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[192635_at] nuclear hormone receptor

Description C02B4.2 /REP_DB=WormBase Gene ID /WP=CE02111 /GEN=nhr-17 /TR=Q17589 /GB=CAA90291.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 67      6grp_high1_10_10 > 86      4grp_highest_8_8 > 22      4grp_high_8_8 > 06      6grp_highest_nonorm > 94      6grp_total > 76      4grp_total > 09      6grp_highest_sub > In      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2095
1 2 3 4 range
A 329.1
(-3)
P 		326.4
(-3)
P 		505.9
(-2.3)
P 		1872.8
(3)
P 		1546
B 314.2
(-3)
P 		383.8
(-2.8)
P 		533
(-2.4)
P 		2394.2
(3)
P 		2080
C 299.1
(-3)
P 		378.8
(-2.8)
P 		549.7
(-2.2)
P 		2276.9
(3)
P 		1978
avr 314.1
(-3) 		363
(-2.8) 		529.5
(-2.3) 		2181.3
(3) 		1867

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 806
1 2 3 4 5 6 range
A 318.4
(-2.6)
P 		273.6
(-3)
P 		336.8
(-2.5)
P 		445.3
(-1.6)
P 		548.7
(-0.7)
P 		984.1
(3)
P 		711
B 294.1
(-2.8)
P 		273.1
(-3)
P 		511
(-0.9)
P 		429.9
(-1.6)
P 		511.5
(-0.9)
P 		942.7
(3)
P 		670
C 331.8
(-2.5)
P 		265.1
(-3)
P 		519.3
(-1.1)
P 		535.2
(-1)
P 		453.7
(-1.6)
P 		1071.2
(3)
P 		806
avr 314.8
(-2.6) 		270.6
(-3) 		455.7
(-1.5) 		470.1
(-1.4) 		504.6
(-1.1) 		999.3
(3) 		729
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 439
1 2 3 4 range
A 119.8
(-1.6)
P 		70.9
(-3)
P 		132.3
(-1.2)
P 		274.1
(3)
P 		203
B 100.2
(-2.9)
P 		94.8
(-3)
P 		123.5
(-2.6)
P 		510.2
(3)
P 		415
C 99
(-3)
P 		108.9
(-2.8)
P 		191.6
(-1)
P 		383.9
(3)
P 		285
avr 106.3
(-2.7) 		91.5
(-3) 		149.1
(-1.8) 		389.4
(3) 		298

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 300
1 2 3 4 5 6 range
A 58.7
(-3)
P 		97.3
(-1.7)
P 		73.4
(-2.5)
P 		112.9
(-1.2)
P 		165.6
(0.5)
P 		239.6
(3)
P 		181
B 102.3
(-2.7)
P 		90.9
(-3)
P 		124.1
(-2.2)
P 		113.9
(-2.5)
P 		207.8
(-0.3)
P 		351.5
(3)
P 		261
C 123
(-2.1)
P 		80.9
(-3)
P 		132.2
(-1.9)
P 		107.6
(-2.4)
P 		146.8
(-1.6)
P 		358.6
(3)
P 		278
avr 94.7
(-2.9) 		89.7
(-3) 		109.9
(-2.5) 		111.5
(-2.4) 		173.4
(-0.8) 		316.6
(3) 		227
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192635_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18046
Sequence Type Exemplar sequence
Representative Public ID C02B4.2 NCBI
Target Description C02B4.2 /REP_DB=WormBase Gene ID /WP=CE02111 /GEN=nhr-17 /TR=Q17589 /GB=CAA90291.1 /SUBMIT=HINXTON /CHR=X /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_077714(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077714 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-17) (nhr-17) mRNA, complete cds. 11/11 None
GENEFINDER00000024962 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12660278:12667769:-1 11/11 None
C02B4.2 ENSEMBL cdna:known chromosome:CEL140:X:12663762:12667771:-1 gene:C02B4.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000024958 6/11 Cross Hyb Matching Probes None
SNAP00000024959 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:12664159-12667769(-) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-17
Ensembl C02B4.2
Entrez Gene 191719 Entrez gene
SwissProt Q17589 EMBL-EBI
WormBase CE02111 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 CAA90291 Hypothetical protein C02B4.2 [Caenorhabditis elegans] ref|NP_510115.1| Nuclear Hormone Receptor family member (nhr-17) [Caenorhabditis elegans] 0.0
blast CAE57227 Hypothetical protein CBG00093 [Caenorhabditis briggsae] 0.0
blast NP_001024855 Nuclear Hormone Receptor family member (nhr-1) [Caenorhabditis elegans] gb|AAO39168.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAO39167.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAC48174.4| Nuclear hormone receptor family protein 1, isoform c [Caenorhabditis elegans] 7.0E-49
blast NP_001024855 Nuclear Hormone Receptor family member (nhr-1) [Caenorhabditis elegans] gb|AAO39168.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAO39167.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAC48174.4| Nuclear hormone receptor family protein 1, isoform c [Caenorhabditis elegans] 1.0E-48
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.2E-44
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.9E-37
Sequence
Target Sequence 
>C. ELEGANS:192635_AT
atcaaaaacgactcttcatccacacggcgttttctaatttagtcttagcagaagcatttc
acactccagaaaaatacaacgatcggatagtgtttccagatggactctgtggatttcgaa
acgttgctcaatcagtttccacggatggtgtttcgaacaaaacgtttggattgacgccga
ccgtggttgccgtaataaatgacgttctcgttccaataagaagaatgcgactaacaaaag
ttgaatatgttttgctgcaagcaattattttcttcgatcctgattgtctttccctgacaa
aacacggctcccaactcattgctgccaaacgcaagcgacttctggattcccttcaaaaat
ggcttcatcaacaaacgaaagactcaattgaagcgtccaccagatttgcggaaatcctcc
tcagaatctgtaatgtacagaaagtggcggcattcaaacgagaaacactgtgcacaattg
agacattcgaattgatgcagccacatccgttca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCAAAAACGACTCTTCATCCACAC 510 25 647 Antisense
CTTCATCCACACGGCGTTTTCTAAT 313 221 660 Antisense
GACTCTGTGGATTTCGAAACGTTGC 408 373 749 Antisense
AACGTTGCTCAATCAGTTTCCACGG 118 145 766 Antisense
TTTTCTTCGATCCTGATTGTCTTTC 661 675 914 Antisense
CCAACTCATTGCTGCCAAACGCAAG 278 277 957 Antisense
CAAACGCAAGCGACTTCTGGATTCC 404 191 972 Antisense
GGATTCCCTTCAAAAATGGCTTCAT 628 507 990 Antisense
ATTGAAGCGTCCACCAGATTTGCGG 330 3 1033 Antisense
CGGAAATCCTCCTCAGAATCTGTAA 264 243 1055 Antisense
GAATTGATGCAGCCACATCCGTTCA 301 323 1135 Antisense
Sequence Source Affymetrix Proprietary Database