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[193566_at] Zinc finger, C4 type (two domains)

Description C06C6.4 /REP_DB=WormBase Gene ID /WP=CE28202 /GEN=nhr-63 /TR=O62034 /GB=CAB07558.2 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_total > 27      4grp_total > 39      6grp_cgc > 14      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 228
1 2 3 4 range
A 247.4
(3)
P 		124.8
(-2.3)
A 		109.4
(-3)
A 		124.6
(-2.3)
A 		138
B 301.8
(3)
P 		94.9
(-2.4)
A 		73.5
(-3)
A 		149.8
(-1)
A 		228
C 282.8
(3)
P 		147.7
(-1.4)
A 		97.2
(-3)
A 		105.1
(-2.7)
A 		186
avr 277.3
(3) 		122.5
(-2.1) 		93.4
(-3) 		126.5
(-1.9) 		184

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 258
1 2 3 4 5 6 range
A 270.1
(3)
P 		197.9
(0.5)
P 		140.4
(-1.5)
P 		96.9
(-3)
A 		144.4
(-1.4)
A 		121.3
(-2.2)
A 		173
B 339.9
(3)
P 		212.3
(0)
P 		95.9
(-2.7)
A 		162
(-1.1)
P 		82
(-3)
A 		184.3
(-0.6)
P 		258
C 278.7
(3)
P 		224.4
(1.2)
P 		106.2
(-2.8)
A 		114.7
(-2.5)
A 		101.4
(-3)
A 		169.5
(-0.7)
P 		177
avr 296.2
(3) 		211.5
(0.3) 		114.2
(-2.8) 		124.5
(-2.5) 		109.3
(-3) 		158.4
(-1.4) 		187
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 90.1
(3)
P 		27.1
(-2.3)
A 		28.6
(-2.1)
A 		18.2
(-3)
A 		72
B 96.2
(3)
P 		23.4
(-2.5)
A 		17
(-3)
A 		31.9
(-1.9)
A 		79
C 93.6
(3)
P 		42.5
(-1)
A 		33.9
(-1.7)
A 		17.7
(-3)
A 		76
avr 93.3
(3) 		31
(-2.3) 		26.5
(-2.7) 		22.6
(-3) 		71

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 95
1 2 3 4 5 6 range
A 49.8
(0.3)
P 		70.4
(3)
P 		30.6
(-2.2)
P 		24.6
(-3)
A 		43.6
(-0.5)
A 		29.5
(-2.4)
A 		46
B 118.3
(3)
P 		70.7
(-0)
P 		23.3
(-3)
A 		42.9
(-1.8)
P 		33.3
(-2.4)
A 		68.7
(-0.1)
P 		95
C 103.3
(3)
P 		68.5
(0.4)
P 		27
(-2.7)
A 		23.1
(-3)
A 		32.8
(-2.3)
A 		56.7
(-0.5)
P 		80
avr 90.5
(3) 		69.9
(1.1) 		27
(-3) 		30.2
(-2.7) 		36.6
(-2.1) 		51.6
(-0.7) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193566_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13497
Sequence Type Exemplar sequence
Representative Public ID C06C6.4 NCBI
Target Description C06C6.4 /REP_DB=WormBase Gene ID /WP=CE28202 /GEN=nhr-63 /TR=O62034 /GB=CAB07558.2 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
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_171557(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171557 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-63) (nhr-63) mRNA, complete cds. 11/11 None
SNAP00000040512 ENSEMBL cdna:SNAP chromosome:CEL140:V:16005874:16007263:1 10/11 None
GENEFINDER00000040523 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16005178:16007263:1 11/11 None
C06C6.4 ENSEMBL cdna:known chromosome:CEL140:V:16005172:16007317:1 gene:C06C6.4 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:16005177-16007263(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-63
Ensembl C06C6.4
Entrez Gene 180068 Entrez gene
SwissProt O62034 EMBL-EBI
WormBase CE28202 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 CAB07558 Hypothetical protein C06C6.4 [Caenorhabditis elegans] ref|NP_741645.3| Nuclear Hormone Receptor family member (nhr-63) [Caenorhabditis elegans] 0.0
blast AAG15164 nuclear receptor NHR-63 [Caenorhabditis elegans] 0.0
blast CAB07558 Hypothetical protein C06C6.4 [Caenorhabditis elegans] ref|NP_741645.3| Nuclear Hormone Receptor family member (nhr-63) [Caenorhabditis elegans] 1.0E-166
blast AAG15164 nuclear receptor NHR-63 [Caenorhabditis elegans] 1.0E-166
blast CAB07558 Hypothetical protein C06C6.4 [Caenorhabditis elegans] ref|NP_741645.3| Nuclear Hormone Receptor family member (nhr-63) [Caenorhabditis elegans] 1.0E-123
blast AAG15164 nuclear receptor NHR-63 [Caenorhabditis elegans] 1.0E-123
blast CAB07555 Hypothetical protein C06C6.5a [Caenorhabditis elegans] ref|NP_507015.3| Nuclear Hormone Receptor family member (nhr-50) [Caenorhabditis elegans] 4.0E-94
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.3E-7
Sequence
Target Sequence 
>C. ELEGANS:193566_AT
ttttccgcaaattcaatcgctttcaaatttggataaggcagatttttcaaagctttctaa
atttgctttttttttatttcagaatgctgttttacgaaacttcagccccaaatggtccct
cctggcatcgtccattgattttgagagaaattgtcatctttatgaagatgttgtaacagt
tgacgattatcttgatatgatcgtgaaattctactccggttccatgtacggcgataataa
aattagtccaaaggaaatattaagagtcttcgagccattcctcacctattatggagttgt
tttggtacttcctatgaatgcgaaaatgttcaattcaattgaatatatggctcttgcaat
gcttttgctgttcgatggagctcatgccaacatttctgcagattgctcgaaaatgtgcca
tgacatcaaaaatgttattctgcgagagcttcgtgactattacatagacaatggtgtcga
tgaaatgcgattttttgaaactatcgacacagtgaatcatgtggagaaaggggaaagtaa
atttattgaagagctgctggcttgtgagcttcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTTCCGCAAATTCAATCGCTTTCA 605 675 522 Antisense
TACGAAACTTCAGCCCCAAATGGTC 533 639 614 Antisense
CTCCTGGCATCGTCCATTGATTTTG 395 235 640 Antisense
GATCGTGAAATTCTACTCCGGTTCC 173 415 720 Antisense
TACTCCGGTTCCATGTACGGCGATA 361 643 733 Antisense
TTAAGAGTCTTCGAGCCATTCCTCA 86 685 781 Antisense
GGCTCTTGCAATGCTTTTGCTGTTC 421 539 870 Antisense
TTTGCTGTTCGATGGAGCTCATGCC 457 667 885 Antisense
GAGCTCATGCCAACATTTCTGCAGA 113 389 899 Antisense
GCGAGAGCTTCGTGACTATTACATA 585 289 963 Antisense
AGAGCTGCTGGCTTGTGAGCTTCAT 341 69 1071 Antisense
Sequence Source Affymetrix Proprietary Database