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[190872_at] nuclear hormone receptor

Description F16B4.9 /REP_DB=WormBase Gene ID /WP=CE17019 /TR=O44635 /GB=AAB94240.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_total > 67      4grp_total > 02      6grp_cgc > 38      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 620
1 2 3 4 range
A 96.6
(-2)
A 		12.6
(-3)
A 		52
(-2.5)
A 		496.6
(3)
P 		484
B 94
(-2.2)
A 		7.8
(-3)
A 		43.2
(-2.7)
A 		627.6
(3)
P 		620
C 80.5
(-2.2)
A 		8.8
(-3)
A 		54.4
(-2.5)
A 		526.9
(3)
P 		518
avr 90.4
(-2.1) 		9.7
(-3) 		49.9
(-2.6) 		550.4
(3) 		541

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 871
1 2 3 4 5 6 range
A 226.6
(-2)
P 		157.6
(-2.5)
A 		105.7
(-2.9)
A 		229
(-2)
A 		86
(-3)
A 		946.9
(3)
P 		861
B 206.2
(-1.9)
P 		118.8
(-2.7)
M 		85.4
(-2.9)
P 		76.1
(-3)
M 		112.9
(-2.7)
A 		816.6
(3)
P 		741
C 276.7
(-1.6)
P 		156.1
(-2.5)
P 		164.1
(-2.4)
A 		164.7
(-2.4)
A 		79.1
(-3)
A 		925.5
(3)
P 		846
avr 236.5
(-1.9) 		144.2
(-2.6) 		118.4
(-2.8) 		156.6
(-2.5) 		92.7
(-3) 		896.3
(3) 		804
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 132
1 2 3 4 range
A 35.2
(-0.2)
A 		2.7
(-3)
A 		13.6
(-2.1)
A 		72.7
(3)
P 		70
B 30
(-1.7)
A 		1.9
(-3)
A 		10
(-2.6)
A 		133.7
(3)
P 		132
C 26.6
(-1.3)
A 		2.5
(-3)
A 		19
(-1.9)
A 		88.9
(3)
P 		86
avr 30.6
(-1.2) 		2.4
(-3) 		14.2
(-2.3) 		98.4
(3) 		96

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 290
1 2 3 4 5 6 range
A 41.8
(-2.5)
P 		56
(-2)
A 		23
(-3)
A 		58.1
(-2)
A 		26
(-2.9)
A 		230.5
(3)
P 		208
B 71.7
(-1.9)
P 		39.5
(-2.6)
M 		20.7
(-3)
P 		20.1
(-3)
M 		45.9
(-2.5)
A 		304.5
(3)
P 		284
C 102.6
(-1.4)
P 		47.6
(-2.5)
P 		41.8
(-2.7)
A 		33.1
(-2.8)
A 		25.6
(-3)
A 		309.8
(3)
P 		284
avr 72
(-2) 		47.7
(-2.5) 		28.5
(-3) 		37.1
(-2.8) 		32.5
(-2.9) 		281.6
(3) 		253
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190872_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15768
Sequence Type Exemplar sequence
Representative Public ID F16B4.9 NCBI
Target Description F16B4.9 /REP_DB=WormBase Gene ID /WP=CE17019 /TR=O44635 /GB=AAB94240.1 /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_071053(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071053 NCBI Caenorhabditis elegans F16B4.9 (F16B4.9) mRNA, complete cds. 11/11 None
SNAP00000004022 ENSEMBL cdna:SNAP chromosome:CEL140:V:1602145:1604563:-1 11/11 None
GENEFINDER00000004038 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:1603805:1607644:-1 11/11 None
F16B4.9 ENSEMBL cdna:known chromosome:CEL140:V:1603805:1607644:-1 gene:F16B4.9 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:1603804-1607644(-) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-178
Ensembl F16B4.9
Entrez Gene 184560 Entrez gene
SwissProt O44635 EMBL-EBI
WormBase CE17680 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 AAB94240 Hypothetical protein F16B4.9 [Caenorhabditis elegans] ref|NP_503454.2| F16B4.9 [Caenorhabditis elegans] 0.0
blast CAE62506 Hypothetical protein CBG06611 [Caenorhabditis briggsae] 1.0E-122
blast AAB94240 Hypothetical protein F16B4.9 [Caenorhabditis elegans] ref|NP_503454.2| F16B4.9 [Caenorhabditis elegans] 1.0E-103
blast CAB03298 Hypothetical protein T06C12.6 [Caenorhabditis elegans] ref|NP_506967.1| Nuclear Hormone Receptor family member (nhr-102) [Caenorhabditis elegans] 8.0E-96
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.4E-20
Sequence
Target Sequence 
>C. ELEGANS:190872_AT
gatagttgccacatggctggcacattgtccatactttcaaaaactagaatcaacgttgaa
gtatcaaatgttcaaagttgtctggaatgtatggagaaggtttgagcgtgtggagatgtc
agtgaaaatgtatgaaagggagactcctggggaggttatgaaattcgcaatttctgacaa
gtactatgttactccgaagctgaaaattgacatatcaaaagtcacgaattggcccgtacc
atttatgggtggaatattccgacggtcaattcaaaatatgtttgagcaaactggagttcc
acttgcctatctggaaccatcatcgatggaaatggcatatatgttgagccaactaagctg
gcagttagcagcacaagctctccaaggaaaagtaatggaactagctgaagctcaacaaga
agagttagcaaataatctccacgatcactacctccaaattaaacggcgatcgaactacgc
gggtcgtcttgttaaactga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATAGTTGCCACATGGCTGGCACAT 469 425 579 Antisense
GGCTGGCACATTGTCCATACTTTCA 697 539 593 Antisense
GTACTATGTTACTCCGAAGCTGAAA 673 457 759 Antisense
AAAGTCACGAATTGGCCCGTACCAT 582 113 796 Antisense
GGTGGAATATTCCGACGGTCAATTC 537 497 826 Antisense
CACTTGCCTATCTGGAACCATCATC 588 195 878 Antisense
GGCAGTTAGCAGCACAAGCTCTCCA 216 537 938 Antisense
AAATAATCTCCACGATCACTACCTC 674 115 1008 Antisense
ACGATCACTACCTCCAAATTAAACG 595 83 1019 Antisense
TAAACGGCGATCGAACTACGCGGGT 680 565 1038 Antisense
TACGCGGGTCGTCTTGTTAAACTGA 223 365 1054 Antisense
Sequence Source Affymetrix Proprietary Database