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[173903_at] retinoic acid

Description AU109527 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=B0280.8 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AU109527 /WB_GENE_ID=B0280.8 /WP=CE00815 /CHR=3 /FEA=Genomic Cluster /GEN=nhr-10 /DEF=retinoic acid; Caenorhabditis elegans cDNA clone:yk708c4 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 95      6grp_high1_10_10 > 58      4grp_highest_8_8 > 39      4grp_high_8_8 > 04      6grp_highest_nonorm > 75      6grp_total > 48      4grp_total > 05      6grp_highest_sub > Cu      6grp_cgc > 19      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 965
1 2 3 4 range
A 1121.6
(0)
P 		815.1
(-3)
P 		886.6
(-2.3)
P 		1423.7
(3)
P 		609
B 1101.2
(-0.8)
P 		879.8
(-2.2)
P 		754.4
(-3)
P 		1719.6
(3)
P 		965
C 1153.3
(-0.7)
P 		954.1
(-3)
P 		1028.4
(-2.2)
P 		1483.3
(3)
P 		529
avr 1125.4
(-0.8) 		883
(-3) 		889.8
(-2.9) 		1542.2
(3) 		659

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 581
1 2 3 4 5 6 range
A 768.8
(-1.8)
P 		950.1
(3)
P 		775.6
(-1.7)
P 		725.6
(-3)
P 		801.6
(-1)
P 		864.6
(0.7)
P 		225
B 936.4
(-0)
P 		983.5
(0.5)
P 		679.9
(-3)
P 		750.2
(-2.2)
P 		904.3
(-0.4)
P 		1195.4
(3)
P 		516
C 1003.3
(1.8)
P 		862.8
(0.1)
P 		614.5
(-3)
P 		728.2
(-1.6)
P 		765.7
(-1.1)
P 		1102.2
(3)
P 		488
avr 902.8
(0.5) 		932.1
(1) 		690
(-3) 		734.7
(-2.3) 		823.9
(-0.8) 		1054.1
(3) 		364
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 234
1 2 3 4 range
A 408.4
(3)
P 		176.9
(-3)
P 		231.8
(-1.6)
P 		208.4
(-2.2)
P 		232
B 351.2
(2.5)
P 		217.3
(-1.7)
P 		174.8
(-3)
P 		366.4
(3)
P 		192
C 381.8
(3)
P 		274.3
(-1.9)
P 		358.4
(1.9)
P 		250.1
(-3)
P 		132
avr 380.5
(3) 		222.8
(-3) 		255
(-1.8) 		275
(-1) 		158

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 304
1 2 3 4 5 6 range
A 141.7
(-3)
P 		337.9
(3)
P 		168.9
(-2.2)
P 		184
(-1.7)
P 		241.9
(0.1)
P 		210.5
(-0.9)
P 		196
B 325.8
(0.4)
P 		327.4
(0.5)
P 		165.1
(-3)
P 		198.7
(-2.3)
P 		367.4
(1.3)
P 		445.7
(3)
P 		281
C 371.9
(3)
P 		263.3
(0.1)
P 		156.4
(-2.7)
P 		146.4
(-3)
P 		247.8
(-0.3)
P 		369
(2.9)
P 		226
avr 279.8
(0.9) 		309.5
(1.9) 		163.5
(-3) 		176.4
(-2.6) 		285.7
(1.1) 		341.7
(3) 		178
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173903_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24143
Sequence Type Exemplar sequence
Representative Public ID AU109527 NCBI
Target Description AU109527 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=B0280.8 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AU109527 /WB_GENE_ID=B0280.8 /WP=CE00815 /CHR=3 /FEA=Genomic Cluster /GEN=nhr-10 /DEF=retinoic acid; Caenorhabditis elegans cDNA clone:yk708c4 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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
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:7112294-7115357(-) 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:173903_AT
gaaacagtttccattatcgtcatagcgtatccataagtataatttcattcccatatctgg
taataactctttctctacattttgtcgatatccatcaactgtgccttaccgttttacaaa
tcagtgatattttatttccaactcatattaattctaatcacaccatgaatttattgttgc
caacgggtcaaaatctttcatcatcatctagaaaatgttcatcttctacacctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAACAGTTTCCATTATCGTCATAG 125 357 1208 Antisense
ATCGTCATAGCGTATCCATAAGTAT 686 35 1223 Antisense
GTATAATTTCATTCCCATATCTGGT 128 453 1244 Antisense
ATATCTGGTAATAACTCTTTCTCTA 326 21 1260 Antisense
CTTTCTCTACATTTTGTCGATATCC 86 223 1276 Antisense
TCGATATCCATCAACTGTGCCTTAC 117 603 1292 Antisense
GTGCCTTACCGTTTTACAAATCAGT 692 477 1308 Antisense
AGTGATATTTTATTTCCAACTCATA 484 59 1330 Antisense
CACCATGAATTTATTGTTGCCAACG 157 201 1368 Antisense
GGGTCAAAATCTTTCATCATCATCT 582 497 1392 Antisense
GAAAATGTTCATCTTCTACACCTCA 555 353 1418 Antisense
Sequence Source Affymetrix Proprietary Database