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[192819_at] nuclear hormone receptor

Description Y67A6A.2 /REP_DB=WormBase Gene ID /WP=CE27305 /GEN=nhr-62 /TR=O02279 /GB=CAA21675.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=nuclear hormone receptor
Cluster 6grp_highest_10_10 > 14      6grp_high1_10_10 > 30      4grp_highest_8_8 > 23      4grp_high_8_8 > 13      6grp_highest_nonorm > 52      6grp_total > 43      4grp_total > 03      6grp_cgc > 81      6grp_high1_sub > 03      6grp_cgc_sub > 03      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 293
1 2 3 4 range
A 216.5
(-2.6)
P 		210.7
(-2.7)
P 		198.2
(-3)
P 		463.5
(3)
P 		265
B 259.2
(-1.2)
P 		192.8
(-2.7)
P 		178.6
(-3)
P 		448.9
(3)
P 		270
C 170.6
(-3)
P 		205.7
(-1.6)
P 		189.6
(-2.2)
P 		320
(3)
P 		149
avr 215.4
(-2.3) 		203.1
(-2.6) 		188.8
(-3) 		410.8
(3) 		222

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 501
1 2 3 4 5 6 range
A 713.4
(0.8)
P 		583.1
(-0.7)
P 		894.6
(3)
P 		639.8
(-0.1)
P 		757.9
(1.4)
P 		393.9
(-3)
P 		501
B 823.6
(2.2)
P 		509.7
(-2.6)
P 		877
(3)
P 		482.4
(-3)
P 		537.6
(-2.2)
P 		639.5
(-0.6)
P 		395
C 544.2
(-1.2)
P 		828.4
(3)
P 		802.1
(2.6)
P 		665.1
(0.6)
P 		417.9
(-3)
P 		561.8
(-0.9)
P 		411
avr 693.7
(-0) 		640.4
(-1) 		857.9
(3) 		595.8
(-1.8) 		571.1
(-2.3) 		531.7
(-3) 		326
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 54
1 2 3 4 range
A 78.8
(3)
P 		45.7
(-3)
P 		51.8
(-1.9)
P 		67.8
(1)
P 		33
B 82.7
(1.6)
P 		47.6
(-2.3)
P 		41.4
(-3)
P 		95.7
(3)
P 		54
C 56.5
(-1.8)
P 		59.2
(-0.4)
P 		66.1
(3)
P 		54
(-3)
P 		12
avr 72.7
(3) 		50.8
(-3) 		53.1
(-2.4) 		72.5
(2.9) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 191
1 2 3 4 5 6 range
A 131.5
(-1.4)
P 		207.4
(2)
P 		194.8
(1.5)
P 		162.3
(0)
P 		228.7
(3)
P 		95.9
(-3)
P 		133
B 286.6
(3)
P 		169.6
(-1.4)
P 		213
(0.2)
P 		127.8
(-3)
P 		218.4
(0.4)
P 		238.5
(1.2)
P 		159
C 201.7
(0.4)
P 		252.8
(3)
P 		204.2
(0.6)
P 		133.7
(-3)
P 		135.2
(-2.9)
P 		188.1
(-0.3)
P 		119
avr 206.6
(2.7) 		209.9
(3) 		204
(2.5) 		141.3
(-3) 		194.1
(1.6) 		174.2
(-0.1) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192819_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1451
Sequence Type Exemplar sequence
Representative Public ID Y67A6A.2 NCBI
Target Description Y67A6A.2 /REP_DB=WormBase Gene ID /WP=CE27305 /GEN=nhr-62 /TR=O02279 /GB=CAA21675.2 /SUBMIT=HINXTON /CHR=1 /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_060206(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060206 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-62) (nhr-62) mRNA, complete cds. 11/11 None
SNAP00000018520 ENSEMBL cdna:SNAP chromosome:CEL140:I:9851617:9852828:1 11/11 None
GENEFINDER00000018526 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9851617:9854449:1 11/11 None
Y67A6A.2 ENSEMBL cdna:known chromosome:CEL140:I:9847719:9852930:1 gene:Y67A6A.2 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
chrI:9847660-9852759(+) 100.0 100.0
Public Domain and Genome References
Gene Title nuclear hormone receptor
Gene Symbol nhr-62
Ensembl Y67A6A.2
Entrez Gene 172836 Entrez gene
SwissProt O02279 EMBL-EBI
WormBase CE27305 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 CAA21675 Hypothetical protein Y67A6A.2 [Caenorhabditis elegans] emb|CAB05776.2| Hypothetical protein Y67A6A.2 [Caenorhabditis elegans] ref|NP_492607.1| Nuclear Hormone Receptor family member (nhr-62) [Caenorhabditis elegans] 0.0
blast AAG15163 nuclear receptor NHR-62 [Caenorhabditis elegans] 0.0
blast AAG15162 nuclear receptor NHR-62 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.9E-29
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.2E-37
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.9E-29
Sequence
Target Sequence 
>C. ELEGANS:192819_AT
gatacgggacatttcactggtggatgtgtgcaaattggactgtacaagcaggatgtgagg
gagtatgttactcgaatggagcatatttcccaaaacaaccagaagctcaatgtattcctg
atgttaaaggatcaagtggacgaatgtatgactcattgagtattccaattaaagaattga
atcttgatgaaactgaaattgttctaatgttggcagttatcattttcagtgatggtaagt
ggagcatgatgcttggtagattagaaatatttgaattttctatttcagagattacagaac
ttgctgatttgacaccagctggaaaagaacatgttcgaatggttggaaaccgattcgttc
gcatgcttcatcatcatgtgaactcaaaagaatatggagaggcgatggaaaatggagatg
atacacaaaatagtagtgaaagtcaagcagcagttcgaattgccaaaatgatgattcttc
tctcggcgactacgaatctcgtgtatctcacttctgacaacattcaattgatggaggtcc
tacacgttgtgccaagtgaatatctttgccatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATACGGGACATTTCACTGGTGGAT 296 423 1004 Antisense
GAGCATATTTCCCAAAACAACCAGA 593 387 1082 Antisense
GAAGCTCAATGTATTCCTGATGTTA 117 343 1105 Antisense
GAACTTGCTGATTTGACACCAGCTG 342 351 1300 Antisense
AAACCGATTCGTTCGCATGCTTCAT 302 125 1350 Antisense
GTCAAGCAGCAGTTCGAATTGCCAA 84 465 1445 Antisense
AAAATGATGATTCTTCTCTCGGCGA 207 133 1468 Antisense
TCTCGGCGACTACGAATCTCGTGTA 474 609 1484 Antisense
GAATCTCGTGTATCTCACTTCTGAC 395 329 1497 Antisense
TGATGGAGGTCCTACACGTTGTGCC 336 567 1532 Antisense
GTGCCAAGTGAATATCTTTGCCATG 660 477 1552 Antisense
Sequence Source Affymetrix Proprietary Database