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[193721_at] Ligand-binding domain of nuclear hormone receptors

Description F54B8.2 /REP_DB=WormBase Gene ID /WP=CE16104 /TR=O45560 /GB=CAB07624.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors
Cluster 6grp_total > 53      4grp_total > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5
1 2 3 4 range
A 3.2
(0.6)
A 		1.4
(-3)
A 		1.5
(-2.8)
A 		4.4
(3)
A 		3
B 2.8
(3)
A 		1.3
(-3)
A 		2.1
(0.2)
A 		2.8
(3)
A 		2
C 1.2
(-3)
A 		1.7
(-2.4)
A 		1.2
(-3)
A 		6.3
(3)
A 		5
avr 2.4
(-1.2) 		1.5
(-3) 		1.6
(-2.8) 		4.5
(3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 3.1
(-2.9)
A 		3.6
(-2.8)
A 		39.2
(3)
A 		19.2
(-0.2)
A 		3.1
(-2.9)
A 		2.2
(-3)
A 		37
B 2.3
(-3)
A 		3
(-2.8)
A 		22.2
(3)
A 		3.5
(-2.6)
A 		2.9
(-2.8)
A 		2.3
(-3)
A 		20
C 1.5
(-3)
A 		2.5
(-1.2)
A 		1.7
(-2.6)
A 		4.8
(3)
A 		2.1
(-1.9)
A 		2.5
(-1.2)
A 		3
avr 2.3
(-3) 		3
(-2.8) 		21
(3) 		9.2
(-0.8) 		2.7
(-2.9) 		2.3
(-3) 		19
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1
1 2 3 4 range
A 1.2
(3)
A 		0.3
(-3)
A 		0.4
(-2.3)
A 		0.6
(-1)
A 		1
B 0.9
(3)
A 		0.3
(-3)
A 		0.5
(-1)
A 		0.6
(-0)
A 		1
C 0.4
(-3)
A 		0.5
(-2.1)
A 		0.4
(-3)
A 		1.1
(3)
A 		1
avr 0.8
(3) 		0.4
(-3) 		0.4
(-3) 		0.8
(3) 		0

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8
1 2 3 4 5 6 range
A 0.6
(-2.9)
A 		1.3
(-2.4)
A 		8.5
(3)
A 		4.9
(0.3)
A 		0.9
(-2.7)
A 		0.5
(-3)
A 		8
B 0.8
(-3)
A 		1
(-2.7)
A 		5.4
(3)
A 		0.9
(-2.9)
A 		1.2
(-2.5)
A 		0.9
(-2.9)
A 		5
C 0.6
(-1)
A 		0.8
(1)
A 		0.4
(-3)
A 		1
(3)
A 		0.7
(-0)
A 		0.8
(1)
A 		1
avr 0.7
(-3) 		1
(-2.6) 		4.8
(3) 		2.3
(-0.7) 		0.9
(-2.7) 		0.7
(-3) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193721_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13482
Sequence Type Exemplar sequence
Representative Public ID F54B8.2 NCBI
Target Description F54B8.2 /REP_DB=WormBase Gene ID /WP=CE16104 /TR=O45560 /GB=CAB07624.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors
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_074546(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074546 NCBI Caenorhabditis elegans F54B8.2 (F54B8.2) mRNA, complete cds. 11/11 None
F54B8.2 ENSEMBL cdna:known chromosome:CEL140:V:15814866:15815688:1 gene:F54B8.2 11/11 None
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
chrV:15814865-15815688(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ligand-binding domain of nuclear hormone receptors
Ensembl F54B8.2
Entrez Gene 186200 Entrez gene
SwissProt O45560 EMBL-EBI
WormBase CE16104 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
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07624 Hypothetical protein F54B8.2 [Caenorhabditis elegans] ref|NP_506947.1| F54B8.2 [Caenorhabditis elegans] 1.0E-130
blast CAB03437 Hypothetical protein T26E4.8 [Caenorhabditis elegans] ref|NP_506938.1| T26E4.8 [Caenorhabditis elegans] 3.0E-81
blast CAA21008 Hypothetical protein Y32B12B.6 [Caenorhabditis elegans] ref|NP_507191.1| Temporarily Assigned Gene name family member (tag-122) [Caenorhabditis elegans] 3.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.0E-42
Sequence
Target Sequence 
>C. ELEGANS:193721_AT
gagtacatccctagatgtcatcctatgaactatagagattggttttatctggttgcagtt
tctacctcggattttttgagaaaattcccattcgtatatcaatcaagttcacgtgatcaa
tcgtttattctacaaaagaattttgtgaaagtcgcaagtttttgtgaagcatttcgatat
tatctgttgggagagaaacaattgacatttcccgatgggtcgaatattttgatagaggat
ttgggaatcgaactcggagaacggatcaaattcagattggttgccaaatgttgtgagctt
caaattacaaacgaggagtttttattactattggtattgatatttagtagtccagctatt
gaagatctctcagatacgggaaaccttcttctatcttcgttccaaagttattacagttca
agtcttcttaaatattgtatgcttactttttatcaagatggtccaatcaggttcacaaaa
ttattggacgtatttcaagttgttgggcaacactatgaagatctcaatcgatactttgta
ttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTACATCCCTAGATGTCATCCTA 305 399 166 Antisense
TATCTGGTTGCAGTTTCTACCTCGG 363 659 211 Antisense
TTGCAGTTTCTACCTCGGATTTTTT 374 701 218 Antisense
AAATTCCCATTCGTATATCAATCAA 639 113 247 Antisense
GTTCACGTGATCAATCGTTTATTCT 252 445 272 Antisense
GGGAATCGAACTCGGAGAACGGATC 426 489 408 Antisense
GTAGTCCAGCTATTGAAGATCTCTC 257 457 512 Antisense
GATCTCTCAGATACGGGAAACCTTC 221 417 529 Antisense
CTTCTTCTATCTTCGTTCCAAAGTT 141 221 550 Antisense
AAGATGGTCCAATCAGGTTCACAAA 591 153 620 Antisense
AGATCTCAATCGATACTTTGTATTC 192 67 684 Antisense
Sequence Source Affymetrix Proprietary Database