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[193508_at] Zinc finger, C4 type (two domains)

Description F41D3.1 /REP_DB=WormBase Gene ID /WP=CE16020 /GEN=nhr-82 /TR=O45505 /GB=CAB04372.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_total > 01      4grp_total > 40      6grp_cgc > 53      6grp_cgc_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 15.3
(-0.2)
A 		5.9
(-3)
A 		25.8
(3)
A 		22.9
(2.1)
A 		20
B 9.9
(-0.1)
A 		15.4
(3)
A 		9
(-0.7)
A 		4.9
(-3)
A 		11
C 11.5
(-0.7)
A 		15.8
(3)
A 		8.8
(-3)
A 		11.5
(-0.7)
A 		7
avr 12.2
(-3) 		12.4
(-2.5) 		14.5
(3) 		13.1
(-0.7) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28
1 2 3 4 5 6 range
A 14.2
(3)
A 		10.6
(0.8)
A 		4.2
(-3)
A 		12
(1.7)
A 		10.5
(0.8)
A 		7.7
(-0.9)
A 		10
B 10.3
(-0.8)
A 		22.7
(3)
A 		8.7
(-1.3)
A 		3.7
(-2.8)
A 		3.2
(-3)
A 		18.2
(1.6)
A 		20
C 7.5
(-1.8)
A 		30.3
(3)
A 		2
(-3)
A 		3.1
(-2.8)
A 		18.1
(0.4)
A 		5.4
(-2.3)
A 		28
avr 10.7
(-0.9) 		21.2
(3) 		5
(-3) 		6.3
(-2.5) 		10.6
(-0.9) 		10.4
(-1) 		16
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6
1 2 3 4 range
A 5.6
(1.8)
A 		1.3
(-3)
A 		6.7
(3)
A 		3.3
(-0.8)
A 		5
B 3.1
(1.5)
A 		3.8
(3)
A 		2.1
(-0.6)
A 		1
(-3)
A 		3
C 3.8
(1.4)
A 		4.5
(3)
A 		3.1
(-0.2)
A 		1.9
(-3)
A 		3
avr 4.2
(3) 		3.2
(0.1) 		4
(2.4) 		2.1
(-3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 2.6
(0.5)
A 		3.8
(3)
A 		0.9
(-3)
A 		3.1
(1.6)
A 		3.2
(1.8)
A 		1.9
(-0.9)
A 		3
B 3.6
(-0.6)
A 		7.6
(3)
A 		2.1
(-2)
A 		1
(-3)
A 		1.3
(-2.7)
A 		6.8
(2.3)
A 		7
C 2.8
(-1.4)
A 		9.3
(3)
A 		0.5
(-3)
A 		0.6
(-2.9)
A 		5.9
(0.7)
A 		1.8
(-2.1)
A 		9
avr 3
(-1.1) 		6.9
(3) 		1.2
(-3) 		1.6
(-2.6) 		3.5
(-0.6) 		3.5
(-0.6) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193508_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1968
Sequence Type Exemplar sequence
Representative Public ID F41D3.1 NCBI
Target Description F41D3.1 /REP_DB=WormBase Gene ID /WP=CE16020 /GEN=nhr-82 /TR=O45505 /GB=CAB04372.1 /SUBMIT=HINXTON /CHR=1 /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_060689(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060689 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-82) (nhr-82) mRNA, complete cds. 11/11 None
GENEFINDER00000037784 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:12253578:12254873:1 11/11 None
SNAP00000037766 ENSEMBL cdna:SNAP chromosome:CEL140:I:12253746:12254873:1 11/11 None
F41D3.1 ENSEMBL cdna:known chromosome:CEL140:I:12253578:12254873:1 gene:F41D3.1 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
chrI:12253508-12254804(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-82
Ensembl F41D3.1
Entrez Gene 191729 Entrez gene
WormBase CE16020 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 CAB04372 Hypothetical protein F41D3.1 [Caenorhabditis elegans] ref|NP_493090.1| Nuclear Hormone Receptor family member (nhr-82) [Caenorhabditis elegans] 0.0
blast CAB04372 Hypothetical protein F41D3.1 [Caenorhabditis elegans] ref|NP_493090.1| Nuclear Hormone Receptor family member (nhr-82) [Caenorhabditis elegans] 1.0E-171
blast CAA15840 Hypothetical protein C47F8.8 [Caenorhabditis elegans] ref|NP_493118.2| Nuclear Hormone Receptor family member (nhr-81) [Caenorhabditis elegans] 1.0E-86
blast CAA18369 Hypothetical protein ZK1025.10 [Caenorhabditis elegans] ref|NP_492932.1| ZK1025.10 [Caenorhabditis elegans] 2.0E-81
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0047
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.1E-11
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0047
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.7E-12
Sequence
Target Sequence 
>C. ELEGANS:193508_AT
tcgtcgagctccacaagatttctgaaatggaaaacaacgtggttttggatgactgtttga
attgtccgggtgtcgatgttctggagcaagatgatgtagaagttttgctcaaatatttca
aattcgtgaatatctgggtgtattctgcacttgcatcttctagcacatgtctggagcaat
ttccagagcaaactggggacaattccaatcagctcttcgacttccttcaccaagtccgat
caactctgggatcatcacttgttcgtctgaacctcaacattttcgagtatgcagctttca
agtcattttgcatttggaatctgaagttcttcgggacaagtaccgcgatgaagattgtcg
cagaagaacatcacattggtatcacatgggcgctcaggaaatattataaggaatccacca
atatgaccgaagtggaaattgcggctcgaattggtgatatcactttacaactgctcactg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCGTCGAGCTCCACAAGATTTCTGA 434 605 455 Antisense
GAATTGTCCGGGTGTCGATGTTCTG 354 323 513 Antisense
GGTGTATTCTGCACTTGCATCTTCT 207 501 591 Antisense
GCATCTTCTAGCACATGTCTGGAGC 351 309 607 Antisense
TGGGGACAATTCCAATCAGCTCTTC 545 553 648 Antisense
TCACCAAGTCCGATCAACTCTGGGA 620 625 681 Antisense
ACTCTGGGATCATCACTTGTTCGTC 60 101 697 Antisense
GTTCGTCTGAACCTCAACATTTTCG 670 441 715 Antisense
GTTCTTCGGGACAAGTACCGCGATG 514 441 780 Antisense
TGGTATCACATGGGCGCTCAGGAAA 216 551 831 Antisense
GATATCACTTTACAACTGCTCACTG 327 425 910 Antisense
Sequence Source Affymetrix Proprietary Database