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[176503_at]

Description Y54F10AM.M /REP_DB=WormBase Gene ID /WP=CE26181 /CHR=3 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_total > 77      4grp_total > 30      6grp_cgc > 58      6grp_cgc_sub > In      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 6.4
(-1.3)
A 		9.9
(0.5)
A 		2.9
(-3)
A 		14.9
(3)
A 		12
B 29.8
(3)
A 		13
(-1.9)
A 		9.4
(-3)
A 		13
(-1.9)
A 		20
C 11.2
(2.1)
A 		9.7
(-1.1)
A 		8.8
(-3)
A 		11.6
(3)
A 		3
avr 15.8
(3) 		10.9
(-0.3) 		7
(-3) 		13.2
(1.2) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 5.3
(-2.4)
A 		9.4
(-1.3)
A 		3.1
(-3)
A 		3.4
(-2.9)
A 		16.3
(0.6)
A 		25.2
(3)
A 		22
B 3.3
(-3)
A 		8.5
(-0.5)
A 		9.5
(0)
A 		15.7
(3)
A 		8.4
(-0.5)
A 		7.2
(-1.1)
A 		12
C 2.3
(-3)
A 		9.1
(-1.6)
A 		2.4
(-3)
A 		4.3
(-2.6)
A 		5.3
(-2.4)
A 		32.4
(3)
A 		30
avr 3.6
(-3) 		9
(-1.2) 		5
(-2.5) 		7.8
(-1.6) 		10
(-0.9) 		21.6
(3) 		18
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9
1 2 3 4 range
A 2.3
(3)
A 		2.1
(2.2)
A 		0.8
(-3)
A 		2.2
(2.6)
A 		2
B 9.5
(3)
A 		3.2
(-2.2)
A 		2.2
(-3)
A 		2.8
(-2.5)
A 		7
C 3.7
(3)
A 		2.8
(-0.2)
A 		3.1
(0.9)
A 		2
(-3)
A 		2
avr 5.2
(3) 		2.7
(-1.7) 		2
(-3) 		2.3
(-2.4) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10
1 2 3 4 5 6 range
A 1
(-2.7)
A 		3.3
(-0.1)
A 		0.7
(-3)
A 		0.9
(-2.8)
A 		4.9
(1.7)
A 		6.1
(3)
A 		5
B 1.2
(-3)
A 		2.8
(0.2)
A 		2.3
(-0.8)
A 		4.2
(3)
A 		3.4
(1.4)
A 		2.7
(0)
A 		3
C 0.8
(-2.9)
A 		2.8
(-1.7)
A 		0.6
(-3)
A 		0.9
(-2.8)
A 		1.7
(-2.4)
A 		10.9
(3)
A 		10
avr 1
(-3) 		3
(-0.9) 		1.2
(-2.8) 		2
(-1.9) 		3.3
(-0.5) 		6.6
(3) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176503_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18920
Sequence Type Exemplar sequence
Representative Public ID Y54F10AM.M NCBI
Target Description Y54F10AM.M /REP_DB=WormBase Gene ID /WP=CE26181 /CHR=3 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
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_065178(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065178 NCBI Caenorhabditis elegans Y54F10AM.1 (Y54F10AM.1) mRNA, complete cds. 11/11 None
Y54F10AM.1 ENSEMBL cdna:known chromosome:CEL140:III:2562040:2564789:1 gene:Y54F10AM.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000034924 5/11 Cross Hyb Matching Probes None
GENEFINDER00000034927 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:2562039-2564789(+) 63.43 100.0
Public Domain and Genome References
Gene Title
Gene Symbol nhr-239
Ensembl Y54F10AM.1
Entrez Gene 190264 Entrez gene
SwissProt Q9BKZ8 EMBL-EBI
WormBase CE26181 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
4879 ligand-dependent nuclear receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK29938 Hypothetical protein Y54F10AM.1 [Caenorhabditis elegans] ref|NP_497579.1| Y54F10AM.1 [Caenorhabditis elegans] 1.0E-120
blast CAE65008 Hypothetical protein CBG09846 [Caenorhabditis briggsae] 9.0E-42
blast XP_795547 PREDICTED: similar to photoreceptor-specific nuclear receptor isoform b [Strongylocentrotus purpuratus] 1.0E-25
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 8.1E-28
Sequence
Target Sequence 
>C. ELEGANS:176503_AT
cacggcagccgtgaactgtgagatttgtggagacaagtcttacggtagacactatggagt
atgggcatgtgatggatgcagttgctttttcaagagaagtgtacgcaagaatattatcta
tacttgtattgcgggaaattggaagtgcgtcgtggataaaggccgaaggaattggtgccc
ggcgtgtcggcttgcaaaatgcacaaggttgaagatgaatagactcggccccgccttttt
ctcgtccactcacggagaaaaggcaaaaatttggggaccaaccaatatcaggccgccgac
atcctacgggttccgcgcgccgctatgtttaactcgctgtgggcgtggtgctgtctccgc
ccgctgcgagttaaacaaagttttcacaaacctgcttccccacgtggaacttccgctcct
ccaccaccacgattgcgtcgaacacgagctcctttggcatcgagaagtccattccagcca
ttgtctcgttagaactgctggcggtgctga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACGGCAGCCGTGAACTGTGAGATT 237 199 114 Antisense
GATGGATGCAGTTGCTTTTTCAAGA 467 407 184 Antisense
GGAAGTGCGTCGTGGATAAAGGCCG 693 529 254 Antisense
CCGAAGGAATTGGTGCCCGGCGTGT 465 261 276 Antisense
CGGCGTGTCGGCTTGCAAAATGCAC 109 235 293 Antisense
TTGAAGATGAATAGACTCGGCCCCG 616 703 322 Antisense
CACGATTGCGTCGAACACGAGCTCC 631 199 541 Antisense
GAGCTCCTTTGGCATCGAGAAGTCC 220 385 559 Antisense
CATCGAGAAGTCCATTCCAGCCATT 659 211 571 Antisense
ATTCCAGCCATTGTCTCGTTAGAAC 252 7 584 Antisense
TCGTTAGAACTGCTGGCGGTGCTGA 168 581 599 Antisense
Sequence Source Affymetrix Proprietary Database