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[194072_at] Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)

Description C13C4.2 /REP_DB=WormBase Gene ID /WP=CE08127 /TR=O01931 /GB=CAB07316.1 /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 > 22      6grp_high1_10_10 > 03      4grp_highest_8_8 > 53      4grp_high_8_8 > 17      6grp_highest_nonorm > 50      6grp_total > 24      4grp_total > 31      6grp_highest_sub > De      6grp_cgc > 31      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.
4 421
1 2 3 4 range
A 556.6
(3)
P 		274.9
(-2.9)
P 		271.6
(-3)
P 		445
(0.7)
P 		285
B 603.4
(3)
P 		259.8
(-1.9)
P 		182
(-3)
P 		495
(1.5)
P 		421
C 550.8
(3)
P 		278.5
(-3)
P 		281.1
(-2.9)
P 		370.6
(-1)
P 		272
avr 570.3
(3) 		271.1
(-2.5) 		244.9
(-3) 		436.9
(0.5) 		325

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 431
1 2 3 4 5 6 range
A 520.6
(1.9)
P 		576.7
(3)
P 		475.8
(1.1)
P 		376.6
(-0.8)
P 		261.6
(-3)
P 		283.9
(-2.6)
P 		315
B 692.4
(3)
P 		564.4
(1.1)
P 		620.1
(1.9)
P 		375.4
(-1.7)
P 		320.8
(-2.5)
P 		284
(-3)
P 		408
C 628.5
(3)
P 		556.5
(1.7)
P 		454.1
(-0.1)
P 		393.1
(-1.2)
P 		305.8
(-2.8)
P 		295.7
(-3)
P 		333
avr 613.8
(3) 		565.9
(2.1) 		516.7
(1.2) 		381.7
(-1.3) 		296.1
(-2.8) 		287.9
(-3) 		326
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 202.7
(3)
P 		59.7
(-3)
P 		71
(-2.5)
P 		65.1
(-2.8)
P 		143
B 192.4
(3)
P 		64.2
(-2.1)
P 		42.2
(-3)
P 		105.5
(-0.5)
P 		150
C 182.3
(3)
P 		80.1
(-2.1)
P 		98
(-1.2)
P 		62.5
(-3)
P 		120
avr 192.5
(3) 		68
(-3) 		70.4
(-2.9) 		77.7
(-2.5) 		125

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 172
1 2 3 4 5 6 range
A 96
(-1.8)
P 		205.1
(3)
P 		103.6
(-1.5)
P 		95.5
(-1.8)
P 		78.9
(-2.6)
P 		69.1
(-3)
P 		136
B 240.9
(3)
P 		187.9
(0.8)
P 		150.6
(-0.8)
P 		99.4
(-3)
P 		130.3
(-1.7)
P 		105.9
(-2.7)
P 		142
C 233
(3)
P 		169.8
(0.5)
P 		115.6
(-1.6)
P 		79
(-3)
P 		98.9
(-2.2)
P 		99
(-2.2)
P 		154
avr 190
(3) 		187.6
(2.9) 		123.3
(-1.1) 		91.3
(-3) 		102.7
(-2.3) 		91.3
(-3) 		99
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194072_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13758
Sequence Type Exemplar sequence
Representative Public ID C13C4.2 NCBI
Target Description C13C4.2 /REP_DB=WormBase Gene ID /WP=CE08127 /TR=O01931 /GB=CAB07316.1 /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_073636(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073636 NCBI Caenorhabditis elegans C13C4.2 (C13C4.2) mRNA, complete cds. 11/11 None
SNAP00000013559 ENSEMBL cdna:SNAP chromosome:CEL140:V:12104521:12105874:1 11/11 None
GENEFINDER00000013571 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12104521:12111725:1 11/11 None
C13C4.2 ENSEMBL cdna:known chromosome:CEL140:V:12104266:12105874:1 gene:C13C4.2 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:12104265-12105874(+) 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-154
Ensembl C13C4.2
Entrez Gene 182565 Entrez gene
SwissProt O01931 EMBL-EBI
WormBase CE08127 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 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 CAE75392 Hypothetical protein CBG23380 [Caenorhabditis briggsae] 0.0
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 CAE75392 Hypothetical protein CBG23380 [Caenorhabditis briggsae] 1.0E-176
blast CAB07313 Hypothetical protein C13C4.1 [Caenorhabditis elegans] ref|NP_506038.1| C13C4.1 [Caenorhabditis elegans] 1.0E-111
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.6E-48
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.4E-27
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.6E-48
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.3E-18
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 7.5E-22
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.3E-29
Sequence
Target Sequence 
>C. ELEGANS:194072_AT
ttcaccaactacgttcacacaagttacctggcttctcttgaatcttcaaaaatgtttgaa
ttttcttcacaacttgatttggaatccagaattcttttaatgaaacacgcgacactaatt
tgttcgaatatgatgaatgcattcttttcgattaacgaaatgaaatcagatattcttagg
catccggatgggagcatgtcaggacatatgagaaaattcgatcgagagaatgatgtcatg
acagatcatgtcaaattgatacagaagacattgatcactttcctaaatcataaagtcgac
aaaattgaatatcttttattcaaagctattatgctttgcaatccagctgtgcccggatta
gattcctggaaccaagaaatcatcgaaaaggaacgaaatcaatacgttaaagctcttcta
aattattgtctccttcaacatggaaaacttcaaggcccaacaagattcgcaactattctc
gcaatggct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCACCAACTACGTTCACACAAGTT 612 683 622 Antisense
TTCACACAAGTTACCTGGCTTCTCT 683 685 635 Antisense
GAAACACGCGACACTAATTTGTTCG 389 355 723 Antisense
GATGAATGCATTCTTTTCGATTAAC 645 411 753 Antisense
ATCAGATATTCTTAGGCATCCGGAT 571 27 786 Antisense
GGCATCCGGATGGGAGCATGTCAGG 386 535 800 Antisense
GAAGACATTGATCACTTTCCTAAAT 687 339 885 Antisense
GCTGTGCCCGGATTAGATTCCTGGA 481 295 967 Antisense
GCTCTTCTAAATTATTGTCTCCTTC 276 301 1033 Antisense
AAGGCCCAACAAGATTCGCAACTAT 337 161 1073 Antisense
ATTCGCAACTATTCTCGCAATGGCT 399 9 1086 Antisense
Sequence Source Affymetrix Proprietary Database