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[186628_at]

Description Y38E10A.18 /REP_DB=WormBase Gene ID /WP=CE21598 /TR=Q9NAJ3 /GB=CAB54409.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_total > 92      4grp_total > 13      6grp_cgc > 98      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 118
1 2 3 4 range
A 66.6
(-1.5)
A 		37.5
(-3)
A 		43.2
(-2.7)
A 		154.4
(3)
A 		117
B 101.4
(1.3)
P 		73.3
(-1.3)
A 		54.5
(-3)
A 		119.2
(3)
A 		65
C 98.3
(1.9)
A 		74.4
(-0)
A 		36.6
(-3)
A 		112.3
(3)
A 		76
avr 88.8
(0.2) 		61.7
(-1.8) 		44.8
(-3) 		128.6
(3) 		84

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 86
1 2 3 4 5 6 range
A 28.9
(-3)
A 		86.4
(1.6)
A 		75.4
(0.7)
A 		104.7
(3)
A 		82.1
(1.2)
M 		64.5
(-0.2)
A 		76
B 80.6
(3)
A 		67.5
(1.7)
A 		18.3
(-3)
A 		46.5
(-0.3)
A 		76.1
(2.6)
A 		50.9
(0.1)
A 		62
C 40
(-2.3)
A 		39.2
(-2.4)
A 		63.2
(0.7)
A 		40.9
(-2.2)
A 		81.4
(3)
P 		34.8
(-3)
A 		47
avr 49.8
(-3) 		64.4
(-0.1) 		52.3
(-2.5) 		64
(-0.2) 		79.9
(3) 		50.1
(-2.9) 		30
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 24.2
(3)
A 		8.1
(-3)
A 		11.3
(-1.8)
A 		22.6
(2.4)
A 		16
B 32.3
(3)
P 		18.1
(-1.3)
A 		12.6
(-3)
A 		25.4
(0.9)
A 		20
C 32.6
(3)
A 		21.4
(-0.4)
A 		12.8
(-3)
A 		18.9
(-1.2)
A 		20
avr 29.7
(3) 		15.9
(-1.7) 		12.2
(-3) 		22.3
(0.5) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 26
1 2 3 4 5 6 range
A 5.3
(-3)
A 		30.7
(3)
A 		16.4
(-0.4)
A 		26.5
(2)
A 		24.8
(1.6)
M 		15.7
(-0.5)
A 		25
B 28
(2.3)
A 		22.5
(1.1)
A 		4.5
(-3)
A 		12.3
(-1.2)
A 		30.9
(3)
A 		19
(0.3)
A 		26
C 14.8
(-0.8)
A 		12
(-1.7)
A 		16.1
(-0.4)
A 		8.2
(-3)
A 		26.3
(3)
P 		11.7
(-1.8)
A 		18
avr 16
(-1.5) 		21.7
(0.8) 		12.3
(-3) 		15.7
(-1.6) 		27.3
(3) 		15.5
(-1.7) 		15
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 186628_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3205
Sequence Type Exemplar sequence
Representative Public ID Y38E10A.18 NCBI
Target Description Y38E10A.18 /REP_DB=WormBase Gene ID /WP=CE21598 /TR=Q9NAJ3 /GB=CAB54409.1 /SUBMIT=HINXTON /CHR=2 /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_064300(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064300 NCBI Caenorhabditis elegans Y38E10A.18 (Y38E10A.18) mRNA, complete cds. 11/11 None
SNAP00000017444 ENSEMBL cdna:SNAP chromosome:CEL140:II:12631270:12638348:1 11/11 None
GENEFINDER00000017456 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12636599:12638348:1 11/11 None
Y38E10A.18 ENSEMBL cdna:known chromosome:CEL140:II:12636599:12638348:1 gene:Y38E10A.18 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
chrII:12636595-12638345(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol nhr-234
Ensembl Y38E10A.18
Entrez Gene 189663 Entrez gene
SwissProt Q9NAJ3 EMBL-EBI
WormBase CE21598 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
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB54409 Hypothetical protein Y38E10A.18 [Caenorhabditis elegans] ref|NP_496701.1| Y38E10A.18 [Caenorhabditis elegans] 0.0
blast CAB54409 Hypothetical protein Y38E10A.18 [Caenorhabditis elegans] ref|NP_496701.1| Y38E10A.18 [Caenorhabditis elegans] 1.0E-139
blast CAE65383 Hypothetical protein CBG10329 [Caenorhabditis briggsae] 1.0E-105
blast CAE62521 Hypothetical protein CBG06626 [Caenorhabditis briggsae] 3.0E-98
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.5E-4
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.6E-6
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.5E-4
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.8E-20
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000017444 3 31-50,70-92,113-135
Sequence
Target Sequence 
>C. ELEGANS:186628_AT
cagggtggcattgttatgtccccccaaaacttcctcgaaaccaaacaccgtactgaccaa
tttgctctggacatttgcacaatgtgcccgggaaccgacttgcttgagaatccagatttt
gaagttctctacaaatactgctccttttcaagtctctggatggatttatcttggattaat
gctagccaggacgattggaacaaggttttggtggaaaaagattacacggaaatacctctt
atcacctacatgaaccagttccaagctaccgtaaccgcccagttggctcgtcttcagctt
gacattttcgagtacgccgcgctcaaatccatgtgcatttggaaacttgggcttctggat
tcaactctcacgttgaaaattgtatcggctgagcattattatggaatcacatgtgccttg
agcaaatattatcgggtcacaaaacgcttggaacaatttgaaatggctacaagaatagca
gaaatcacattgctaattggtccgatctttaatgtctatcgagacatgctcgtgctctac
ca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGGTGGCATTGTTATGTCCCCCC 269 207 508 Antisense
AACACCGTACTGACCAATTTGCTCT 6 137 551 Antisense
ACAATGTGCCCGGGAACCGACTTGC 188 115 586 Antisense
GAACCGACTTGCTTGAGAATCCAGA 628 345 599 Antisense
CAAATACTGCTCCTTTTCAAGTCTC 658 191 639 Antisense
ATACCTCTTATCACCTACATGAACC 477 23 739 Antisense
CATGAACCAGTTCCAAGCTACCGTA 701 209 756 Antisense
GCTCGTCTTCAGCTTGACATTTTCG 269 299 793 Antisense
TTTTCGAGTACGCCGCGCTCAAATC 343 673 812 Antisense
GGAAACTTGGGCTTCTGGATTCAAC 39 529 848 Antisense
ATCGAGACATGCTCGTGCTCTACCA 625 35 1025 Antisense
Sequence Source Affymetrix Proprietary Database