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[192260_at]

Description T09A12.4 /REP_DB=WormBase Gene ID /WP=CE18229 /GEN=nhr-66 /TR=O45184 /GB=AAC04434.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 25      4grp_highest_8_8 > 44      4grp_high_8_8 > 16      6grp_highest_nonorm > 75      6grp_total > 26      4grp_total > 31      6grp_highest_sub > 01_02      6grp_cgc > 14      6grp_high1_sub > 01_02      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 711
1 2 3 4 range
A 1030.3
(3)
P 		388.2
(-3)
P 		509.7
(-1.9)
P 		751.5
(0.4)
P 		642
B 935.7
(3)
P 		560
(-2.4)
P 		516.7
(-3)
P 		726.6
(0)
P 		419
C 1099.5
(3)
P 		464.9
(-3)
P 		531.4
(-2.4)
P 		648.1
(-1.3)
P 		635
avr 1021.8
(3) 		471
(-3) 		519.3
(-2.5) 		708.7
(-0.4) 		551

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 479
1 2 3 4 5 6 range
A 911.5
(0.6)
P 		1061.2
(3)
P 		682.8
(-3)
P 		805.6
(-1.1)
P 		847.2
(-0.4)
P 		918.3
(0.7)
P 		378
B 1054.3
(2.4)
P 		1093
(3)
P 		803.4
(-1.5)
P 		860.3
(-0.6)
P 		708.2
(-3)
P 		855.9
(-0.7)
P 		385
C 1161.8
(3)
P 		1154.7
(2.9)
P 		853.8
(-1.7)
P 		772.5
(-3)
P 		797.4
(-2.6)
P 		829.9
(-2.1)
P 		389
avr 1042.5
(1.9) 		1103
(3) 		780
(-3) 		812.8
(-2.4) 		784.3
(-2.9) 		868
(-1.4) 		323
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 291
1 2 3 4 range
A 375.1
(3)
P 		84.3
(-3)
P 		133.2
(-2)
P 		110
(-2.5)
P 		291
B 298.4
(3)
P 		138.3
(-2.4)
P 		119.7
(-3)
P 		154.8
(-1.8)
P 		179
C 364
(3)
P 		133.7
(-2.4)
P 		185.2
(-1.2)
P 		109.3
(-3)
P 		255
avr 345.8
(3) 		118.8
(-3) 		146
(-2.3) 		124.7
(-2.8) 		227

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 282
1 2 3 4 5 6 range
A 168
(-2.5)
P 		377.4
(3)
P 		148.7
(-3)
P 		204.3
(-1.5)
P 		255.6
(-0.2)
P 		223.6
(-1)
P 		229
B 366.8
(3)
P 		363.8
(2.9)
P 		195.1
(-3)
P 		227.9
(-1.9)
P 		287.7
(0.2)
P 		319.2
(1.3)
P 		172
C 430.6
(3)
P 		352.3
(1.3)
P 		217.3
(-1.6)
P 		155.3
(-3)
P 		258
(-0.8)
P 		277.8
(-0.3)
P 		275
avr 321.8
(1.6) 		364.5
(3) 		187
(-3) 		195.8
(-2.7) 		267.1
(-0.3) 		273.5
(-0.1) 		178
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192260_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8474
Sequence Type Exemplar sequence
Representative Public ID T09A12.4 NCBI
Target Description T09A12.4 /REP_DB=WormBase Gene ID /WP=CE18229 /GEN=nhr-66 /TR=O45184 /GB=AAC04434.2 /SUBMIT=ST.LOUIS /CHR=4 /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_001028198(11), NM_171397(11), NM_171396(11), NM_171398(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028198 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-66) (nhr-66) mRNA, complete cds. 11/11 None
NM_171397 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-66) (nhr-66) mRNA, complete cds. 11/11 None
NM_171396 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-66) (nhr-66) mRNA, complete cds. 11/11 None
NM_171398 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-66) (nhr-66) mRNA, complete cds. 11/11 None
SNAP00000044389 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8226724:8229335:-1 11/11 None
GENEFINDER00000044397 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8226724:8236558:-1 11/11 None
T09A12.4d.1 ENSEMBL cdna:known chromosome:CEL140:IV:8226315:8236583:-1 gene:T09A12.4 11/11 None
T09A12.4d.2 ENSEMBL cdna:known chromosome:CEL140:IV:8226315:8236184:-1 gene:T09A12.4 11/11 None
T09A12.4a.1 ENSEMBL cdna:known chromosome:CEL140:IV:8226317:8231817:-1 gene:T09A12.4 11/11 A 
T09A12.4c ENSEMBL cdna:known chromosome:CEL140:IV:8226724:8236558:-1 gene:T09A12.4 11/11 A 
T09A12.4b ENSEMBL cdna:known chromosome:CEL140:IV:8226724:8229483:-1 gene:T09A12.4 11/11 A 
T09A12.4a.2 ENSEMBL cdna:known chromosome:CEL140:IV:8226724:8232088:-1 gene:T09A12.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
AF273817 6/11 Cross Hyb Matching Probes A 
AF273818 4/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:8226729-8232127(-) 97.1 100.0
Public Domain and Genome References
Ensembl T09A12.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM54168 Nuclear hormone receptor family protein 66, isoform c [Caenorhabditis elegans] ref|NP_741462.1| Nuclear Hormone Receptor family member (nhr-66) [Caenorhabditis elegans] 0.0
blast AAV34786 Nuclear hormone receptor family protein 66, isoform d [Caenorhabditis elegans] ref|NP_001023369.1| Nuclear Hormone Receptor family member (nhr-66) [Caenorhabditis elegans] 0.0
blast AAG15169 nuclear receptor NHR-66 [Caenorhabditis elegans] 0.0
blast AAM54166 Nuclear hormone receptor family protein 66, isoform a [Caenorhabditis elegans] ref|NP_741463.1| Nuclear Hormone Receptor family member (nhr-66) [Caenorhabditis elegans] 0.0
blast AAG15168 nuclear receptor NHR-66 [Caenorhabditis elegans] 0.0
blast AAM54167 Nuclear hormone receptor family protein 66, isoform b [Caenorhabditis elegans] ref|NP_741464.1| Nuclear Hormone Receptor family member (nhr-66) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.4E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.1E-25
Sequence
Target Sequence 
>C. ELEGANS:192260_AT
ccttccttcattcacacatgcaatggacacaatcggagaaaaaatgaagaaaaataatat
aacggaaacagagctcaccattcttctcgggcttgtgctcctcgatccaggaatatacgg
aatccatgagagcactagaaaatttttgaaaagaattcgagatcagcttattcatgatgt
ttatatgtactatgaagatgaaatgtcacatttgtatgatccagaaattcgaatggctga
tattttcatgcttgtcgccgctataaagattcactcgatcaaaacgtcagaaaatatgca
catgctccgagtgtttgatttaatcccggcggatgcatgtttcaaccagatgcttgacgt
ggaaagtgtaaacgtttctccagatggacaaaaagactcagaagctgagcaaggaccaag
tcctgtttccgtcccagaagcggcacgtggcagctaccaagatgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCTTCCTTCATTCACACATGCAATG 150 269 1545 Antisense
GAAACAGAGCTCACCATTCTTCTCG 705 355 1609 Antisense
CTTGTGCTCCTCGATCCAGGAATAT 175 219 1636 Antisense
CTGATATTTTCATGCTTGTCGCCGC 665 237 1781 Antisense
TTGTCGCCGCTATAAAGATTCACTC 417 705 1796 Antisense
ATATGCACATGCTCCGAGTGTTTGA 429 21 1838 Antisense
GAGTGTTTGATTTAATCCCGGCGGA 278 401 1853 Antisense
GGCGGATGCATGTTTCAACCAGATG 62 541 1872 Antisense
GTGTAAACGTTTCTCCAGATGGACA 67 487 1910 Antisense
GCAAGGACCAAGTCCTGTTTCCGTC 624 315 1953 Antisense
GGCACGTGGCAGCTACCAAGATGAT 216 535 1986 Antisense
Sequence Source Affymetrix Proprietary Database