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[194128_s_at] Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)

Description F57A10.5 /REP_DB=WormBase Gene ID /WP=CE16151 /GEN=nhr-60 /TR=O17898 /GB=CAB09422.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Cluster 6grp_high1_10_10 > 13      4grp_high_8_8 > 51      6grp_total > 25      4grp_total > 61      6grp_cgc > 33      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 132.8
(1.7)
P 		101.3
(-1.2)
P 		147.7
(3)
P 		80.9
(-3)
A 		67
B 115.2
(2)
P 		122
(3)
P 		97.6
(-0.4)
P 		79.4
(-3)
P 		43
C 113.4
(2.1)
P 		117.3
(3)
P 		93.8
(-2.5)
P 		91.7
(-3)
P 		26
avr 120.5
(3) 		113.5
(1.8) 		113
(1.8) 		84
(-3) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 131.5
(2.5)
P 		137.6
(3)
P 		123.8
(2)
P 		85.3
(-1)
P 		58.3
(-3)
P 		79.5
(-1.4)
P 		79
B 141.2
(3)
P 		123.4
(2)
P 		71.5
(-1)
P 		70.7
(-1)
P 		71.1
(-1)
P 		36.6
(-3)
P 		105
C 99.7
(0.6)
P 		126.6
(3)
P 		88.9
(-0.3)
P 		58.9
(-3)
A 		80.3
(-1.1)
P 		67.1
(-2.3)
P 		68
avr 124.1
(2.6) 		129.2
(3) 		94.7
(-0) 		71.6
(-2.1) 		69.9
(-2.2) 		61.1
(-3) 		68
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 37
1 2 3 4 range
A 48.4
(3)
P 		22
(-1.3)
P 		38.6
(1.4)
P 		11.8
(-3)
A 		37
B 36.7
(3)
P 		30.1
(1)
P 		22.6
(-1.3)
P 		16.9
(-3)
P 		20
C 37.5
(3)
P 		33.7
(2)
P 		32.7
(1.7)
P 		15.5
(-3)
P 		22
avr 40.9
(3) 		28.6
(0.2) 		31.3
(0.8) 		14.7
(-3) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 37
1 2 3 4 5 6 range
A 24.2
(-1.7)
P 		48.9
(3)
P 		27
(-1.2)
P 		21.6
(-2.2)
P 		17.6
(-3)
P 		19.4
(-2.7)
P 		31
B 49.1
(3)
P 		41.1
(1.6)
P 		17.4
(-2.4)
P 		18.7
(-2.2)
P 		28.9
(-0.4)
P 		13.7
(-3)
P 		35
C 37
(2.6)
P 		38.6
(3)
P 		22.6
(-0.6)
P 		11.9
(-3)
A 		26
(0.2)
P 		22.5
(-0.6)
P 		27
avr 36.8
(1.6) 		42.9
(3) 		22.3
(-1.8) 		17.4
(-3) 		24.2
(-1.4) 		18.5
(-2.7) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194128_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12717
Sequence Type Exemplar sequence
Representative Public ID F57A10.5 NCBI
Target Description F57A10.5 /REP_DB=WormBase Gene ID /WP=CE16151 /GEN=nhr-60 /TR=O17898 /GB=CAB09422.1 /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_074529(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074529 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-60) (nhr-60) mRNA, complete cds. 11/11 None
SNAP00000005223 ENSEMBL cdna:SNAP chromosome:CEL140:V:15772945:15775004:-1 11/11 None
GENEFINDER00000005228 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15772945:15775810:-1 11/11 None
F57A10.5 ENSEMBL cdna:known chromosome:CEL140:V:15772945:15775810:-1 gene:F57A10.5 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:15772944-15775810(-) 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-60
Ensembl F57A10.5
Entrez Gene 180059 Entrez gene
SwissProt O17898 EMBL-EBI
WormBase CE16151 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 CAB09422 Hypothetical protein F57A10.5 [Caenorhabditis elegans] ref|NP_506930.1| Nuclear Hormone Receptor family member (nhr-60) [Caenorhabditis elegans] 0.0
blast AAG15157 nuclear receptor NHR-60 [Caenorhabditis elegans] 0.0
blast CAB09422 Hypothetical protein F57A10.5 [Caenorhabditis elegans] ref|NP_506930.1| Nuclear Hormone Receptor family member (nhr-60) [Caenorhabditis elegans] 1.0E-176
blast AAG15157 nuclear receptor NHR-60 [Caenorhabditis elegans] 1.0E-176
blast CAB04069 Hypothetical protein F09C6.9 [Caenorhabditis elegans] ref|NP_507273.2| Nuclear Hormone Receptor family member (nhr-116) [Caenorhabditis elegans] gb|AAO39205.1| nuclear receptor NHR-116 [Caenorhabditis elegans] 1.0E-146
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.2E-53
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.4E-17
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.2E-53
Sequence
Target Sequence 
>C. ELEGANS:194128_S_AT
catccccagggaaaccgagagactcacaacacagtcaaaacataaaacaatggttcttct
acaatttactgacaactgtcgaatacgccaaaacgttcatgttctttcatcgactcagct
ctcgagacaagctgattctaactaggcacgtggcattggcttgtacgaaccttcatatct
cgtactcatcgattagaaggaatttagaggttatcattgagcctgacggatcggaaccca
tgactttcaacgatacccattattcggcttctgtgatgtctgttgcaccgttgatccgtt
gtcaaattaaaaatattgaatatttgttactgaaagccattgtattatgtaatccagccg
tccccgatctctccgccaaatcccaggaaatcatctcactggagcgagtaaaatatgcag
atgctctttttaattattgtctccgaagccggtctgatggtcccccgcatttcgcccaat
taattcaaattattgatgttctcgaacgtcagcagagaatgcaaaaggatttgcatctac
ttctcgtggctccgaaagtagcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATCCCCAGGGAAACCGAGAGACTC 511 209 728 Antisense
TCTTTCATCGACTCAGCTCTCGAGA 586 615 830 Antisense
GTGGCATTGGCTTGTACGAACCTTC 681 489 877 Antisense
CGAACCTTCATATCTCGTACTCATC 329 253 893 Antisense
ATTGAGCCTGACGGATCGGAACCCA 311 3 943 Antisense
ATACCCATTATTCGGCTTCTGTGAT 320 23 980 Antisense
CTTCTGTGATGTCTGTTGCACCGTT 122 219 995 Antisense
TTGCACCGTTGATCCGTTGTCAAAT 386 701 1010 Antisense
TGTCTCCGAAGCCGGTCTGATGGTC 144 559 1165 Antisense
AAAGGATTTGCATCTACTTCTCGTG 441 121 1251 Antisense
ACTTCTCGTGGCTCCGAAAGTAGCG 686 101 1266 Antisense
Sequence Source Affymetrix Proprietary Database