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[174023_at] nuclear hormone receptor

Description g4139079 /REP_DB=GenBank Identifier /CHR=4 /FEA=Genomic Cluster
Cluster 6grp_highest_10_10 > 74      6grp_high1_10_10 > 55      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 84      6grp_total > 46      4grp_total > 26      6grp_highest_sub > Cu      6grp_cgc > 36      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 227
1 2 3 4 range
A 219.9
(-2)
P 		332.8
(2.3)
P 		194.6
(-3)
P 		352.3
(3)
P 		158
B 254.4
(-3)
P 		374.2
(2.1)
P 		280.2
(-1.9)
P 		395.4
(3)
P 		141
C 263.8
(-2.6)
P 		263.5
(-2.6)
P 		251.6
(-3)
P 		421.6
(3)
P 		170
avr 246
(-2.8) 		323.5
(0.3) 		242.1
(-3) 		389.8
(3) 		148

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 546
1 2 3 4 5 6 range
A 499.7
(-0.2)
P 		527.6
(0.2)
P 		739.5
(3)
P 		523.9
(0.1)
P 		288.7
(-3)
P 		590.7
(1)
P 		451
B 682.4
(1.1)
P 		633.5
(0.4)
P 		600.6
(-0)
P 		459.4
(-2.1)
P 		395.1
(-3)
P 		811.7
(3)
P 		417
C 774.3
(2.3)
P 		519.2
(-0.7)
P 		545
(-0.4)
P 		481.5
(-1.2)
P 		329.4
(-3)
P 		834.5
(3)
P 		505
avr 652.1
(1.6) 		560.1
(0.3) 		628.4
(1.3) 		488.3
(-0.8) 		337.7
(-3) 		745.6
(3) 		408
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 42
1 2 3 4 range
A 80.1
(3)
P 		72.2
(1.4)
P 		50.9
(-3)
P 		51.6
(-2.9)
P 		29
B 81.1
(0.5)
P 		92.4
(3)
P 		64.9
(-3)
P 		84.3
(1.2)
P 		28
C 87.3
(2.9)
P 		75.8
(-1.3)
P 		87.7
(3)
P 		71.1
(-3)
P 		17
avr 82.8
(3) 		80.1
(1.9) 		67.8
(-3) 		69
(-2.5) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 216
1 2 3 4 5 6 range
A 92.1
(-2.7)
P 		187.6
(3)
P 		161
(1.4)
P 		132.9
(-0.3)
P 		87.1
(-3)
P 		143.8
(0.4)
P 		101
B 237.5
(0.8)
P 		210.9
(-0)
P 		145.8
(-2.2)
P 		121.7
(-3)
P 		160.5
(-1.7)
P 		302.7
(3)
P 		181
C 287
(3)
P 		158.4
(-1.1)
P 		138.7
(-1.7)
P 		96.8
(-3)
P 		106.6
(-2.7)
P 		279.4
(2.8)
P 		190
avr 205.5
(1.2) 		185.6
(0.3) 		148.5
(-1.5) 		117.1
(-3) 		118.1
(-3) 		242
(3) 		125
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174023_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21498
Sequence Type Exemplar sequence
Representative Public ID 4139079 NCBI
Target Description g4139079 /REP_DB=GenBank Identifier /CHR=4 /FEA=Genomic Cluster
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(11)
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. 11/11 A 
SNAP00000030922 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9072147:9073500:1 11/11 None
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
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
chrIV:9072858-9073511(+) 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 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:174023_AT
gaaggcacttacagtatggcaagctacatacttcaagctaactgaaaatggccgtgaaaa
atgtcgtagacaaaggaatatcataattggctttctatcaaaaatgtgtcattcaccagg
tggaggcggagagcatcgtgttggagaacttctgatgagtatgaattatctcagggaatc
tgctcaaaaactcacaacttcttacgtgatgctcacagttttcaatgttctcaactgtga
ttcaatgcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGGCACTTACAGTATGGCAAGCT 658 333 14 Antisense
GGCAAGCTACATACTTCAAGCTAAC 330 535 31 Antisense
CAAGCTAACTGAAAATGGCCGTGAA 64 185 47 Antisense
TGGCCGTGAAAAATGTCGTAGACAA 115 543 62 Antisense
GGAATATCATAATTGGCTTTCTATC 579 533 88 Antisense
ACCAGGTGGAGGCGGAGAGCATCGT 228 85 128 Antisense
AGAGCATCGTGTTGGAGAACTTCTG 134 69 143 Antisense
CAGGGAATCTGCTCAAAAACTCACA 351 205 185 Antisense
CACAACTTCTTACGTGATGCTCACA 382 195 206 Antisense
GATGCTCACAGTTTTCAATGTTCTC 585 413 221 Antisense
GTTCTCAACTGTGATTCAATGCTTC 5 443 240 Antisense
Sequence Source GenBank