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[192634_at] nuclear hormone receptor

Description ZC410.1 /REP_DB=WormBase Gene ID /WP=CE26841 /GEN=nhr-11 /TR=Q23294 /GB=CAA92572.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 64      6grp_high1_10_10 > 46      4grp_highest_8_8 > 04      4grp_high_8_8 > 37      6grp_highest_nonorm > 76      6grp_total > 46      4grp_total > 34      6grp_highest_sub > Cu      6grp_cgc > 35      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 342
1 2 3 4 range
A 478.6
(-3)
P 		789.8
(3)
P 		586.1
(-0.9)
P 		613.1
(-0.4)
P 		311
B 538
(-3)
P 		820.4
(3)
P 		554.9
(-2.6)
P 		690.4
(0.2)
P 		282
C 511.7
(-3)
P 		790.1
(3)
P 		547.3
(-2.2)
P 		777.1
(2.7)
P 		278
avr 509.4
(-3) 		800.1
(3) 		562.8
(-1.9) 		693.5
(0.8) 		291

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1010
1 2 3 4 5 6 range
A 1535
(3)
P 		1016.8
(-0.1)
P 		1073.5
(0.2)
P 		1141.9
(0.6)
P 		533.5
(-3)
P 		1292.2
(1.5)
P 		1002
B 1207
(3)
P 		1043
(1.3)
P 		1087.1
(1.8)
P 		856.1
(-0.5)
P 		612
(-3)
P 		1086.3
(1.8)
P 		595
C 1304.9
(3)
P 		1000.9
(0.7)
P 		1140.7
(1.7)
P 		1026.6
(0.9)
P 		525.5
(-3)
P 		1181.2
(2)
P 		779
avr 1349
(3) 		1020.2
(0.5) 		1100.4
(1.1) 		1008.2
(0.4) 		557
(-3) 		1186.6
(1.8) 		792
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 138
1 2 3 4 range
A 174.3
(3)
P 		171.4
(2.8)
P 		153.2
(1.5)
P 		89.7
(-3)
P 		85
B 171.6
(0.5)
P 		202.6
(3)
P 		128.6
(-3)
P 		147.1
(-1.5)
P 		74
C 169.4
(-0.6)
P 		227.2
(3)
P 		190.7
(0.7)
P 		131
(-3)
P 		96
avr 171.8
(0.8) 		200.4
(3) 		157.5
(-0.3) 		122.6
(-3) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 323
1 2 3 4 5 6 range
A 283
(0.6)
P 		361.6
(3)
P 		233.8
(-0.8)
P 		289.6
(0.8)
P 		161
(-3)
P 		314.6
(1.6)
P 		201
B 420
(3)
P 		347.2
(0.7)
P 		264
(-1.8)
P 		226.7
(-3)
P 		248.6
(-2.3)
P 		405.1
(2.5)
P 		193
C 483.7
(3)
P 		305.4
(-0.4)
P 		290.3
(-0.7)
P 		206.4
(-2.3)
P 		170.1
(-3)
P 		395.4
(1.3)
P 		314
avr 395.6
(3) 		338.1
(1.3) 		262.7
(-0.9) 		240.9
(-1.6) 		193.2
(-3) 		371.7
(2.3) 		202
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192634_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9641
Sequence Type Exemplar sequence
Representative Public ID ZC410.1 NCBI
Target Description ZC410.1 /REP_DB=WormBase Gene ID /WP=CE26841 /GEN=nhr-11 /TR=Q23294 /GB=CAA92572.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_069174(11), AF083227(11), AY305843(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069174 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-11) (nhr-11) mRNA, complete cds. 11/11 A 
AF083227 NCBI Caenorhabditis elegans nuclear receptor NHR-11 (nhr-11) mRNA, partial cds. 11/11 None
AY305843 NCBI Caenorhabditis elegans clone yk726g1 nuclear receptor nuclear receptor NHR-11 mRNA, complete sequence. 9/11 A 
GENEFINDER00000030938 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9070670:9073500:1 11/11 None
ZC410.1 ENSEMBL cdna:known chromosome:CEL140:IV:9069990:9073580:1 gene:ZC410.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000030921 1/11 Cross Hyb Matching Probes None
SNAP00000030922 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:9070675-9072727(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-11
Ensembl ZC410.1
Entrez Gene 177724 Entrez gene
SwissProt Q23294 EMBL-EBI
WormBase CE26841 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 AAR11983 nuclear receptor NHR-11 [Caenorhabditis elegans] emb|CAA92572.2| Hypothetical protein ZC410.1 [Caenorhabditis elegans] ref|NP_501575.3| Nuclear Hormone Receptor family member (nhr-11) [Caenorhabditis elegans] sp|Q23294|NHR11_CAEEL Nuclear hormone receptor family member nhr-11 0.0
blast CAE74096 Hypothetical protein CBG21756 [Caenorhabditis briggsae] 0.0
blast CAE74096 Hypothetical protein CBG21756 [Caenorhabditis briggsae] 1.0E-158
blast AAD03685 nuclear receptor NHR-11 [Caenorhabditis elegans] 1.0E-146
blast AAR11983 nuclear receptor NHR-11 [Caenorhabditis elegans] emb|CAA92572.2| Hypothetical protein ZC410.1 [Caenorhabditis elegans] ref|NP_501575.3| Nuclear Hormone Receptor family member (nhr-11) [Caenorhabditis elegans] sp|Q23294|NHR11_CAEEL Nuclear hormone receptor family member nhr-11 1.0E-146
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.5E-27
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.1E-16
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.5E-7
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.0E-8
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.5E-27
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.0E-8
Sequence
Target Sequence 
>C. ELEGANS:192634_AT
atcttccattaacaccttctatatctcatccaccattaccaactcagctaatgccagaag
aatcttcacgaacatcgtcatttgatgggggatactgttcatcttatccatcatcatcag
cagccacccatccatctccacctggaatgttatattcaattgaaaacaattcaattttac
aatactatcattcaatggaaactggattatgctcgaaaagaagaataatgtacacaaata
ctggtatggacttcattctggatactcatgcaaatttgcaatgtccgttcacagtcaatg
atctacgcccacacgattaccgaaattttcgtggaatgctcagacatgattttgtaatgc
tttttgactacgcaacacgatttccagagtttaatagttttacgagtcatgagaaaaata
tgttctatcggcaaattgttgctgttgattttatattgtcttccgcatattacacggcaa
aactcggtcaagcacatcgtcaaatggtattgacaaatggtgaatatctgaatatggatc
ctttaccaatgtccggaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCTTCCATTAACACCTTCTATATC 434 29 245 Antisense
TTACCAACTCAGCTAATGCCAGAAG 692 677 280 Antisense
GTTCATCTTATCCATCATCATCAGC 319 445 341 Antisense
GGACTTCATTCTGGATACTCATGCA 8 525 492 Antisense
ATTTGCAATGTCCGTTCACAGTCAA 57 19 518 Antisense
TCACAGTCAATGATCTACGCCCACA 641 627 533 Antisense
GACTACGCAACACGATTTCCAGAGT 470 373 610 Antisense
GTTGATTTTATATTGTCTTCCGCAT 509 437 688 Antisense
TTGTCTTCCGCATATTACACGGCAA 540 707 700 Antisense
AAACTCGGTCAAGCACATCGTCAAA 61 125 724 Antisense
ATGGATCCTTTACCAATGTCCGGAA 376 51 778 Antisense
Sequence Source Affymetrix Proprietary Database