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[191884_s_at] retinoic acid

Description B0280.8 /REP_DB=WormBase Gene ID /WP=CE00815 /GEN=nhr-10 /TR=SW:P41999 /GB=AAA19086.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=retinoic acid
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 57      4grp_highest_8_8 > 47      4grp_high_8_8 > 12      6grp_highest_nonorm > 85      6grp_total > 47      4grp_total > 20      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 599
1 2 3 4 range
A 874.6
(0.8)
P 		735.1
(-0.6)
P 		492.6
(-3)
P 		1091.1
(3)
P 		599
B 816.4
(-0.1)
P 		715.6
(-1.5)
P 		602.7
(-3)
P 		1045.9
(3)
P 		443
C 778.2
(-1.5)
P 		731
(-2.2)
P 		673.9
(-3)
P 		1088.7
(3)
P 		415
avr 823.1
(-0.1) 		727.2
(-1.3) 		589.7
(-3) 		1075.2
(3) 		486

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 376
1 2 3 4 5 6 range
A 828.7
(3)
P 		711
(-1.1)
P 		654.5
(-3)
P 		763.4
(0.8)
P 		724.1
(-0.6)
P 		812.6
(2.4)
P 		174
B 842.2
(1.6)
P 		685.3
(-2.9)
P 		682.4
(-3)
P 		705.9
(-2.3)
P 		722.8
(-1.8)
P 		891.2
(3)
P 		209
C 682.3
(-0.9)
P 		842.8
(1.7)
P 		633.7
(-1.6)
P 		746.3
(0.2)
P 		548.6
(-3)
P 		924.3
(3)
P 		376
avr 784.4
(0.5) 		746.4
(-0.5) 		656.9
(-3) 		738.5
(-0.8) 		665.2
(-2.8) 		876
(3) 		219
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 190
1 2 3 4 range
A 318.4
(3)
P 		159.6
(-2)
P 		128.8
(-3)
P 		159.7
(-2)
P 		190
B 260.3
(3)
P 		176.7
(-1.2)
P 		139.7
(-3)
P 		222.9
(1.1)
P 		121
C 257.6
(3)
P 		210.2
(-0.8)
P 		234.9
(1.2)
P 		183.6
(-3)
P 		74
avr 278.8
(3) 		182.2
(-2.2) 		167.8
(-3) 		188.7
(-1.9) 		111

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 190
1 2 3 4 5 6 range
A 152.8
(-2.4)
P 		252.9
(3)
P 		142.5
(-3)
P 		193.6
(-0.2)
P 		218.5
(1.1)
P 		197.8
(0)
P 		110
B 293.1
(1.6)
P 		228.1
(-0.8)
P 		165.7
(-3)
P 		187
(-2.2)
P 		293.7
(1.6)
P 		332.3
(3)
P 		167
C 252.9
(0.9)
P 		257.2
(1)
P 		161.3
(-2.6)
P 		150.1
(-3)
P 		177.5
(-2)
P 		309.4
(3)
P 		159
avr 232.9
(0.7) 		246.1
(1.4) 		156.5
(-3) 		176.9
(-2) 		229.9
(0.6) 		279.8
(3) 		123
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191884_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6854
Sequence Type Exemplar sequence
Representative Public ID B0280.8 NCBI
Target Description B0280.8 /REP_DB=WormBase Gene ID /WP=CE00815 /GEN=nhr-10 /TR=SW:P41999 /GB=AAA19086.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=retinoic acid
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_066153(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066153 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-10) (nhr-10) mRNA, complete cds. 11/11 None
SNAP00000041609 ENSEMBL cdna:SNAP chromosome:CEL140:III:7112573:7115358:-1 11/11 None
GENEFINDER00000041627 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7112573:7115358:-1 11/11 None
B0280.8 ENSEMBL cdna:known chromosome:CEL140:III:7112223:7115362:-1 gene:B0280.8 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:7112570-7115356(-) 100.0 100.0
Public Domain and Genome References
Gene Title retinoic acid
Gene Symbol nhr-10
Ensembl B0280.8
Entrez Gene 175993 Entrez gene
SwissProt P41999 EMBL-EBI
WormBase CE00815 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
3707 steroid hormone receptor 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 AAA19086 Nuclear hormone receptor family protein 10 [Caenorhabditis elegans] ref|NP_498554.1| Nuclear Hormone Receptor family member (nhr-10) [Caenorhabditis elegans] sp|P41999|NHR10_CAEEL Nuclear hormone receptor family member nhr-10 0.0
blast AAO39172 nuclear receptor NHR-10 [Caenorhabditis elegans] 0.0
blast CAE70133 Hypothetical protein CBG16594 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.8E-50
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.0E-49
Sequence
Target Sequence 
>C. ELEGANS:191884_S_AT
aaagacgttgccagttttccaatcacttccattcacggataagcttgctcttcttcgaca
ttcagccatcacatatccatcattggttcatgtattcaattctccagatcatggtcttga
cacgattgtcttcccagacggtgcctattttgacagaacacctgaaccaactcgtcctct
tggattcaacaaaaagaagtatcaaatgcttgatcaattgttgaaaccaatgagatcaat
ggaaattgacatgactgaatttgctgcattcaaagcaattttctttttgaatccagacgc
tgatgatgttgattcgaatgcaaaaaagacgttgagtgatggaagaagtgcaattacaaa
tgctctttatcggtatatggtcaagaaaaaaggagcagaagatgctggggatagattcgg
acgtcttcttcttctcggtactgtcctcgccacaatggctgttgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAGACGTTGCCAGTTTTCCAATCA 542 123 642 Antisense
TTCCAATCACTTCCATTCACGGATA 608 701 658 Antisense
ACGGATAAGCTTGCTCTTCTTCGAC 465 95 676 Antisense
TTCAGCCATCACATATCCATCATTG 526 685 702 Antisense
GGTTCATGTATTCAATTCTCCAGAT 240 507 726 Antisense
GTCTTGACACGATTGTCTTCCCAGA 131 469 755 Antisense
TCTTCCCAGACGGTGCCTATTTTGA 94 617 770 Antisense
GACAGAACACCTGAACCAACTCGTC 32 355 793 Antisense
CAACTCGTCCTCTTGGATTCAACAA 265 187 809 Antisense
GGATAGATTCGGACGTCTTCTTCTT 280 507 1050 Antisense
TGTCCTCGCCACAATGGCTGTTGAA 627 557 1083 Antisense
Sequence Source Affymetrix Proprietary Database