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[194102_at] Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)

Description C13C4.3 /REP_DB=WormBase Gene ID /WP=CE08128 /TR=O01930 /GB=CAB07314.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 31      6grp_high1_10_10 > 13      4grp_high_8_8 > 17      6grp_highest_nonorm > 80      6grp_total > 13      4grp_total > 30      6grp_highest_sub > De      6grp_cgc > 30      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 188
1 2 3 4 range
A 271.2
(3)
P 		89
(-2.8)
M 		83.4
(-3)
A 		190.9
(0.4)
P 		188
B 197.9
(3)
P 		131.5
(-1)
P 		99.3
(-3)
A 		187.8
(2.4)
P 		99
C 207.5
(3)
P 		112.5
(-2.3)
P 		99.5
(-3)
P 		144.6
(-0.5)
P 		108
avr 225.5
(3) 		111
(-2.2) 		94.1
(-3) 		174.4
(0.7) 		131

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 222
1 2 3 4 5 6 range
A 303.9
(3)
P 		252.7
(1.6)
P 		200.5
(0.2)
P 		246.2
(1.4)
P 		149.5
(-1.2)
P 		82
(-3)
P 		222
B 281.4
(2.8)
P 		287.9
(3)
P 		237.8
(1.3)
P 		174.6
(-0.7)
P 		112.3
(-2.8)
P 		106.2
(-3)
P 		182
C 247.8
(1.7)
P 		287.7
(3)
P 		176.8
(-0.6)
P 		139.3
(-1.8)
P 		117.3
(-2.6)
P 		103.6
(-3)
P 		184
avr 277.7
(3) 		276.1
(2.9) 		205
(0.6) 		186.7
(-0) 		126.4
(-2) 		97.3
(-3) 		180
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 80
1 2 3 4 range
A 98.8
(3)
P 		19.3
(-3)
M 		21.8
(-2.8)
A 		27.9
(-2.4)
P 		80
B 63.1
(3)
P 		32.5
(-1.6)
P 		23
(-3)
A 		40
(-0.5)
P 		40
C 68.7
(3)
P 		32.3
(-1.9)
P 		34.7
(-1.6)
P 		24.4
(-3)
P 		44
avr 76.9
(3) 		28
(-2.8) 		26.5
(-3) 		30.8
(-2.5) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 78
1 2 3 4 5 6 range
A 56
(0.1)
P 		89.9
(3)
P 		43.7
(-1)
P 		62.4
(0.6)
P 		45.1
(-0.8)
P 		20
(-3)
P 		70
B 97.9
(3)
P 		95.8
(2.8)
P 		57.8
(-1.1)
P 		46.2
(-2.3)
P 		45.6
(-2.4)
P 		39.6
(-3)
P 		58
C 91.9
(3)
P 		87.8
(2.6)
P 		45
(-1.4)
P 		28
(-3)
P 		38
(-2.1)
P 		34.7
(-2.4)
P 		64
avr 81.9
(2.1) 		91.2
(3) 		48.8
(-1.3) 		45.5
(-1.6) 		42.9
(-1.8) 		31.4
(-3) 		60
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194102_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13973
Sequence Type Exemplar sequence
Representative Public ID C13C4.3 NCBI
Target Description C13C4.3 /REP_DB=WormBase Gene ID /WP=CE08128 /TR=O01930 /GB=CAB07314.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, 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_073638(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073638 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-136) (nhr-136) mRNA, complete cds. 11/11 None
SNAP00000013561 ENSEMBL cdna:SNAP chromosome:CEL140:V:12110016:12111725:1 11/11 None
GENEFINDER00000013571 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12104521:12111725:1 11/11 None
C13C4.3 ENSEMBL cdna:known chromosome:CEL140:V:12109730:12111725:1 gene:C13C4.3 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:12110196-12111725(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Gene Symbol nhr-136
Ensembl C13C4.3
Entrez Gene 182566 Entrez gene
SwissProt O01930 EMBL-EBI
WormBase CE08128 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 CAB07314 Hypothetical protein C13C4.3 [Caenorhabditis elegans] ref|NP_506039.1| Nuclear Hormone Receptor family member (nhr-136) [Caenorhabditis elegans] sp|O01930|NH136_CAEEL Nuclear hormone receptor family member nhr-136 0.0
blast CAB07313 Hypothetical protein C13C4.1 [Caenorhabditis elegans] ref|NP_506038.1| C13C4.1 [Caenorhabditis elegans] 0.0
blast CAB00126 Hypothetical protein C13C4.2 [Caenorhabditis elegans] emb|CAB07316.1| Hypothetical protein C13C4.2 [Caenorhabditis elegans] ref|NP_506037.1| C13C4.2 [Caenorhabditis elegans] 0.0
blast CAE75394 Hypothetical protein CBG23383 [Caenorhabditis briggsae] 1.0E-178
blast CAE75394 Hypothetical protein CBG23383 [Caenorhabditis briggsae] 1.0E-176
blast CAB00126 Hypothetical protein C13C4.2 [Caenorhabditis elegans] emb|CAB07316.1| Hypothetical protein C13C4.2 [Caenorhabditis elegans] ref|NP_506037.1| C13C4.2 [Caenorhabditis elegans] 1.0E-105
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.4E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.3E-29
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.4E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.3E-29
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.6E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.4E-39
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.4E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.3E-18
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-22
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.3E-29
Sequence
Target Sequence 
>C. ELEGANS:194102_AT
agcccagtggagcttgctacatacattgcggctacctagctagtatagaatattcaaaaa
tgtttgactttgctcataaaatagatgttgctagcaaagcaactctgataaaacatgcaa
caattatgtgcgcagatatcatgacagctttcttctcttactatcaacgtaaatccgatc
gactgattcatccaaatggaatgtttgcaggaccaccaaaatacagatatggtgaagccg
gtacaaaatatcaagcttcaatgcaaagaactctggcaacagtgctccgacatgaactta
atcgaattgaatatatgctactcaaagctattgtgctttgcaatccagcagtctctagtc
tttctatttcggtacaacaaataattggaaaagaacgtgaagaatatgttcgaactctac
ttacatactgtcttctcaattatggttctgttcatggaccatcaagattttctgcccttc
ttgctattatgtcagttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCCCAGTGGAGCTTGCTACATACA 248 83 575 Antisense
TACATACATTGCGGCTACCTAGCTA 282 645 592 Antisense
GATATCATGACAGCTTTCTTCTCTT 204 427 709 Antisense
GCTTTCTTCTCTTACTATCAACGTA 698 303 721 Antisense
ATCCGATCGACTGATTCATCCAAAT 268 39 747 Antisense
AAGAACTCTGGCAACAGTGCTCCGA 248 153 840 Antisense
GCTTTGCAATCCAGCAGTCTCTAGT 605 303 909 Antisense
GTCTCTAGTCTTTCTATTTCGGTAC 467 469 925 Antisense
AACTCTACTTACATACTGTCTTCTC 91 141 987 Antisense
ATCAAGATTTTCTGCCCTTCTTGCT 293 25 1035 Antisense
GCCCTTCTTGCTATTATGTCAGTTC 418 287 1048 Antisense
Sequence Source Affymetrix Proprietary Database