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[175833_s_at] Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors

Description g538372 /REP_DB=GenBank Identifier /GB=U13076.1 /PROTEIN_GB=AAA96984.1 /CHR=3 /FEA=Mapped Transcript /DEF=steroid hormone receptor family member CNR8
Cluster 6grp_high1_10_10 > 38      4grp_highest_8_8 > 62      4grp_high_8_8 > 18      6grp_total > 38      4grp_total > 22      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 636
1 2 3 4 range
A 775.7
(3)
P 		435.2
(-0.7)
P 		228.5
(-3)
P 		725.8
(2.5)
P 		547
B 863.3
(3)
P 		453
(-0.9)
P 		227.1
(-3)
P 		811.6
(2.5)
P 		636
C 723.8
(3)
P 		498.9
(0.1)
P 		259.7
(-3)
P 		702.4
(2.7)
P 		464
avr 787.6
(3) 		462.4
(-0.6) 		238.4
(-3) 		746.6
(2.6) 		549

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 779
1 2 3 4 5 6 range
A 846.8
(3)
P 		357.2
(-0.8)
P 		125
(-2.6)
P 		73.7
(-3)
P 		291.2
(-1.3)
P 		513.6
(0.4)
P 		773
B 760.9
(3)
P 		409.6
(-0.1)
P 		89.4
(-3)
P 		183
(-2.2)
P 		173.7
(-2.2)
P 		456.4
(0.3)
P 		672
C 615
(3)
P 		376
(0.4)
P 		140
(-2.2)
P 		67.4
(-3)
A 		193.3
(-1.6)
P 		403.8
(0.7)
P 		548
avr 740.9
(3) 		380.9
(-0.4) 		118.1
(-2.9) 		108
(-3) 		219.4
(-1.9) 		457.9
(0.3) 		633
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 282.4
(3)
P 		94.5
(-2.1)
P 		59.7
(-3)
P 		106.2
(-1.7)
P 		223
B 275.3
(3)
P 		111.9
(-1.4)
P 		52.6
(-3)
P 		172.9
(0.2)
P 		223
C 239.6
(3)
P 		143.4
(-0.9)
P 		90.5
(-3)
P 		118.4
(-1.9)
P 		149
avr 265.8
(3) 		116.6
(-1.5) 		67.6
(-3) 		132.5
(-1) 		198

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 251
1 2 3 4 5 6 range
A 156.1
(3)
P 		127
(1.7)
P 		27.2
(-2.6)
P 		18.7
(-3)
P 		87.9
(0)
P 		125
(1.6)
P 		137
B 264.8
(3)
P 		136.3
(-0.2)
P 		21.7
(-3)
P 		48.5
(-2.3)
P 		70.6
(-1.8)
P 		170.2
(0.7)
P 		243
C 228
(3)
P 		114.7
(-0.2)
P 		35.6
(-2.4)
P 		13.5
(-3)
A 		62.6
(-1.6)
P 		135.2
(0.4)
P 		215
avr 216.3
(3) 		126
(0.1) 		28.2
(-3) 		26.9
(-3) 		73.7
(-1.5) 		143.5
(0.7) 		189
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175833_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19790
Sequence Type Exemplar sequence
Representative Public ID 538372 NCBI
Target Description g538372 /REP_DB=GenBank Identifier /GB=U13076.1 /PROTEIN_GB=AAA96984.1 /CHR=3 /FEA=Mapped Transcript /DEF=steroid hormone receptor family member CNR8
Cluster Evidence This cluster is supported by a Mapped Transcript.
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_065330(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065330 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-6) (nhr-6) mRNA, complete cds. 11/11 A 
C48D5.1.1 ENSEMBL cdna:known chromosome:CEL140:III:3563728:3578757:1 gene:C48D5.1 11/11 None
C48D5.1.2 ENSEMBL cdna:known chromosome:CEL140:III:3573682:3578750:1 gene:C48D5.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000020151 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:3576341-3578750(+) 96.98 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors
Gene Symbol nhr-6
Ensembl C48D5.1
Entrez Gene 175462 Entrez gene
SwissProt P41829 EMBL-EBI
WormBase CE24859 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 CAA85271 Hypothetical protein C48D5.1 [Caenorhabditis elegans] ref|NP_497731.1| Nuclear Hormone Receptor family member (nhr-6) [Caenorhabditis elegans] gb|AAO39171.1| nuclear receptor NHR-6 [Caenorhabditis elegans] gb|AAD03682.1| nuclear receptor NHR-6 [Caenorhabditis elegans] sp|P41829|NHR6_CAEEL Nuclear hormone receptor family member nhr-6 (Cnr8) 0.0
blast G88408 protein nhr-6 [imported] - Caenorhabditis elegans 0.0
blast AAG15119 nuclear receptor NHR-6 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.8E-17
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.4E-52
Sequence
Target Sequence 
>C. ELEGANS:175833_S_AT
tatttttcaaaatcgctagccccattgaattgcatatcgcaaagatttctaatttatttt
gtttccccactactgtctcaaacaaaaaatcacttccagaaaaatttcaaataacttgtt
accggtactttcccaacaatttttgctccttgaacctcaaatctctcagaatttgtcccc
ccattcggtttttattttatgaaaagcctctagtttttgtgtgaattccaatccccgaat
atcaattttgttttgtttcaattttcagagtttat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATTTTTCAAAATCGCTAGCCCCAT 97 663 1501 Antisense
CAAAATCGCTAGCCCCATTGAATTG 198 189 1508 Antisense
TAGCCCCATTGAATTGCATATCGCA 391 651 1517 Antisense
GCATATCGCAAAGATTTCTAATTTA 119 307 1532 Antisense
TTCCCCACTACTGTCTCAAACAAAA 108 697 1563 Antisense
CAACAATTTTTGCTCCTTGAACCTC 115 189 1634 Antisense
CCTTGAACCTCAAATCTCTCAGAAT 470 269 1648 Antisense
GAAAAGCCTCTAGTTTTTGTGTGAA 97 355 1701 Antisense
TTTTGTGTGAATTCCAATCCCCGAA 229 677 1715 Antisense
CCAATCCCCGAATATCAATTTTGTT 333 271 1728 Antisense
TTTTGTTTCAATTTTCAGAGTTTAT 185 677 1751 Antisense
Sequence Source GenBank