9
(-3)
A 		63.3
(-2.8)
A 		834.9
(3)
P 		800
B 224.1
(-1.5)
P 		24.4
(-3)
A 		35.5
(-2.9)
A 		837.2
(3)
P 		813
C 210.1
(-1.9)
P 		82.2
(-3)
A 		84.2
(-3)
A 		777.8
(3)
P 		696
avr 208.4
(-1.7) 		47.2
(-3) 		61
(-2.9) 		816.6
(3) 		769

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 160
1 2 3 4 5 6 range
A 163.9
(3)
P 		127.5
(1)
A 		88.4
(-1.1)
A 		52.8
(-3)
A 		54.1
(-2.9)
A 		81.4
(-1.5)
A 		111
B 128.7
(3)
P 		125.1
(2.8)
P 		4.1
(-3)
A 		10.6
(-2.7)
A 		31.3
(-1.7)
A 		42.6
(-1.1)
A 		125
C 125
(3)
P 		90.4
(1.1)
A 		15.8
(-3)
A 		37.2
(-1.8)
A 		18.1
(-2.9)
A 		78.5
(0.4)
A 		109
avr 139.2
(3) 		114.3
(1.6) 		36.1
(-2.9) 		33.5
(-3) 		34.5
(-2.9) 		67.5
(-1.1) 		106
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 172
1 2 3 4 range
A 69.5
(0.2)
P 		7.6
(-3)
A 		16.5
(-2.5)
A 		122.2
(3)
P 		115
B 71.5
(-0.7)
P 		6
(-3)
A 		8.2
(-2.9)
A 		178.4
(3)
P 		172
C 69.6
(-0.4)
P 		23.6
(-3)
A 		29.3
(-2.7)
A 		131.1
(3)
P 		108
avr 70.2
(-0.4) 		12.4
(-3) 		18
(-2.7) 		143.9
(3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 45
1 2 3 4 5 6 range
A 30.2
(0.2)
P 		45.3
(3)
A 		19.3
(-1.9)
A 		13.4
(-3)
A 		16.3
(-2.5)
A 		19.8
(-1.8)
A 		32
B 44.8
(3)
P 		41.6
(2.6)
P 		1
(-3)
A 		2.8
(-2.8)
A 		12.7
(-1.4)
A 		15.9
(-1)
A 		44
C 46.3
(3)
P 		27.6
(0.3)
A 		4
(-3)
A 		7.5
(-2.5)
A 		5.9
(-2.7)
A 		26.3
(0.2)
A 		42
avr 40.4
(3) 		38.2
(2.6) 		8.1
(-3) 		7.9
(-3) 		11.6
(-2.3) 		20.7
(-0.6) 		33
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189858_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5591
Sequence Type Exemplar sequence
Representative Public ID K08A2.7 NCBI
Target Description K08A2.7 /REP_DB=WormBase Gene ID /WP=CE23862 /TR=Q9N5J7 /GB=AAF39918.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=zinc finger protein
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(10), NM_001027065(10), NM_001027066(10)
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. 10/11 None
NM_001027065 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-88) (nhr-88) mRNA, complete cds. 10/11 None
NM_001027066 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-88) (nhr-88) mRNA, complete cds. 10/11 None
SNAP00000036641 ENSEMBL cdna:SNAP chromosome:CEL140:II:2977047:2980633:1 10/11 None
GENEFINDER00000036647 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:2978420:2980311:1 10/11 None
K08A2.5a.4 ENSEMBL cdna:known chromosome:CEL140:II:2976634:2986976:1 gene:K08A2.5 10/11 None
K08A2.5a.3 ENSEMBL cdna:known chromosome:CEL140:II:2978404:2986976:1 gene:K08A2.5 10/11 None
K08A2.5a.2 ENSEMBL cdna:known chromosome:CEL140:II:2978404:2986976:1 gene:K08A2.5 10/11 A 
K08A2.5a.1 ENSEMBL cdna:known chromosome:CEL140:II:2978411:2986976:1 gene:K08A2.5 10/11 A 
K08A2.5c ENSEMBL cdna:known chromosome:CEL140:II:2978420:2980925:1 gene:K08A2.5 10/11 None
K08A2.5b ENSEMBL cdna:known chromosome:CEL140:II:2978420:2982056:1 gene:K08A2.5 10/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
AF273831 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:2976461-2980471(+) 90.19 100.0
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
blast AAO21381 Nuclear hormone receptor family protein 88, isoform b [Caenorhabditis elegans] ref|NP_001022236.1| Nuclear Hormone Receptor family member (nhr-88) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
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 IPR002492 EMBL-EBI Transposase, Tc1/Tc3 7.2E-31
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 9.3E-48
Sequence
Target Sequence 
>C. ELEGANS:189858_AT
tatggttgtaagggcttcttccgccgaacaatccgatcccaacagacctacacctgccga
ttcacccaaaaatgcgccatcgacaaggatcaacgcaacgcatgccgttactgccggttc
cagcgttgcctgacagttggcatggagccagaagccattcgaccggatcgtgacgtcatc
ggcaagcagaagaatccacggaagaagaagatgaagtccgacacgaatagtggaagcatc
gatgcatccctaccctcaccgaatggctgcgattctccagtttccaataatgaagatgtt
attttgtcatttttattggatgttgaagatcaggcgacttgcgggaataatcatatcaca
atgcctattggaatatcaatgatgatgaagaatgacccggatttcgatgtgtccactttg
ttccatagtcaatatgtcagaaatcaggagagctttccgaagtttatctcaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATGGTTGTAAGGGCTTCTTCCGCC 492 655 385 Antisense
GATTCACCCAAAAATGCGCCATCGA 430 431 443 Antisense
TCAACGCAACGCATGCCGTTACTGC 402 631 474 Antisense
GTTCCAGCGTTGCCTGACAGTTGGC 26 441 501 Antisense
GCATGGAGCCAGAAGCCATTCGACC 70 209 524 Antisense
TCGACCGGATCGTGACGTCATCGGC 535 597 543 Antisense
GTGGAAGCATCGATGCATCCCTACC 98 491 614 Antisense
TGCGATTCTCCAGTTTCCAATAATG 480 583 652 Antisense
ATGACCCGGATTTCGATGTGTCCAC 539 45 776 Antisense
ATGTGTCCACTTTGTTCCATAGTCA 15 51 791 Antisense
AGAGCTTTCCGAAGTTTATCTCAAA 576 69 833 Antisense
Sequence Source Affymetrix Proprietary Database