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[186589_at]

Description Y77E11A.5 /REP_DB=WormBase Gene ID /WP=CE25619 /TR=Q9N4B8 /GB=AAF36075.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 21      4grp_total > 10      6grp_cgc > 54      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 3
(-3)
A 		6.3
(-2.7)
A 		4.1
(-2.9)
A 		70.3
(3)
A 		67
B 2.9
(-3)
A 		3.6
(-1.4)
A 		3
(-2.8)
A 		5.5
(3)
A 		3
C 3.8
(-2.6)
A 		3.6
(-2.7)
A 		2.8
(-3)
A 		18.1
(3)
A 		15
avr 3.2
(-3) 		4.5
(-2.7) 		3.3
(-3) 		31.3
(3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 11
1 2 3 4 5 6 range
A 3.2
(1.4)
A 		2.6
(-0.3)
A 		2.4
(-0.8)
A 		1.6
(-3)
A 		3.8
(3)
A 		2.8
(0.3)
A 		2
B 2.9
(-2.9)
A 		2.8
(-2.9)
A 		12.7
(3)
A 		3.2
(-2.7)
A 		2.8
(-2.9)
A 		2.7
(-3)
A 		10
C 3
(-2.5)
A 		11.9
(3)
A 		2.2
(-3)
A 		4.1
(-1.8)
A 		4.4
(-1.6)
A 		2.5
(-2.8)
A 		10
avr 3
(-2.4) 		5.8
(3) 		5.8
(3) 		3
(-2.4) 		3.7
(-1.1) 		2.7
(-3) 		3
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 1.1
(-3)
A 		1.4
(-2.8)
A 		1.1
(-3)
A 		10.3
(3)
A 		9
B 0.9
(-0.6)
A 		0.9
(-0.6)
A 		0.7
(-3)
A 		1.2
(3)
A 		1
C 1.3
(-2.1)
A 		1
(-3)
A 		1
(-3)
A 		3.1
(3)
A 		2
avr 1.1
(-2.7) 		1.1
(-2.7) 		0.9
(-3) 		4.9
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 0.6
(-1.3)
A 		0.9
(1.3)
A 		0.5
(-2.1)
A 		0.4
(-3)
A 		1.1
(3)
A 		0.7
(-0.4)
A 		1
B 1
(-2.5)
A 		0.9
(-2.7)
A 		3.1
(3)
A 		0.8
(-3)
A 		1.1
(-2.2)
A 		1
(-2.5)
A 		2
C 1.1
(-2)
A 		3.6
(3)
A 		0.6
(-3)
A 		0.8
(-2.6)
A 		1.4
(-1.4)
A 		0.9
(-2.4)
A 		3
avr 0.9
(-1.9) 		1.8
(3) 		1.4
(0.8) 		0.7
(-3) 		1.2
(-0.3) 		0.9
(-1.9) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 186589_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11179
Sequence Type Exemplar sequence
Representative Public ID Y77E11A.5 NCBI
Target Description Y77E11A.5 /REP_DB=WormBase Gene ID /WP=CE25619 /TR=Q9N4B8 /GB=AAF36075.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=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_067672(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067672 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-41) (nhr-41) mRNA, complete cds. 11/11 None
SNAP00000027300 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1393898:1400617:1 11/11 None
Y104H12A.1 ENSEMBL cdna:known chromosome:CEL140:IV:1386162:1399352:1 gene:Y104H12A.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000027326 7/11 Cross Hyb Matching Probes None
GENEFINDER00000027332 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:1393903-1399211(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol nhr-41
Ensembl Y104H12A.1
Entrez Gene 190865 Entrez gene
WormBase CE37054 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.7797.1.S1_S_AT similar to nuclear receptor subfamily 2, group C, member 2 cfa
CHICKEN:GGA.15703.1.S1_AT nuclear receptor subfamily 2, group C, member 2 gga
CHICKEN:GGA.15703.2.S1_AT nuclear receptor subfamily 2, group C, member 2 gga
CHICKEN:GGA.15703.2.S1_S_AT nuclear receptor subfamily 2, group C, member 2 gga
CHICKEN:GGA.164.1.S1_S_AT nuclear receptor subfamily 2, group C, member 2 gga
CHICKEN:GGAAFFX.22615.2.S1_S_AT nuclear receptor subfamily 2, group C, member 2 gga
HG-U133A_2:206038_S_AT nuclear receptor subfamily 2, group C, member 2 hs
HG-U133_PLUS_2:206038_S_AT nuclear receptor subfamily 2, group C, member 2 hs
HG-U133A:206038_S_AT nuclear receptor subfamily 2, group C, member 2 hs
HG-FOCUS:206038_S_AT nuclear receptor subfamily 2, group C, member 2 hs
HG-U95AV2:36714_AT nuclear receptor subfamily 2, group C, member 2 hs
HU35KSUBC:RC_AA427575_AT nuclear receptor subfamily 2, group C, member 2 hs
HUGENEFL:L27586_AT nuclear receptor subfamily 2, group C, member 2 hs
U133_X3P:G4507674_3P_A_AT nuclear receptor subfamily 2, group C, member 2 hs
HU35KSUBA:RC_AA176496_AT Nuclear receptor subfamily 2, group C, member 2 hs
HU35KSUBC:RC_T71249_AT Nuclear receptor subfamily 2, group C, member 2 hs
U133_X3P:HS2.385636.1.S1_3P_AT Nuclear receptor subfamily 2, group C, member 2 hs
U133_X3P:HS.76962.0.A1_3P_AT Nuclear receptor subfamily 2, group C, member 2 hs
U133_X3P:HS.29904.0.A1_3P_X_AT Nuclear receptor subfamily 2, group C, member 2 hs
U133_X3P:HS.29904.0.A1_3P_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U133_PLUS_2:1561546_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U133_PLUS_2:226848_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U133B:226848_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U133_PLUS_2:244019_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U133B:244019_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U95B:44538_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U95C:60210_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U95B:42040_AT Nuclear receptor subfamily 2, group C, member 2 hs
HG-U95C:53080_AT Nuclear receptor subfamily 2, group C, member 2 hs
HU35KSUBC:RC_AA258789_AT Nuclear receptor subfamily 2, group C, member 2 hs
MOUSE430A_2:1454167_AT nuclear receptor subfamily 2, group C, member 2 mm
MOE430A:1454167_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430_2:1454167_AT nuclear receptor subfamily 2, group C, member 2 mm
MU11KSUBA:U11688_S_AT nuclear receptor subfamily 2, group C, member 2 mm
MU11KSUBB:MSA.1798.0_S_AT nuclear receptor subfamily 2, group C, member 2 mm
MG-U74BV2:106588_AT nuclear receptor subfamily 2, group C, member 2 mm
MOE430A:1425014_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430A_2:1425014_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430_2:1425014_AT nuclear receptor subfamily 2, group C, member 2 mm
MOE430A:1451569_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430A_2:1451569_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430_2:1451569_AT nuclear receptor subfamily 2, group C, member 2 mm
MOE430B:1454851_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430_2:1454851_AT nuclear receptor subfamily 2, group C, member 2 mm
MOE430B:1439696_AT nuclear receptor subfamily 2, group C, member 2 mm
MOUSE430_2:1439696_AT nuclear receptor subfamily 2, group C, member 2 mm
MG-U74AV2:98479_F_AT nuclear receptor subfamily 2, group C, member 2 mm
RG-U34A:L27513_AT TR4 orphan receptor rn
RG-U34B:RC_AA899464_I_AT TR4 orphan receptor rn
RG-U34B:RC_AA899464_F_AT TR4 orphan receptor rn
RAE230A:1369243_AT TR4 orphan receptor rn
RAT230_2:1369243_AT TR4 orphan receptor rn
RAE230B:1380135_AT TR4 orphan receptor rn
RAT230_2:1380135_AT TR4 orphan receptor rn
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
4879 ligand-dependent nuclear receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_500073 Nuclear Hormone Receptor family member (nhr-41) [Caenorhabditis elegans] 0.0
blast Q9N4B8 Nuclear hormone receptor family member nhr-41 0.0
blast AAQ55494 NHR-41A [Caenorhabditis elegans] 0.0
blast AAQ55495 NHR-41B [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.4E-52
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.4E-52
Sequence
Target Sequence 
>C. ELEGANS:186589_AT
ggccagctcctggacaatttaacgaatcaaatggcaatgggcatggagtgcggccaatac
tcggcggaaaaattcgaaaaaattagcgaacagatgcagaggctgttgcaattgtcacag
ttgttcgcctcgcgagagctcaccgccgtggagtatgcctatcttaaaatgatctcattt
accgcacaagatctcccgagctcaatggcttcccccgagacgcgtagcgtgaatcaaatg
gcgtcacaggagctgttcgagtacgtttcctcatcgaaaagcacacaaaatcatatgtca
aatgagcacataaatgtggacgactcgacgtcagaggacaatgacacgcacgtgacgtca
cagcaatcaagtgtgaatattgctgctgaaagattttcacggatcctgcagcttctcccc
tgtctccgctggttcgatcctgcaacaattgtggaaatattcttttcgggcctaattggc
ccaatgtctattgaaaccatcatcccatttgtcctgcaaatgaatttgatgagctttttc
gaccaaaaaatggagctcggcagcggcggagcatcggatactctctcaacatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCCAGCTCCTGGACAATTTAACGA 571 541 211 Antisense
GCATGGAGTGCGGCCAATACTCGGC 98 311 251 Antisense
CGCCGTGGAGTATGCCTATCTTAAA 162 257 354 Antisense
TCATTTACCGCACAAGATCTCCCGA 569 619 385 Antisense
TTCCCCCGAGACGCGTAGCGTGAAT 426 669 420 Antisense
AGGAGCTGTTCGAGTACGTTTCCTC 43 55 458 Antisense
TGACACGCACGTGACGTCACAGCAA 668 571 552 Antisense
AAAGATTTTCACGGATCCTGCAGCT 709 121 599 Antisense
CTGGTTCGATCCTGCAACAATTGTG 221 241 639 Antisense
AAAAATGGAGCTCGGCAGCGGCGGA 411 129 756 Antisense
GAGCATCGGATACTCTCTCAACATC 154 389 779 Antisense
Sequence Source Affymetrix Proprietary Database