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[192777_at] nuclear hormone receptor

Description F44C8.3 /REP_DB=WormBase Gene ID /WP=CE17824 /GEN=nhr-18 /TR=O16360 /GB=AAB65890.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 45      6grp_high1_10_10 > 54      4grp_high_8_8 > 13      6grp_highest_nonorm > 81      6grp_total > 40      4grp_total > 03      6grp_cgc > 35      6grp_cgc_sub > Cu      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1470
1 2 3 4 range
A 312.4
(-2.2)
P 		193.3
(-2.7)
P 		116
(-3)
P 		1552
(3)
P 		1436
B 223
(-2.6)
P 		230.8
(-2.6)
P 		129.6
(-3)
P 		1586.2
(3)
P 		1457
C 251.6
(-2.5)
P 		156.4
(-2.9)
P 		134
(-3)
M 		1563.5
(3)
P 		1430
avr 262.3
(-2.4) 		193.5
(-2.7) 		126.5
(-3) 		1567.2
(3) 		1441

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 269
1 2 3 4 5 6 range
A 246.9
(-1.2)
P 		232.1
(-1.5)
P 		434.8
(3)
P 		232.4
(-1.5)
P 		166.4
(-3)
P 		166
(-3)
P 		269
B 315.3
(3)
P 		260.4
(0.3)
P 		312.9
(2.9)
P 		288.9
(1.7)
P 		193.1
(-3)
P 		263
(0.4)
P 		122
C 265.4
(-0.1)
P 		343.4
(2.3)
P 		234.4
(-1)
P 		313.9
(1.4)
P 		167.8
(-3)
P 		367.9
(3)
P 		200
avr 275.9
(1) 		278.6
(1.1) 		327.4
(3) 		278.4
(1.1) 		175.8
(-3) 		265.6
(0.6) 		152
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 308
1 2 3 4 range
A 113.7
(-0.5)
P 		42
(-2.6)
P 		30.3
(-3)
P 		227.2
(3)
P 		197
B 71.1
(-2.2)
P 		57
(-2.5)
P 		30
(-3)
P 		338
(3)
P 		308
C 83.3
(-1.9)
P 		45
(-3)
P 		46.7
(-3)
M 		263.6
(3)
P 		219
avr 89.4
(-1.7) 		48
(-2.7) 		35.7
(-3) 		276.3
(3) 		241

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 83
1 2 3 4 5 6 range
A 45.5
(-2.4)
P 		82.6
(1.7)
P 		94.7
(3)
P 		58.9
(-1)
P 		50.2
(-1.9)
P 		40.4
(-3)
P 		54
B 109.7
(3)
P 		86.7
(-1.1)
P 		76
(-3)
P 		76.5
(-2.9)
P 		78.5
(-2.6)
P 		98.1
(0.9)
P 		34
C 98.4
(0.8)
P 		104.8
(1.4)
P 		59.7
(-2.5)
P 		63.1
(-2.2)
P 		54.3
(-3)
P 		123.2
(3)
P 		69
avr 84.5
(1.6) 		91.4
(3) 		76.8
(0.1) 		66.2
(-2) 		61
(-3) 		87.2
(2.2) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192777_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15956
Sequence Type Exemplar sequence
Representative Public ID F44C8.3 NCBI
Target Description F44C8.3 /REP_DB=WormBase Gene ID /WP=CE17824 /GEN=nhr-18 /TR=O16360 /GB=AAB65890.1 /SUBMIT=ST.LOUIS /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_071207(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071207 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-18) (nhr-18) mRNA, complete cds. 11/11 None
SNAP00000011144 ENSEMBL cdna:SNAP chromosome:CEL140:V:2227973:2234966:1 11/11 None
GENEFINDER00000011149 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:2221907:2228797:1 11/11 None
F44C8.3 ENSEMBL cdna:known chromosome:CEL140:V:2227031:2228808:1 gene:F44C8.3 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:2227030-2228797(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-18
Ensembl F44C8.3
Entrez Gene 178702 Entrez gene
SwissProt O16360 EMBL-EBI
WormBase CE30796 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 AAK84533 Nuclear hormone receptor family protein 18 [Caenorhabditis elegans] ref|NP_503608.2| Nuclear Hormone Receptor family member (nhr-18) [Caenorhabditis elegans] sp|O16360|NHR18_CAEEL Nuclear hormone receptor family member nhr-18 0.0
blast AAD03690 nuclear receptor NHR-18 [Caenorhabditis elegans] pir||T43356 nuclear receptor NHR-18 - Caenorhabditis elegans (fragment) 0.0
blast T31792 hypothetical protein F44C8.3 - Caenorhabditis elegans 0.0
blast T31793 hypothetical protein F44C8.2 - Caenorhabditis elegans 0.0
blast AAR11990 nuclear receptor NHR-126 [Caenorhabditis elegans] gb|AAK84530.2| Nuclear hormone receptor family protein 126 [Caenorhabditis elegans] ref|NP_503609.2| Nuclear Hormone Receptor family member (nhr-126) [Caenorhabditis elegans] 1.0E-180
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 6.7E-5
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.4E-18
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 6.7E-5
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.1E-4
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.2E-5
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.5E-6
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-5
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 6.7E-5
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.1E-17
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.5E-5
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.4E-18
Sequence
Target Sequence 
>C. ELEGANS:192777_AT
gtaaagtcatgttggttctcctggacacggttggataagctatcggaaacggctaacaag
cagattaacaaaatgctcggtaaatcgcagttgatggtcggtaatggtgcatgtatgaat
atgaacaacttcgagattgatttatcttggtgcacgaattattcgttggagcagctgaaa
tacttttttcaaacaccgaatggtaagaaaaacttccaacagtcgatacaggatatgatc
gatttgaatcccagcagcattgaagtcagttacatgctcctacatctttctctggagcac
gcaggaaaacgattacatggagatgcactggatgctactgaaaatttagtgcaagttcag
gcaaacaacttgcataaatattatgtggagaaattgaagttggcaaattattcgtcacga
ctgacgcagttgatgaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAAAGTCATGTTGGTTCTCCTGGA 654 461 691 Antisense
GGTTCTCCTGGACACGGTTGGATAA 5 507 704 Antisense
ATCGCAGTTGATGGTCGGTAATGGT 211 35 774 Antisense
GATTGATTTATCTTGGTGCACGAAT 80 435 825 Antisense
GAAAAACTTCCAACAGTCGATACAG 693 351 897 Antisense
GAATCCCAGCAGCATTGAAGTCAGT 550 329 936 Antisense
AAGTCAGTTACATGCTCCTACATCT 464 157 953 Antisense
GCTCCTACATCTTTCTCTGGAGCAC 276 299 966 Antisense
GGAGATGCACTGGATGCTACTGAAA 517 517 1009 Antisense
GTTGGCAAATTATTCGTCACGACTG 709 435 1089 Antisense
GTCACGACTGACGCAGTTGATGAGA 687 465 1104 Antisense
Sequence Source Affymetrix Proprietary Database