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[173147_s_at] --- /// Zinc finger, C4 type (two domains)

Description AU113586_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AU113586 /DEF=Caenorhabditis elegans cDNA clone:yk709d2 : 3prime end, single read.
Cluster 6grp_total > 24      4grp_total > 50      6grp_cgc > 31      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 707
1 2 3 4 range
A 40.9
(-3)
A 		715.8
(3)
P 		606.2
(2)
P 		61.9
(-2.8)
A 		675
B 66.4
(-2.5)
A 		632.4
(2.6)
P 		681.9
(3)
P 		13.1
(-3)
A 		669
C 63.7
(-2.9)
A 		720.5
(3)
P 		578.1
(1.7)
P 		56.1
(-3)
A 		664
avr 57
(-2.9) 		689.6
(3) 		622.1
(2.4) 		43.7
(-3) 		646

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 224
1 2 3 4 5 6 range
A 228.5
(3)
P 		137.9
(0.3)
P 		94.9
(-1)
P 		75.4
(-1.6)
A 		30
(-3)
A 		29.1
(-3)
A 		199
B 128.7
(1.3)
P 		179.8
(3)
P 		139.2
(1.6)
P 		92.4
(0)
A 		39.9
(-1.8)
A 		4.1
(-3)
A 		176
C 161.6
(3)
P 		158.4
(2.8)
P 		92.8
(-0.3)
A 		65.3
(-1.7)
A 		54.8
(-2.2)
A 		37.9
(-3)
A 		124
avr 172.9
(3) 		158.7
(2.4) 		109
(0.4) 		77.7
(-0.8) 		41.6
(-2.3) 		23.7
(-3) 		149
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 204
1 2 3 4 range
A 14.9
(-2.8)
A 		155.4
(2.9)
P 		158.5
(3)
P 		9.1
(-3)
A 		149
B 21.2
(-2.3)
A 		156.2
(2.9)
P 		158
(3)
P 		2.8
(-3)
A 		155
C 21.1
(-2.6)
A 		207.1
(3)
P 		201.5
(2.8)
P 		9.5
(-3)
A 		198
avr 19.1
(-2.6) 		172.9
(3) 		172.7
(3) 		7.1
(-3) 		166

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 58
1 2 3 4 5 6 range
A 42.1
(2)
P 		49
(3)
P 		20.7
(-1.1)
P 		19.1
(-1.3)
A 		9.1
(-2.7)
A 		7.1
(-3)
A 		42
B 44.8
(1.5)
P 		59.8
(3)
P 		33.8
(0.3)
P 		24.5
(-0.6)
A 		16.2
(-1.5)
A 		1.5
(-3)
A 		58
C 59.9
(3)
P 		48.3
(1.5)
P 		23.6
(-1.6)
A 		13.1
(-2.9)
A 		17.7
(-2.4)
A 		12.7
(-3)
A 		47
avr 48.9
(2.5) 		52.4
(3) 		26
(-0.5) 		18.9
(-1.4) 		14.3
(-2) 		7.1
(-3) 		45
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173147_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27485
Sequence Type Exemplar sequence
Representative Public ID AU113586 NCBI
Target Description AU113586_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AU113586 /DEF=Caenorhabditis elegans cDNA clone:yk709d2 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST 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_060530(11), NM_060521(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060530 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-113) (nhr-113) mRNA, complete cds. 11/11 A 
NM_060521 NCBI Caenorhabditis elegans C27C7.8 (C27C7.8) mRNA, complete cds. 11/11 A 
SNAP00000039062 ENSEMBL cdna:SNAP chromosome:CEL140:I:11441500:11445529:1 11/11 None
GENEFINDER00000039069 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11444904:11445529:1 11/11 None
GENEFINDER00000038824 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11480273:11485526:-1 11/11 None
C27C7.8 ENSEMBL cdna:known chromosome:CEL140:I:11444881:11445589:1 gene:C27C7.8 11/11 A 
ZK1025.9 ENSEMBL cdna:known chromosome:CEL140:I:11481400:11483741:-1 gene:ZK1025.9 11/11 A 
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:11445107-11445422(+) 89.33 89.33
Public Domain and Genome References
Gene Title
Zinc finger, C4 type (two domains)
Gene Symbol nhr-259
nhr-113
Ensembl C27C7.8
ZK1025.9
Entrez Gene 173033 Entrez gene
182960 Entrez gene
SwissProt Q9U3N8 EMBL-EBI
WormBase CE18538 Wormbase
CE19335 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 CAA18368 Hypothetical protein ZK1025.9 [Caenorhabditis elegans] ref|NP_492931.1| Nuclear Hormone Receptor family member (nhr-113) [Caenorhabditis elegans] 0.0
blast AAO39200 nuclear receptor NHR-113 [Caenorhabditis elegans] 0.0
blast CAA18368 Hypothetical protein ZK1025.9 [Caenorhabditis elegans] ref|NP_492931.1| Nuclear Hormone Receptor family member (nhr-113) [Caenorhabditis elegans] 1.0E-101
blast AAO39200 nuclear receptor NHR-113 [Caenorhabditis elegans] 1.0E-101
blast CAB03930 Hypothetical protein C27C7.8 [Caenorhabditis elegans] ref|NP_492922.1| C27C7.8 [Caenorhabditis elegans] 1.0E-97
blast CAA18368 Hypothetical protein ZK1025.9 [Caenorhabditis elegans] ref|NP_492931.1| Nuclear Hormone Receptor family member (nhr-113) [Caenorhabditis elegans] 1.0E-97
blast AAO39200 nuclear receptor NHR-113 [Caenorhabditis elegans] 1.0E-97
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.012
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.9E-17
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.012
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.012
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.012
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.9E-17
Sequence
Target Sequence 
>C. ELEGANS:173147_S_AT
gtcaggacaacattgggatcttccctggcaaatttgaaattgaacatgtatgaatactct
gctttcaagttgttttgcatctggaatctgaaattccacaaaacctccactgctctgaaa
attgttgctcaagagcactatgaaggagtttgctccgcgctgagaaactattatgagaca
cagacaaaaatggacgattttgaaattgcaattaggataggggatattactttgcaaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCAGGACAACATTGGGATCTTCCC 11 467 13 Antisense
GACAACATTGGGATCTTCCCTGGCA 366 365 18 Antisense
GATCTTCCCTGGCAAATTTGAAATT 23 417 29 Antisense
ACATGTATGAATACTCTGCTTTCAA 537 107 56 Antisense
AATACTCTGCTTTCAAGTTGTTTTG 166 173 65 Antisense
GCATCTGGAATCTGAAATTCCACAA 30 309 89 Antisense
AAAACCTCCACTGCTCTGAAAATTG 620 131 112 Antisense
TATGAAGGAGTTTGCTCCGCGCTGA 294 657 151 Antisense
GTTTGCTCCGCGCTGAGAAACTATT 69 451 160 Antisense
GAGAAACTATTATGAGACACAGACA 41 393 174 Antisense
GGATAGGGGATATTACTTTGCAAAT 546 507 227 Antisense
Sequence Source Affymetrix Proprietary Database