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[193670_at] Zinc finger, C4 type (two domains)

Description K06B4.2 /REP_DB=WormBase Gene ID /WP=CE11784 /GEN=nhr-52 /TR=SW:O17928 /GB=CAB05761.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_total > 15      4grp_total > 46      6grp_cgc > 32      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 61.7
(3)
A 		12.2
(-2.4)
A 		7.1
(-3)
A 		35.9
(0.2)
A 		55
B 79.6
(3)
A 		61.3
(0.8)
A 		29.1
(-3)
A 		28.7
(-3)
A 		51
C 32.1
(1.8)
A 		33.1
(2)
A 		37.9
(3)
A 		8.7
(-3)
A 		29
avr 57.8
(3) 		35.5
(-1) 		24.7
(-2.9) 		24.4
(-3) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 83
1 2 3 4 5 6 range
A 92.7
(3)
A 		44.2
(-0.5)
A 		54.9
(0.3)
A 		54.3
(0.2)
A 		39.1
(-0.9)
A 		9.5
(-3)
A 		83
B 47.1
(-0)
A 		84.7
(3)
A 		19.5
(-2.3)
A 		11
(-3)
A 		10.6
(-3)
A 		19.3
(-2.3)
A 		74
C 68.2
(1.2)
A 		87.9
(3)
M 		42.1
(-1.3)
A 		23.9
(-3)
A 		44.5
(-1.1)
A 		27.7
(-2.6)
A 		64
avr 69.3
(2.7) 		72.3
(3) 		38.8
(-0.8) 		29.7
(-1.8) 		31.4
(-1.6) 		18.8
(-3) 		54
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 24
1 2 3 4 range
A 22.5
(3)
A 		2.6
(-2.8)
A 		1.8
(-3)
A 		5.2
(-2)
A 		21
B 25.4
(3)
A 		15.1
(-0.2)
A 		6.8
(-2.8)
A 		6.1
(-3)
A 		19
C 10.6
(1.7)
A 		9.5
(1.1)
A 		13.2
(3)
A 		1.5
(-3)
A 		12
avr 19.5
(3) 		9.1
(-1.1) 		7.3
(-1.8) 		4.3
(-3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26
1 2 3 4 5 6 range
A 17.1
(3)
A 		15.7
(2.4)
A 		12
(0.9)
A 		13.8
(1.7)
A 		11.8
(0.9)
A 		2.3
(-3)
A 		15
B 16.4
(0.2)
A 		28.2
(3)
A 		4.7
(-2.6)
A 		2.9
(-3)
A 		4.3
(-2.7)
A 		7.2
(-2)
A 		25
C 25.3
(2.6)
A 		26.8
(3)
M 		10.7
(-1.4)
A 		4.8
(-3)
A 		14.4
(-0.4)
A 		9.3
(-1.8)
A 		22
avr 19.6
(1.6) 		23.6
(3) 		9.1
(-2) 		7.2
(-2.7) 		10.2
(-1.6) 		6.3
(-3) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193670_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13094
Sequence Type Exemplar sequence
Representative Public ID K06B4.2 NCBI
Target Description K06B4.2 /REP_DB=WormBase Gene ID /WP=CE11784 /GEN=nhr-52 /TR=SW:O17928 /GB=CAB05761.1 /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_074498(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074498 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-52) (nhr-52) mRNA, complete cds. 11/11 None
SNAP00000010510 ENSEMBL cdna:SNAP chromosome:CEL140:V:15681531:15682631:1 9/11 None
GENEFINDER00000010518 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15676859:15683227:1 11/11 None
K06B4.2 ENSEMBL cdna:known chromosome:CEL140:V:15680166:15682631:1 gene:K06B4.2 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:15680165-15682631(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-52
Ensembl K06B4.2
Entrez Gene 3565623 Entrez gene
SwissProt O17928 EMBL-EBI
WormBase CE11784 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 CAB05761 Hypothetical protein K06B4.2 [Caenorhabditis elegans] ref|NP_506899.1| Nuclear Hormone Receptor family member (nhr-52) [Caenorhabditis elegans] gb|AAG15146.1| nuclear receptor NHR-52 [Caenorhabditis elegans] sp|O17928|NHR52_CAEEL Nuclear hormone receptor family member nhr-52 0.0
blast CAB05760 Hypothetical protein K06B4.1 [Caenorhabditis elegans] ref|NP_506898.2| Nuclear Hormone Receptor family member (nhr-51) [Caenorhabditis elegans] 1.0E-159
blast AAG15145 nuclear receptor NHR-51 [Caenorhabditis elegans] 1.0E-159
blast CAB05761 Hypothetical protein K06B4.2 [Caenorhabditis elegans] ref|NP_506899.1| Nuclear Hormone Receptor family member (nhr-52) [Caenorhabditis elegans] gb|AAG15146.1| nuclear receptor NHR-52 [Caenorhabditis elegans] sp|O17928|NHR52_CAEEL Nuclear hormone receptor family member nhr-52 2.0E-97
blast CAB05759 Hypothetical protein K06B4.8 [Caenorhabditis elegans] ref|NP_506903.2| K06B4.8 [Caenorhabditis elegans] 6.0E-85
blast CAB05760 Hypothetical protein K06B4.1 [Caenorhabditis elegans] ref|NP_506898.2| Nuclear Hormone Receptor family member (nhr-51) [Caenorhabditis elegans] 6.0E-85
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.8E-5
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.5E-6
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.5E-43
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.6E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.5E-6
Sequence
Target Sequence 
>C. ELEGANS:193670_AT
cacgagtggacatttctgggctcctactacaaaatagctcagtttctggactttgacttt
gtcaaaactatgagccttgccgataggaaaatcttattctcctacaatactcttcgaatg
ggatctctatctcgatccatgcgtacataccttgataaacgagattgcctgatgactcca
agtggcgatgacttattttcacctgccgtacgcgggttgttcgacaaaacgccagaaata
atcaataggatcttgtgccaggtggttggaagactgatggaaattaaaattacatatgaa
gaatacttgcttttgatcatgattgtgttctgcaatccatcaatatctcacgaactgtcc
gattcagcacgagaaactctatccaaatatcaaaatatgtatgcatcatttttgttccgc
ttctgccaactcaagaaccaacacaaggcgccaactcggttcaatgatatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACGAGTGGACATTTCTGGGCTCCT 73 201 433 Antisense
AGCTCAGTTTCTGGACTTTGACTTT 558 75 468 Antisense
CTTATTCTCCTACAATACTCTTCGA 172 219 525 Antisense
ACTCTTCGAATGGGATCTCTATCTC 272 101 541 Antisense
TCTATCTCGATCCATGCGTACATAC 642 613 558 Antisense
GAGATTGCCTGATGACTCCAAGTGG 462 397 593 Antisense
TGGCGATGACTTATTTTCACCTGCC 526 545 615 Antisense
TCTCACGAACTGTCCGATTCAGCAC 248 613 778 Antisense
GTATGCATCATTTTTGTTCCGCTTC 284 455 831 Antisense
CGCTTCTGCCAACTCAAGAACCAAC 335 253 850 Antisense
GGCGCCAACTCGGTTCAATGATATT 379 543 879 Antisense
Sequence Source Affymetrix Proprietary Database