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[190876_at] nuclear hormone receptor

Description C54F6.8 /REP_DB=WormBase Gene ID /WP=CE17603 /TR=O16443 /GB=AAG24018.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_total > 34      4grp_total > 21      6grp_cgc > 44      6grp_cgc_sub > 02      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 60.9
(-3)
M 		106.1
(2.7)
P 		74
(-1.3)
A 		108.3
(3)
P 		47
B 108.8
(3)
P 		69.7
(-1.3)
A 		54.7
(-3)
A 		87.2
(0.6)
A 		54
C 106.3
(0.7)
A 		41.8
(-2.8)
A 		37.1
(-3)
A 		150.6
(3)
P 		114
avr 92
(0.7) 		72.5
(-1.3) 		55.3
(-3) 		115.4
(3) 		60

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 85
1 2 3 4 5 6 range
A 67.1
(-0.9)
A 		57.8
(-1.6)
A 		118.3
(3)
A 		51.3
(-2.1)
A 		40.4
(-3)
A 		39.8
(-3)
A 		79
B 69.5
(-0)
A 		83.5
(3)
P 		77.3
(1.7)
A 		55.7
(-3)
A 		68.8
(-0.2)
A 		60
(-2.1)
A 		28
C 68.5
(0)
A 		102.5
(3)
A 		53.9
(-1.2)
A 		55.3
(-1.1)
A 		33.7
(-3)
A 		62.5
(-0.5)
P 		69
avr 68.4
(0.5) 		81.3
(2.7) 		83.2
(3) 		54.1
(-1.9) 		47.6
(-3) 		54.1
(-1.9) 		36
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 22.2
(2.3)
M 		23
(3)
P 		19.3
(-0.1)
A 		15.9
(-3)
P 		7
B 34.7
(3)
P 		17.2
(-1.8)
A 		12.7
(-3)
A 		18.6
(-1.4)
A 		22
C 35.2
(3)
A 		12
(-3)
A 		12.9
(-2.8)
A 		25.4
(0.5)
P 		23
avr 30.7
(3) 		17.4
(-2.1) 		15
(-3) 		20
(-1.1) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 12.4
(-2)
A 		20.6
(1.1)
A 		25.8
(3)
A 		13
(-1.8)
A 		12.2
(-2.1)
A 		9.7
(-3)
A 		16
B 24.2
(1.3)
A 		27.8
(2.9)
P 		18.8
(-1.2)
A 		14.8
(-3)
A 		28
(3)
A 		22.4
(0.5)
A 		13
C 25.4
(1.3)
A 		31.3
(3)
A 		13.7
(-2.2)
A 		11.1
(-2.9)
A 		10.9
(-3)
A 		20.9
(-0.1)
P 		20
avr 20.7
(0.4) 		26.6
(3) 		19.4
(-0.2) 		13
(-3) 		17
(-1.2) 		17.7
(-0.9) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190876_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12129
Sequence Type Exemplar sequence
Representative Public ID C54F6.8 NCBI
Target Description C54F6.8 /REP_DB=WormBase Gene ID /WP=CE17603 /TR=O16443 /GB=AAG24018.1 /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_072533(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072533 NCBI Caenorhabditis elegans C54F6.8 (C54F6.8) mRNA, complete cds. 11/11 None
GENEFINDER00000031634 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:7511636:7517451:1 9/11 None
C54F6.8 ENSEMBL cdna:known chromosome:CEL140:V:7514747:7516276:1 gene:C54F6.8 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000031618 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:7514747-7516277(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-171
Ensembl C54F6.8
Entrez Gene 183807 Entrez gene
SwissProt O16443 EMBL-EBI
WormBase CE17603 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 NP_504934 C54F6.8 [Caenorhabditis elegans] gb|AAG24018.1| Hypothetical protein C54F6.8 [Caenorhabditis elegans] 0.0
blast NP_504933 C54F6.9 [Caenorhabditis elegans] gb|AAG24012.1| Hypothetical protein C54F6.9 [Caenorhabditis elegans] 1.0E-170
blast NP_504934 C54F6.8 [Caenorhabditis elegans] gb|AAG24018.1| Hypothetical protein C54F6.8 [Caenorhabditis elegans] 1.0E-169
blast CAE57784 Hypothetical protein CBG00806 [Caenorhabditis briggsae] 1.0E-103
blast NP_504933 C54F6.9 [Caenorhabditis elegans] gb|AAG24012.1| Hypothetical protein C54F6.9 [Caenorhabditis elegans] 3.0E-99
blast CAE57784 Hypothetical protein CBG00806 [Caenorhabditis briggsae] 5.0E-87
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.8E-49
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.8E-14
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.3E-47
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.9E-42
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.8E-14
Sequence
Target Sequence 
>C. ELEGANS:190876_AT
gtggtcgtttcttgcagcttataacataattgaatattttacatcgtttcattttattga
taaactcaataatgatgataagatgaaactattccaagccaactcattcagatcgaatat
attttgtggcggaatgcgcggatataaagaaaaacgagacaaaatggtaacgccaggtgg
tcaagaaatacttcccgaaattctggtcaagttattgaatacatctccacagttgctgcg
tagagtgtgttgtcaagtgattgcaaggttgattgagctagaaatcacgaatgaggagtt
tgttctgctcaatctgatattctttttcaatactgtagacagcatgtctgactcggcaaa
aagtacacttggctcctggcaaaaactgtacacaaatgcgctatttcaatattgccaatt
gacttacaagcatcgtgctccatctcgtctggttgatctcttatcattatatcaaatcgt
tcaaaaaaatacatcagaaattcagtacattggcatcatgactcaagctctcctacctga
ttttcgggtcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGTCGTTTCTTGCAGCTTATAAC 79 489 480 Antisense
AACTATTCCAAGCCAACTCATTCAG 313 139 566 Antisense
AATACTTCCCGAAATTCTGGTCAAG 212 171 666 Antisense
ACATCTCCACAGTTGCTGCGTAGAG 439 105 700 Antisense
AGGAGTTTGTTCTGCTCAATCTGAT 448 55 773 Antisense
AGACAGCATGTCTGACTCGGCAAAA 109 73 816 Antisense
GCAAAAAGTACACTTGGCTCCTGGC 287 317 835 Antisense
GGCTCCTGGCAAAAACTGTACACAA 6 541 850 Antisense
GACTTACAAGCATCGTGCTCCATCT 40 373 900 Antisense
ATCTCGTCTGGTTGATCTCTTATCA 326 33 921 Antisense
CTCTCCTACCTGATTTTCGGGTCAA 489 227 1007 Antisense
Sequence Source Affymetrix Proprietary Database