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[194121_s_at] Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors

Description C48D5.1 /REP_DB=WormBase Gene ID /WP=CE24859 /GEN=nhr-6 /TR=SW:P41829 /GB=CAA85271.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors
Cluster 4grp_high_8_8 > 19      6grp_total > 27      4grp_total > 29      6grp_cgc > 05      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 365
1 2 3 4 range
A 424.2
(1.2)
P 		304.9
(-0.8)
P 		177.8
(-3)
P 		531.9
(3)
P 		354
B 465.7
(3)
P 		286.5
(-1)
P 		193.5
(-3)
A 		437
(2.4)
P 		272
C 441.1
(3)
P 		303.1
(-0)
P 		167.3
(-3)
P 		380.2
(1.7)
P 		274
avr 443.7
(2.9) 		298.2
(-0.4) 		179.5
(-3) 		449.7
(3) 		270

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 333
1 2 3 4 5 6 range
A 430.6
(3)
P 		258.9
(-0.1)
P 		127.4
(-2.5)
A 		97.5
(-3)
A 		160.5
(-1.9)
A 		294.5
(0.5)
P 		333
B 371.7
(3)
P 		252.9
(0.3)
M 		136.3
(-2.4)
A 		125.1
(-2.7)
A 		110.1
(-3)
A 		234
(-0.2)
P 		262
C 333.8
(3)
P 		266.7
(1.2)
P 		110.2
(-2.9)
A 		104.6
(-3)
A 		117.6
(-2.7)
A 		220.7
(0)
P 		229
avr 378.7
(3) 		259.5
(0.3) 		124.6
(-2.7) 		109.1
(-3) 		129.4
(-2.5) 		249.7
(0.1) 		270
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 154.5
(3)
P 		66.2
(-1.9)
P 		46.5
(-3)
P 		77.9
(-1.3)
P 		108
B 148.5
(3)
P 		70.8
(-1.5)
P 		44.8
(-3)
A 		93.1
(-0.2)
P 		104
C 146
(3)
P 		87.1
(-1)
P 		58.3
(-3)
P 		64.1
(-2.6)
P 		88
avr 149.7
(3) 		74.7
(-1.5) 		49.9
(-3) 		78.4
(-1.3) 		100

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 79.4
(1.9)
P 		92.1
(3)
P 		27.7
(-2.7)
A 		24.7
(-3)
A 		48.4
(-0.9)
A 		71.7
(1.2)
P 		67
B 129.3
(3)
P 		84.2
(0.2)
M 		33.1
(-3)
A 		33.1
(-3)
A 		44.7
(-2.3)
A 		87.3
(0.4)
P 		96
C 123.7
(3)
P 		81.4
(0.5)
P 		28.1
(-2.6)
A 		21
(-3)
A 		38.1
(-2)
A 		73.9
(0.1)
P 		103
avr 110.8
(3) 		85.9
(1.2) 		29.6
(-2.8) 		26.3
(-3) 		43.7
(-1.8) 		77.6
(0.6) 		85
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194121_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6367
Sequence Type Exemplar sequence
Representative Public ID C48D5.1 NCBI
Target Description C48D5.1 /REP_DB=WormBase Gene ID /WP=CE24859 /GEN=nhr-6 /TR=SW:P41829 /GB=CAA85271.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors
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_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 
GENEFINDER00000020151 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3573682:3578529:1 11/11 None
SNAP00000020146 ENSEMBL cdna:SNAP chromosome:CEL140:III:3576139:3578373:1 11/11 None
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
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
chrIII:3573681-3578373(+) 99.68 100.0
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
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:194121_S_AT
gcagatctttcttcgcaatcatggcaatccgcgtggcaaaccgatgtggcaacagcaccg
acacaattatgttcgagtctggagagcttttctcgttgaacgcgttccctgcctgcttcc
aacaaatcattcgattcatggttgacaaagcacgaaccttcagctcattggttgactggg
agcctcaggcattcgccgcctttattgctcttcaatttttggctggaaacacagaacata
acgtacttggattgaccaacaaacctctcgtcgaccaggttcaaagtaccatcatcaatg
ctctcaaggatcattgcagcggatctcagaacaaattggccaagatcgttagattgaccc
aagaattcgatgtattccatgctcttggactccaggccctggacattctctatccatcac
accagcttccagaagagttcatgttccttatcaatcttacacgtgctccattacgatcta
cggatgcaccgccagcttgtggaagcccagttgccccatctggaagttcactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAGATCTTTCTTCGCAATCATGGC 239 313 1307 Antisense
CAATCCGCGTGGCAAACCGATGTGG 107 181 1331 Antisense
GAGAGCTTTTCTCGTTGAACGCGTT 626 389 1388 Antisense
TGCCTGCTTCCAACAAATCATTCGA 137 585 1416 Antisense
AAGCACGAACCTTCAGCTCATTGGT 396 151 1454 Antisense
GGTTGACTGGGAGCCTCAGGCATTC 456 507 1476 Antisense
GACTCCAGGCCCTGGACATTCTCTA 362 373 1694 Antisense
CCATCACACCAGCTTCCAGAAGAGT 286 271 1720 Antisense
GTTCCTTATCAATCTTACACGTGCT 167 441 1749 Antisense
ACACGTGCTCCATTACGATCTACGG 262 109 1765 Antisense
AGTTGCCCCATCTGGAAGTTCACTT 119 65 1815 Antisense
Sequence Source Affymetrix Proprietary Database