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[177331_at]

Description VC5.5 /REP_DB=WormBase Gene ID /WP=CE21226 /TR=Q9TYU3 /GB=AAC78212.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 61      6grp_total > 41      4grp_total > 21      6grp_cgc > 60      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 141
1 2 3 4 range
A 205
(2.7)
P 		179.8
(0.8)
A 		130
(-3)
A 		208.8
(3)
P 		79
B 199.1
(0.5)
P 		136.9
(-3)
A 		141.6
(-2.7)
A 		244
(3)
P 		107
C 176.8
(0.4)
P 		123.7
(-2)
A 		102.9
(-3)
A 		231.8
(3)
P 		129
avr 193.6
(1) 		146.8
(-1.7) 		124.8
(-3) 		228.2
(3) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 229.2
(2.1)
A 		168.1
(0.3)
P 		257.9
(3)
P 		174.4
(0.5)
M 		125.8
(-1)
P 		58.1
(-3)
A 		200
B 141.6
(-0.7)
P 		197.6
(3)
P 		147.8
(-0.3)
P 		158.2
(0.4)
A 		194.8
(2.8)
P 		106.6
(-3)
P 		91
C 140.1
(-1)
P 		185.6
(0.7)
P 		201.6
(1.3)
A 		247.5
(3)
P 		133.8
(-1.3)
M 		87.4
(-3)
A 		160
avr 170.3
(1.4) 		183.8
(2.1) 		202.4
(3) 		193.4
(2.5) 		151.5
(0.4) 		84
(-3) 		118
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 74.6
(3)
P 		39
(-1.9)
A 		34
(-2.5)
A 		30.6
(-3)
P 		44
B 63.5
(3)
P 		33.8
(-2.8)
A 		32.8
(-3)
A 		52
(0.8)
P 		31
C 58.5
(3)
P 		35.6
(-3)
A 		35.9
(-2.9)
A 		39.1
(-2.1)
P 		23
avr 65.5
(3) 		36.1
(-2.6) 		34.2
(-3) 		40.6
(-1.8) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 65
1 2 3 4 5 6 range
A 42.2
(0.7)
A 		59.8
(3)
P 		56.2
(2.5)
P 		44.2
(1)
M 		38
(0.1)
P 		14.1
(-3)
A 		46
B 49.3
(-1.1)
P 		65.8
(1.2)
P 		35.9
(-3)
P 		41.9
(-2.2)
A 		79.1
(3)
P 		39.8
(-2.5)
P 		43
C 51.9
(2)
P 		56.6
(3)
P 		51.3
(1.8)
A 		49.8
(1.5)
P 		43.3
(0.1)
M 		29.3
(-3)
A 		27
avr 47.8
(0.7) 		60.7
(3) 		47.8
(0.7) 		45.3
(0.2) 		53.5
(1.7) 		27.7
(-3) 		33
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177331_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12368
Sequence Type Exemplar sequence
Representative Public ID VC5.5 NCBI
Target Description VC5.5 /REP_DB=WormBase Gene ID /WP=CE21226 /TR=Q9TYU3 /GB=AAC78212.1 /SUBMIT=ST.LOUIS /CHR=5 /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_072397(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072397 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-135) (nhr-135) mRNA, complete cds. 11/11 None
SNAP00000038538 ENSEMBL cdna:SNAP chromosome:CEL140:V:7092208:7094133:-1 11/11 None
GENEFINDER00000038542 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:7092208:7096323:-1 11/11 None
VC5.5 ENSEMBL cdna:known chromosome:CEL140:V:7092208:7096345:-1 gene:VC5.5 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:7092208-7096324(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol nhr-135
Ensembl VC5.5
Entrez Gene 189066 Entrez gene
SwissProt Q9TYU3 EMBL-EBI
WormBase CE21226 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 AAC78212 Nuclear hormone receptor family protein 135 [Caenorhabditis elegans] ref|NP_504798.1| Nuclear Hormone Receptor family member (nhr-135) [Caenorhabditis elegans] 0.0
blast CAE72003 Hypothetical protein CBG19080 [Caenorhabditis briggsae] 1.0E-164
blast CAE72002 Hypothetical protein CBG19079 [Caenorhabditis briggsae] 1.0E-145
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.2E-14
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.8E-19
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.7E-8
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.0E-5
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.8E-19
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.9E-11
Sequence
Target Sequence 
>C. ELEGANS:177331_AT
accacacatttcccgaattttctcgagttttggaaccagatcagcaaaggattctattcc
ggaatttttatatgaaatggacagtgtttgagccggcgtatctagccgttttattaggaa
aacccgacacatatcacttgccaacaggtgacattgtggacgaagtcggggtatattata
cacgtcatttatgcactccaacttcttatagcctagatgaagtatcaagaatattttccc
catactgggcggatttccgtaaaacattggtcgatccagttattgatgcgaaactttcaa
ttcacgaatttctgctcctatgtgcaatatgcctatttgatattggtctcgactatcaat
ctgatgattgcattgaattttgtcaaacaattcgacaagaactcttccgtgaactgaatg
ctgtttgcaagcaattgtgcagttctaattctgaagactattgcttccggttctctaaga
acatgttgttattgccgtctattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCACACATTTCCCGAATTTTCTCG 48 85 1670 Antisense
AATGGACAGTGTTTGAGCCGGCGTA 58 163 1745 Antisense
GAGCCGGCGTATCTAGCCGTTTTAT 614 379 1759 Antisense
TAGGAAAACCCGACACATATCACTT 228 651 1784 Antisense
ATACACGTCATTTATGCACTCCAAC 663 23 1847 Antisense
GCACTCCAACTTCTTATAGCCTAGA 86 317 1862 Antisense
TTCCCCATACTGGGCGGATTTCCGT 222 695 1905 Antisense
AATTCACGAATTTCTGCTCCTATGT 218 177 1968 Antisense
GAACTCTTCCGTGAACTGAATGCTG 677 349 2068 Antisense
ACTATTGCTTCCGGTTCTCTAAGAA 177 103 2126 Antisense
AACATGTTGTTATTGCCGTCTATTC 689 137 2149 Antisense
Sequence Source Affymetrix Proprietary Database