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[173109_s_at]

Description AV182430_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV182430 /DEF=Caenorhabditis elegans cDNA clone:yk637g5 : 3prime end, single read.
Cluster 6grp_total > 68      4grp_total > 08      6grp_cgc > 38      6grp_cgc_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 3.7
(-2.4)
A 		2.1
(-3)
A 		3.8
(-2.4)
A 		17.8
(3)
A 		16
B 2.2
(-2.8)
A 		1.4
(-3)
A 		8.8
(-0.8)
A 		21.9
(3)
A 		21
C 1.7
(-3)
A 		3.3
(-2.8)
A 		14.7
(-1.5)
A 		52.6
(3)
A 		51
avr 2.5
(-3) 		2.3
(-3) 		9.1
(-1.6) 		30.8
(3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 85
1 2 3 4 5 6 range
A 9
(-2.4)
A 		2.4
(-3)
A 		3.1
(-2.9)
A 		5.7
(-2.7)
A 		22.7
(-1.2)
A 		69.8
(3)
P 		67
B 12.8
(-1.9)
A 		2.6
(-2.8)
A 		0.9
(-3)
A 		12.6
(-1.9)
A 		11.3
(-2.1)
A 		67.5
(3)
P 		67
C 30.3
(-1)
A 		1.8
(-3)
A 		24.9
(-1.4)
A 		4.9
(-2.8)
A 		16.9
(-1.9)
A 		85.8
(3)
P 		84
avr 17.4
(-1.7) 		2.3
(-3) 		9.6
(-2.4) 		7.7
(-2.6) 		17
(-1.8) 		74.4
(3) 		72
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9
1 2 3 4 range
A 1.3
(-0.7)
A 		0.5
(-3)
A 		1
(-1.6)
A 		2.6
(3)
A 		2
B 0.7
(-2.5)
A 		0.3
(-3)
A 		2
(-0.7)
A 		4.7
(3)
A 		4
C 0.6
(-3)
A 		1
(-2.7)
A 		5.1
(0.3)
A 		8.9
(3)
A 		8
avr 0.9
(-2.6) 		0.6
(-3) 		2.7
(-0.4) 		5.4
(3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 29
1 2 3 4 5 6 range
A 1.7
(-2.6)
A 		0.9
(-2.9)
A 		0.7
(-3)
A 		1.4
(-2.7)
A 		6.8
(-0.8)
A 		17
(3)
P 		16
B 4.5
(-2)
A 		0.9
(-2.8)
A 		0.2
(-3)
A 		3.3
(-2.3)
A 		4.6
(-1.9)
A 		25.2
(3)
P 		25
C 11.2
(-0.7)
A 		0.5
(-3)
A 		6.3
(-1.8)
A 		1
(-2.9)
A 		5.5
(-1.9)
A 		28.7
(3)
P 		28
avr 5.8
(-1.7) 		0.8
(-3) 		2.4
(-2.6) 		1.9
(-2.7) 		5.6
(-1.7) 		23.6
(3) 		23
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173109_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26804
Sequence Type Exemplar sequence
Representative Public ID AV182430 NCBI
Target Description AV182430_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV182430 /DEF=Caenorhabditis elegans cDNA clone:yk637g5 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_171272(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171272 NCBI Caenorhabditis elegans Y41D4B.26 (Y41D4B.26) mRNA, complete cds. 11/11 A 
SNAP00000005519 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1631977:1633204:1 11/11 None
GENEFINDER00000005550 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1620197:1633204:1 11/11 None
Y41D4B.26 ENSEMBL cdna:known chromosome:CEL140:IV:1631956:1633204:1 gene:Y41D4B.26 11/11 A 
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
chrIV:1632283-1633176(+) 89.33 89.33
Public Domain and Genome References
Gene Title
Gene Symbol nhr-146
Ensembl Y41D4B.26
Entrez Gene 176973 Entrez gene
SwissProt Q8WSN8 EMBL-EBI
WormBase CE36740 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68482 Nuclear hormone receptor family protein 92 [Caenorhabditis elegans] ref|NP_500111.3| Nuclear Hormone Receptor family member (nhr-92) [Caenorhabditis elegans] 0.0
blast AAG15184 nuclear receptor NHR-92 [Caenorhabditis elegans] 0.0
blast AAL32242 Nuclear hormone receptor family protein 87 [Caenorhabditis elegans] ref|NP_500112.2| Nuclear Hormone Receptor family member (nhr-87) [Caenorhabditis elegans] 1.0E-170
blast AAL32241 Hypothetical protein Y41D4B.26 [Caenorhabditis elegans] ref|NP_741322.2| Y41D4B.26 [Caenorhabditis elegans] 8.0E-92
blast CAE67971 Hypothetical protein CBG13577 [Caenorhabditis briggsae] 2.0E-41
blast CAE67972 Hypothetical protein CBG13578 [Caenorhabditis briggsae] 5.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.8E-30
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.0E-23
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.8E-24
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.7E-21
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.2E-9
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.3E-12
Sequence
Target Sequence 
>C. ELEGANS:173109_S_AT
tccagaaactctgaatcttccgttgactggaatnatgtttgagttcaagtgtcaagaaaa
ctggaccggcgaaaaatgtgacgtacgttgtgacaaaaactgcacagaaccatctaagac
tatcaatgacatggaattcgatgtcagttacactgtgaaccctatgaaactggagacnat
tgnggcgatgcttaagaaggataatgaggtcgccaatactttgagtgaga

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAGAAACTCTGAATCTTCCGTTG 652 589 17 Antisense
AACTCTGAATCTTCCGTTGACTGGA 36 141 23 Antisense
GGACCGGCGAAAAATGTGACGTACG 397 521 79 Antisense
GACGTACGTTGTGACAAAAACTGCA 165 377 96 Antisense
AAAACTGCACAGAACCATCTAAGAC 225 131 112 Antisense
GAACCATCTAAGACTATCAATGACA 576 345 123 Antisense
CATGGAATTCGATGTCAGTTACACT 165 207 146 Antisense
GTCAGTTACACTGTGAACCCTATGA 455 465 159 Antisense
CTGTGAACCCTATGAAACTGGAGAC 238 227 169 Antisense
GAAGGATAATGAGGTCGCCAATACT 192 335 212 Antisense
GAGGTCGCCAATACTTTGAGTGAGA 618 401 222 Antisense
Sequence Source Affymetrix Proprietary Database