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[192782_at] nuclear hormone receptor

Description H12C20.3 /REP_DB=WormBase Gene ID /WP=CE18808 /GEN=nhr-68 /TR=Q9XXM8 /GB=CAA18351.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 56      6grp_high1_10_10 > 75      4grp_highest_8_8 > 18      4grp_high_8_8 > 62      6grp_highest_nonorm > 83      6grp_total > 65      4grp_total > 59      6grp_cgc > 56      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 466
1 2 3 4 range
A 227.8
(-0.4)
P 		282.9
(0.9)
P 		367.9
(3)
P 		120.8
(-3)
P 		247
B 317.5
(0.3)
P 		329.1
(0.4)
P 		527.5
(3)
P 		61.6
(-3)
P 		466
C 251.1
(-0.5)
P 		317.2
(0.8)
P 		427
(3)
P 		123.2
(-3)
P 		304
avr 265.5
(-0.1) 		309.7
(0.7) 		440.8
(3) 		101.9
(-3) 		339

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 432
1 2 3 4 5 6 range
A 266.4
(-3)
P 		390
(-1.1)
P 		652
(3)
P 		465.6
(0.1)
P 		350.9
(-1.7)
P 		519.8
(0.9)
P 		386
B 391.4
(-3)
P 		508.3
(-0.7)
P 		567.9
(0.4)
P 		421.7
(-2.4)
P 		460.4
(-1.7)
P 		698.5
(3)
P 		307
C 366.3
(-2.9)
P 		478.8
(-0.5)
P 		450.6
(-1.1)
P 		524.1
(0.5)
P 		360.6
(-3)
P 		643
(3)
P 		282
avr 341.4
(-3) 		459
(-0.5) 		556.8
(1.6) 		470.5
(-0.2) 		390.6
(-1.9) 		620.4
(3) 		279
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 83
(2)
P 		61.4
(0.3)
P 		96.2
(3)
P 		17.7
(-3)
P 		79
B 101.3
(1.9)
P 		81.3
(0.8)
P 		122.2
(3)
P 		13.1
(-3)
P 		109
C 83.1
(-0.1)
P 		91.2
(0.3)
P 		148.8
(3)
P 		20.8
(-3)
P 		128
avr 89.1
(1.1) 		78
(0.5) 		122.4
(3) 		17.2
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 211
1 2 3 4 5 6 range
A 49.1
(-3)
P 		138.7
(2.8)
P 		142
(3)
P 		118.1
(1.5)
P 		105.9
(0.7)
P 		126.5
(2)
P 		93
B 136.2
(-2)
P 		169.2
(-0.7)
P 		137.9
(-1.9)
P 		111.7
(-3)
P 		187
(0)
P 		260.5
(3)
P 		149
C 135.8
(-1.3)
P 		146.1
(-0.8)
P 		114.7
(-2.5)
P 		105.4
(-3)
P 		116.7
(-2.4)
P 		215.2
(3)
P 		110
avr 107
(-3) 		151.3
(-0.2) 		131.5
(-1.4) 		111.7
(-2.7) 		136.5
(-1.1) 		200.7
(3) 		94
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192782_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12944
Sequence Type Exemplar sequence
Representative Public ID H12C20.3 NCBI
Target Description H12C20.3 /REP_DB=WormBase Gene ID /WP=CE18808 /GEN=nhr-68 /TR=Q9XXM8 /GB=CAA18351.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
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_073535(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073535 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-68) (nhr-68) mRNA, complete cds. 11/11 None
SNAP00000002550 ENSEMBL cdna:SNAP chromosome:CEL140:V:11576049:11578143:1 11/11 None
GENEFINDER00000002552 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11576049:11578143:1 11/11 None
H12C20.3 ENSEMBL cdna:known chromosome:CEL140:V:11576029:11578295:1 gene:H12C20.3 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:11576048-11578143(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-68
Ensembl H12C20.3
Entrez Gene 179589 Entrez gene
SwissProt Q9XXM8 EMBL-EBI
WormBase CE18808 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 CAA18351 Hypothetical protein H12C20.3 [Caenorhabditis elegans] ref|NP_505936.1| Nuclear Hormone Receptor family member (nhr-68) [Caenorhabditis elegans] 0.0
blast AAO39181 nuclear receptor NHR-68 [Caenorhabditis elegans] 0.0
blast CAE75338 Hypothetical protein CBG23318 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.1E-37
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.3E-41
Sequence
Target Sequence 
>C. ELEGANS:192782_AT
gatgattatcattactggcacgagagagattggttcgttctcactgaatatgcaaaaacg
ttcaaggtttttaagaatatgccatatcatgataaaacggaattagtttgccatgcagct
attgtcattcctgttctcaatcaagtttataattccccagattatgggcttgataccgta
gtatttccggatggaacatattatgatagaactcatgaacctacaagaccagctggactt
aaccgcaagaagtaccaagtgctagatcttgttttgaaaccgtttagagaaatggaaatt
aatttcaatgaatttgcagcatttaaagcaatcacatttttaaatccagatgcggatatt
tcccttgaatcaaaacatgcaattaatgaggaacgtgttttaatcacaaaacaattgtat
gcgtatatggtacagaaggacgggttggagaaagcaatttacagatttgggcgattaatt
cttatgggtacttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGATTATCATTACTGGCACGAGA 305 411 568 Antisense
GATTGGTTCGTTCTCACTGAATATG 546 435 595 Antisense
GTTTGCCATGCAGCTATTGTCATTC 431 451 673 Antisense
TTGTCATTCCTGTTCTCAATCAAGT 570 707 689 Antisense
ATAATTCCCCAGATTATGGGCTTGA 396 23 716 Antisense
GGGCTTGATACCGTAGTATTTCCGG 161 493 733 Antisense
GAACTCATGAACCTACAAGACCAGC 37 349 776 Antisense
CAAGACCAGCTGGACTTAACCGCAA 551 183 791 Antisense
AGTGCTAGATCTTGTTTTGAAACCG 552 59 825 Antisense
GATGCGGATATTTCCCTTGAATCAA 164 415 916 Antisense
GGCGATTAATTCTTATGGGTACTTC 593 539 1037 Antisense
Sequence Source Affymetrix Proprietary Database