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[176050_at]

Description Y41D4B.E /REP_DB=WormBase Gene ID /WP=CE26089 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_total > 41      4grp_total > 17      6grp_cgc > 81      6grp_cgc_sub > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 7.7
(-2.9)
A 		16.3
(-2.2)
A 		6.9
(-3)
A 		78.8
(3)
A 		72
B 22.4
(-0.4)
A 		6.3
(-2.6)
A 		46.8
(3)
A 		3.3
(-3)
A 		44
C 7.8
(-3)
A 		54.7
(-0.3)
A 		16
(-2.5)
A 		113.7
(3)
A 		106
avr 12.6
(-3) 		25.8
(-1.5) 		23.2
(-1.8) 		65.3
(3) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 104
1 2 3 4 5 6 range
A 83
(1.6)
A 		6.7
(-2.8)
A 		107.3
(3)
A 		27.1
(-1.7)
A 		16.9
(-2.2)
A 		3.9
(-3)
A 		103
B 19.8
(-2)
A 		47.2
(-0.4)
A 		104.1
(3)
A 		57.7
(0.2)
A 		48
(-0.3)
A 		3.3
(-3)
A 		101
C 54.8
(0.1)
A 		87.8
(2.1)
P 		64
(0.6)
A 		101.5
(3)
P 		6.5
(-3)
A 		24.8
(-1.8)
A 		95
avr 52.5
(0.1) 		47.2
(-0.3) 		91.8
(3) 		62.1
(0.8) 		23.8
(-2) 		10.7
(-3) 		81
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 2.8
(-2.4)
A 		3.5
(-1.9)
A 		1.8
(-3)
A 		11.5
(3)
A 		10
B 7.1
(0.8)
A 		1.6
(-2.5)
A 		10.9
(3)
A 		0.7
(-3)
A 		10
C 2.6
(-3)
A 		15.7
(1.7)
A 		5.6
(-1.9)
A 		19.2
(3)
A 		17
avr 4.2
(-3) 		6.9
(-0.4) 		6.1
(-1.2) 		10.5
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26
1 2 3 4 5 6 range
A 15.3
(0.8)
A 		2.4
(-2.6)
A 		23.4
(3)
A 		6.9
(-1.4)
A 		5.1
(-1.9)
A 		0.9
(-3)
A 		23
B 6.9
(-1.6)
A 		15.7
(0.6)
A 		25.3
(3)
A 		15.3
(0.5)
A 		19.5
(1.6)
A 		1.2
(-3)
A 		24
C 20.3
(1.4)
A 		26.8
(3)
P 		16.3
(0.4)
A 		20.4
(1.4)
P 		2.1
(-3)
A 		8.3
(-1.5)
A 		25
avr 14.2
(0.5) 		15
(0.8) 		21.7
(3) 		14.2
(0.5) 		8.9
(-1.2) 		3.5
(-3) 		18
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176050_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19287
Sequence Type Exemplar sequence
Representative Public ID Y41D4B.E NCBI
Target Description Y41D4B.E /REP_DB=WormBase Gene ID /WP=CE26089 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_067709, NM_067710
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000005516 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1617460:1619334:-1 None
Y41D4B.20 ENSEMBL cdna:known chromosome:CEL140:IV:1617460:1618943:-1 gene:Y41D4B.20 None
NM_067709 NCBI Caenorhabditis elegans Y41D4B.20 (Y41D4B.20) mRNA, complete cds. None
GENEFINDER00000005535 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1616735:1619456:-1 None
GENEFINDER00000005550 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1620197:1633204:1 None
SNAP00000005516 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1617460:1619334:-1 None
SNAP00000005517 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1621217:1623725:1 None
NM_067710 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-92) (nhr-92) mRNA, complete cds. A 
Y41D4B.20 ENSEMBL cdna:known chromosome:CEL140:IV:1617460:1618943:-1 gene:Y41D4B.20 None
Y41D4B.8 ENSEMBL cdna:known chromosome:CEL140:IV:1620173:1623731:1 gene:Y41D4B.8 A 
NM_067709 NCBI Caenorhabditis elegans Y41D4B.20 (Y41D4B.20) mRNA, complete cds. None
GENEFINDER00000005535 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1616735:1619456:-1 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
chrIV:1622015-1623727(+) 71.96 71.96
chrIV:1616740-1620338(-) 100.0 100.0
Public Domain and Genome References
Gene Title

Gene Symbol nhr-92
Ensembl Y41D4B.20
Y41D4B.8
Entrez Gene 176971 Entrez gene
189824 Entrez gene
SwissProt Q95Y08 EMBL-EBI
Q95Y07 EMBL-EBI
WormBase CE27627 Wormbase
CE37567 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 AAK68482 Nuclear hormone receptor family protein 92 [Caenorhabditis elegans] ref|NP_500111.3| Nuclear Hormone Receptor family member (nhr-92) [Caenorhabditis elegans] 0.0
blast AAG15184 nuclear receptor NHR-92 [Caenorhabditis elegans] 0.0
blast AAL32242 Nuclear hormone receptor family protein 87 [Caenorhabditis elegans] ref|NP_500112.2| Nuclear Hormone Receptor family member (nhr-87) [Caenorhabditis elegans] 1.0E-170
blast AAK68482 Nuclear hormone receptor family protein 92 [Caenorhabditis elegans] ref|NP_500111.3| Nuclear Hormone Receptor family member (nhr-92) [Caenorhabditis elegans] 1.0E-157
blast AAG15184 nuclear receptor NHR-92 [Caenorhabditis elegans] 1.0E-156
blast CAE67969 Hypothetical protein CBG13575 [Caenorhabditis briggsae] 1.0E-130
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 9.3E-17
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.8E-30
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.7E-21
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.3E-23
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.8E-30
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.6E-24
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.0E-23
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.8E-24
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.2E-9
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.3E-12
Sequence
Target Sequence 
>C. ELEGANS:176050_AT
tgcaaacgactccgccaaaatgaattcgagccgacggaacaccacatacttgacagtaca
accctgctccacaacttctacctacaattcatcatcctcgaaggtggctatttcgcatgt
caatatggcagaacagacattacctacctaccatctgatggacaacagccaatttccgag
gtagaagcttccaaaatgttcgccagctcattcgacacttaccgccgcaatgtgtacgat
ccaatgatccgaattgcgtgtgacaaattcgaatttctggctctaacagccttaactcta
ttcgacacggggctagaaggccagtccgatcaatgcacagaatcatgcagaaggattcgg
gaatccgtgcagcgggaagttctacagtactccaagctgacgagatcagaattagattcg
tcaattcgactaggggatatattgtcaatcctaccgaatttacagagagccactcaacga
ttccatgaagatatgacaatttcgaatgtgatgaatgcgtattcggtggacgagaaattc
tataacttgggcttcaagaccagacaagacaaacgattagaggctggtgatggtttttgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCAAACGACTCCGCCAAAATGAAT 370 577 82 Antisense
TCCGCCAAAATGAATTCGAGCCGAC 254 597 92 Antisense
GAATTCGAGCCGACGGAACACCACA 464 323 103 Antisense
TTCGAGCCGACGGAACACCACATAC 551 693 106 Antisense
GACGGAACACCACATACTTGACAGT 187 377 114 Antisense
ATACTTGACAGTACAACCCTGCTCC 694 23 127 Antisense
ACGAGAAATTCTATAACTTGGGCTT 521 93 611 Antisense
ATAACTTGGGCTTCAAGACCAGACA 513 23 623 Antisense
TGGGCTTCAAGACCAGACAAGACAA 414 553 629 Antisense
GACAAGACAAACGATTAGAGGCTGG 61 365 644 Antisense
ATTAGAGGCTGGTGATGGTTTTTGT 5 3 657 Antisense
Sequence Source Affymetrix Proprietary Database