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[191007_at] nuclear hormone receptor

Description R02C2.4 /REP_DB=WormBase Gene ID /WP=CE18093 /TR=O44543 /GB=AAC48231.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 58      4grp_highest_8_8 > 38      4grp_high_8_8 > 04      6grp_highest_nonorm > 82      6grp_total > 47      4grp_total > 05      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 324
1 2 3 4 range
A 331.2
(-0.4)
P 		261.5
(-3)
P 		308.3
(-1.3)
P 		424
(3)
P 		163
B 308.2
(-1.2)
P 		213.4
(-3)
P 		244
(-2.4)
P 		537.2
(3)
P 		324
C 332.8
(1.9)
P 		218.3
(-3)
P 		284.5
(-0.2)
P 		359.6
(3)
P 		141
avr 324.1
(-0.3) 		231.1
(-3) 		278.9
(-1.6) 		440.3
(3) 		209

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 249
1 2 3 4 5 6 range
A 330.2
(-0.2)
P 		329.9
(-0.2)
P 		217
(-3)
P 		229
(-2.7)
P 		259.4
(-2)
P 		462.3
(3)
P 		245
B 354.8
(3)
P 		343.4
(2.4)
P 		252.5
(-2)
P 		246.9
(-2.2)
P 		231.1
(-3)
P 		341.3
(2.3)
P 		124
C 287.5
(-0.7)
P 		323.5
(0.4)
P 		258.1
(-1.6)
P 		243.8
(-2.1)
P 		213.8
(-3)
P 		409.9
(3)
P 		196
avr 324.2
(0.2) 		332.3
(0.4) 		242.5
(-2.7) 		239.9
(-2.8) 		234.8
(-3) 		404.5
(3) 		170
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 120.6
(3)
P 		56.8
(-3)
P 		80.6
(-0.8)
P 		62.1
(-2.5)
P 		64
B 98.3
(1.4)
P 		52.7
(-3)
P 		56.5
(-2.6)
P 		114.5
(3)
P 		62
C 110.2
(3)
P 		62.8
(-2.7)
P 		99.2
(1.7)
P 		60.6
(-3)
P 		50
avr 109.7
(3) 		57.4
(-3) 		78.8
(-0.5) 		79.1
(-0.5) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 90
1 2 3 4 5 6 range
A 60.9
(-1.8)
P 		117.3
(3)
P 		47.3
(-3)
P 		58.1
(-2.1)
P 		78.3
(-0.3)
P 		112.6
(2.6)
P 		70
B 123.5
(2.7)
P 		114.3
(1.8)
P 		61.3
(-3)
P 		65.4
(-2.6)
P 		93.9
(-0)
P 		127.3
(3)
P 		66
C 106.6
(0.9)
P 		98.7
(0.4)
P 		65.7
(-1.9)
P 		49
(-3)
P 		69.2
(-1.6)
P 		137.2
(3)
P 		88
avr 97
(0.5) 		110.1
(1.6) 		58.1
(-2.9) 		57.5
(-3) 		80.5
(-1) 		125.7
(3) 		68
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191007_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15467
Sequence Type Exemplar sequence
Representative Public ID R02C2.4 NCBI
Target Description R02C2.4 /REP_DB=WormBase Gene ID /WP=CE18093 /TR=O44543 /GB=AAC48231.1 /SUBMIT=ST.LOUIS /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_070764(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070764 NCBI Caenorhabditis elegans R02C2.4 (R02C2.4) mRNA, complete cds. 11/11 None
SNAP00000019097 ENSEMBL cdna:SNAP chromosome:CEL140:V:252193:257809:-1 10/11 None
GENEFINDER00000019103 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:246480:257814:-1 11/11 None
R02C2.4 ENSEMBL cdna:known chromosome:CEL140:V:254806:260247:-1 gene:R02C2.4 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:254805-260518(-) 99.25 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-204
Ensembl R02C2.4
Entrez Gene 187519 Entrez gene
SwissProt O44543 EMBL-EBI
WormBase CE32202 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 AAC48231 Hypothetical protein R02C2.4 [Caenorhabditis elegans] ref|NP_503165.2| R02C2.4 [Caenorhabditis elegans] 0.0
blast AAC48228 Temporarily assigned gene name protein 40 [Caenorhabditis elegans] ref|NP_503163.2| Temporarily Assigned Gene name family member (tag-40) [Caenorhabditis elegans] 0.0
blast CAE58006 Hypothetical protein CBG01075 [Caenorhabditis briggsae] 0.0
blast AAC48230 Seven tm receptor protein 121 [Caenorhabditis elegans] ref|NP_503164.2| Seven TM Receptor family member (str-121) [Caenorhabditis elegans] 6.0E-68
blast AAG15157 nuclear receptor NHR-60 [Caenorhabditis elegans] 1.0E-65
blast CAB09422 Hypothetical protein F57A10.5 [Caenorhabditis elegans] ref|NP_506930.1| Nuclear Hormone Receptor family member (nhr-60) [Caenorhabditis elegans] 1.0E-65
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 6.7E-51
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.6E-12
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.9E-7
Pfam IPR003002 EMBL-EBI 7TM chemoreceptor, subfamily 1 6.9E-39
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.4E-26
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.7E-10
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.6E-12
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.9E-7
Pfam IPR003002 EMBL-EBI 7TM chemoreceptor, subfamily 1 1.1E-55
Pfam IPR003002 EMBL-EBI 7TM chemoreceptor, subfamily 1 3.7E-14
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.0E-49
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.6E-12
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.9E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503165.2 2 10-32,39-61
R02C2.4 2 10-32,39-61
SNAP00000019097 3 413-432,452-474,484-506
GENEFINDER00000019103 18 460-482,494-516,541-563,584-606,630-652,659-681,691-713,720-737,872-894,950-972,987-1009,1036-1055,1111-1133,1171-1193,1208-1225,1246-1263,1278-1300,1312-1334
Sequence
Target Sequence 
>C. ELEGANS:191007_AT
ggatcgccaagaattttaccgccaaatgtaaagaagtggtttagttatgatctactcaca
gtggtggaaatggcgaagacatttgattttttcaagaaactttcagagaatgataggttt
tttctatgccgagacaccagtctaatggtatcgaatcttatgcgggcctatttttcggtg
gaaaacaagaccgataaatttatcagagcagatgggcaaaccttcgtacccccgccaaag
attcccaaagagtatatggataatttgtcaagtgatatcatgatgcgagcaattaaaact
ctgatccgcctggcgtgtacaaaagttgaatatctttttcttagagctattttgttgtgc
aattcagcagctcccgacatctcagcttccggccgaaacatactttctacagaacgggcc
aagtacacggtagcccttctcaactacacaatgacgcatcacggcgctgcgggacccggg
cgttttgctgaaattcttaatgttattgatgttctggaacgacagcagaaggaccagaga
gatgttaacgtttatattacgttgtaccgtccgaaacatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATCGCCAAGAATTTTACCGCCAA 415 513 1120 Antisense
TTTTCTATGCCGAGACACCAGTCTA 566 675 1239 Antisense
GAATCTTATGCGGGCCTATTTTTCG 359 327 1272 Antisense
GAGCAGATGGGCAAACCTTCGTACC 644 389 1325 Antisense
CAATTAAAACTCTGATCCGCCTGGC 700 179 1409 Antisense
ATCCGCCTGGCGTGTACAAAAGTTG 424 33 1423 Antisense
TTGTTGTGCAATTCAGCAGCTCCCG 485 705 1471 Antisense
GGGCCAAGTACACGGTAGCCCTTCT 188 493 1535 Antisense
GCCCTTCTCAACTACACAATGACGC 160 287 1552 Antisense
CACAATGACGCATCACGGCGCTGCG 292 193 1566 Antisense
ATTACGTTGTACCGTCCGAAACATG 696 1 1675 Antisense
Sequence Source Affymetrix Proprietary Database