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[190812_at] nuclear hormone receptor

Description F09C6.9 /REP_DB=WormBase Gene ID /WP=CE18582 /TR=Q9XV98 /GB=CAB04069.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 53      6grp_high1_10_10 > 34      4grp_highest_8_8 > 37      4grp_high_8_8 > 0      6grp_highest_nonorm > 80      6grp_total > 01      4grp_total > 07      6grp_highest_sub > 02      6grp_cgc > 53      6grp_high1_sub > 02      6grp_cgc_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 197.2
(-0.9)
P 		172
(-3)
P 		211.2
(0.3)
P 		242.7
(3)
P 		71
B 266.4
(3)
P 		152
(-3)
P 		216.8
(0.4)
P 		235.2
(1.4)
P 		114
C 227.7
(0.3)
P 		193.2
(-3)
P 		221.1
(-0.3)
P 		255
(3)
P 		62
avr 230.4
(1.8) 		172.4
(-3) 		216.4
(0.7) 		244.3
(3) 		72

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 160
1 2 3 4 5 6 range
A 232.7
(1.4)
P 		260.6
(3)
P 		159.7
(-2.9)
P 		158.6
(-3)
P 		192.6
(-1)
P 		191.2
(-1.1)
P 		102
B 158.1
(-2.5)
P 		304.8
(3)
P 		145.3
(-3)
P 		177.3
(-1.8)
P 		164.6
(-2.3)
P 		209.6
(-0.6)
P 		160
C 216.7
(-0)
P 		270.7
(3)
P 		221.1
(0.2)
P 		201
(-0.9)
P 		164.2
(-3)
P 		216.7
(-0)
P 		107
avr 202.5
(-1.4) 		278.7
(3) 		175.4
(-2.9) 		179
(-2.7) 		173.8
(-3) 		205.8
(-1.2) 		105
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 71.8
(3)
P 		37.3
(-2.7)
P 		55.2
(0.3)
P 		35.5
(-3)
P 		36
B 84.9
(3)
P 		37.5
(-3)
P 		50.2
(-1.4)
P 		50.1
(-1.4)
P 		47
C 75.4
(2.7)
P 		55.5
(-0.8)
P 		77.1
(3)
P 		43
(-3)
P 		34
avr 77.4
(3) 		43.4
(-2.9) 		60.8
(0.1) 		42.9
(-3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 67
1 2 3 4 5 6 range
A 42.9
(-2.2)
P 		92.7
(3)
P 		34.8
(-3)
P 		40.2
(-2.4)
P 		58.1
(-0.6)
P 		46.6
(-1.8)
P 		58
B 55
(-1.2)
P 		101.5
(3)
P 		35.3
(-3)
P 		47
(-1.9)
P 		66.9
(-0.1)
P 		78.2
(0.9)
P 		66
C 80.3
(2.7)
P 		82.6
(3)
P 		56.3
(-0.7)
P 		40.4
(-3)
P 		53.1
(-1.2)
P 		72.5
(1.6)
P 		42
avr 59.4
(-0.9) 		92.3
(3) 		42.1
(-3) 		42.5
(-3) 		59.4
(-0.9) 		65.8
(-0.2) 		50
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190812_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12609
Sequence Type Exemplar sequence
Representative Public ID F09C6.9 NCBI
Target Description F09C6.9 /REP_DB=WormBase Gene ID /WP=CE18582 /TR=Q9XV98 /GB=CAB04069.1 /SUBMIT=HINXTON /CHR=5 /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 identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_074872(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074872 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-116) (nhr-116) mRNA, complete cds. 11/11 None
SNAP00000006353 ENSEMBL cdna:SNAP chromosome:CEL140:V:16914819:16917850:1 11/11 None
GENEFINDER00000006368 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16907496:16917854:1 11/11 None
F09C6.9 ENSEMBL cdna:known chromosome:CEL140:V:16914812:16917929:1 gene:F09C6.9 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:16914548-16918290(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-116
Ensembl F09C6.9
Entrez Gene 180129 Entrez gene
SwissProt Q9XV98 EMBL-EBI
WormBase CE37501 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 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] 0.0
blast CAB04068 Hypothetical protein F09C6.8 [Caenorhabditis elegans] ref|NP_507272.1| F09C6.8 [Caenorhabditis elegans] 0.0
blast AAB70328 Hypothetical protein C38C3.9 [Caenorhabditis elegans] ref|NP_503435.1| C38C3.9 [Caenorhabditis elegans] 1.0E-173
blast CAB09422 Hypothetical protein F57A10.5 [Caenorhabditis elegans] ref|NP_506930.1| Nuclear Hormone Receptor family member (nhr-60) [Caenorhabditis elegans] 1.0E-149
blast AAG15157 nuclear receptor NHR-60 [Caenorhabditis elegans] 1.0E-149
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.9E-54
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 8.2E-22
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.5E-31
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.9E-54
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.9E-25
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 8.2E-22
Sequence
Target Sequence 
>C. ELEGANS:190812_AT
gatgtacttcaacttgttcaccaccgtagagtacgcgaagacgttcatgtttttccatag
gctcgactccagagacaaatttattctgacaaagcatatcacattgtcttgtatgaatct
gcatctctcctacatctcggtcgccaggaaatcagaagttttgacgaatcccgacggaac
aagctttccttccagaacccaagcccactacacttcaaaaacaatgtcggtcgctcctct
aattcggtatcaaattcagtacatcgagtacacgcttctcaaagcaatttgcttatgtaa
tccagccgttcccgatctctctcaccacgctcaggaaatactttcaaaagaacgggaaaa
atatgcggacgctttattcgactattgcctccgaactcgaaatgatgggccatcacactt
tgctcagctgatgcagattttcgatgttctggagcgccaacagaagcttcaaaaagatct
ccatttgctttatattctgccaactttggctcatgctccaaagtgtcttgttatccgtgt
cattg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTACTTCAACTTGTTCACCACC 254 409 822 Antisense
TTTTCCATAGGCTCGACTCCAGAGA 45 675 872 Antisense
TTGTATGAATCTGCATCTCTCCTAC 554 705 930 Antisense
CTACATCTCGGTCGCCAGGAAATCA 212 227 951 Antisense
CCGACGGAACAAGCTTTCCTTCCAG 525 263 992 Antisense
CAAAAACAATGTCGGTCGCTCCTCT 93 191 1037 Antisense
GTACATCGAGTACACGCTTCTCAAA 249 461 1080 Antisense
TCTCTCACCACGCTCAGGAAATACT 264 611 1139 Antisense
GGACGCTTTATTCGACTATTGCCTC 153 523 1188 Antisense
ATCACACTTTGCTCAGCTGATGCAG 418 27 1233 Antisense
AAGTGTCTTGTTATCCGTGTCATTG 53 159 1342 Antisense
Sequence Source Affymetrix Proprietary Database