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[175463_at]

Description AU113761_rc /REP_DB=TREMBL Accession /GB=AU113761 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk711d10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 56      6grp_high1_10_10 > 65      4grp_highest_8_8 > 31      4grp_high_8_8 > 05      6grp_highest_nonorm > 90      6grp_total > 55      4grp_total > 03      6grp_cgc > 46      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 383
1 2 3 4 range
A 199.8
(-1.2)
P 		131.4
(-2.9)
P 		127.7
(-3)
P 		372.9
(3)
P 		245
B 186.3
(-2.2)
P 		143.7
(-2.9)
P 		140.5
(-3)
P 		505.7
(3)
P 		365
C 172.4
(-2.6)
P 		167.4
(-2.7)
P 		148.8
(-3)
P 		510.6
(3)
P 		362
avr 186.2
(-2.1) 		147.5
(-2.8) 		139
(-3) 		463.1
(3) 		324

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 146
1 2 3 4 5 6 range
A 108.3
(-3)
P 		129.6
(-1.9)
P 		162.3
(-0.3)
P 		230
(3)
P 		127.2
(-2.1)
P 		159.9
(-0.5)
P 		122
B 170
(3)
P 		153.2
(0.3)
P 		154
(0.5)
P 		132.3
(-3)
P 		158.3
(1.1)
P 		161.9
(1.7)
P 		38
C 176.2
(2.6)
P 		169.2
(2.1)
P 		183.5
(3)
P 		84.4
(-3)
P 		138.2
(0.3)
P 		175.2
(2.5)
P 		99
avr 151.5
(-0.6) 		150.7
(-0.8) 		166.6
(3) 		148.9
(-1.2) 		141.2
(-3) 		165.7
(2.8) 		25
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 72.8
(3)
P 		28.5
(-3)
P 		33.4
(-2.3)
P 		54.6
(0.5)
P 		44
B 59.4
(-0.9)
P 		35.5
(-2.8)
P 		32.6
(-3)
P 		107.8
(3)
P 		75
C 57.1
(-1.6)
P 		48.1
(-3)
P 		51.9
(-2.4)
P 		86.1
(3)
P 		38
avr 63.1
(0.4) 		37.4
(-3) 		39.3
(-2.7) 		82.8
(3) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 48
1 2 3 4 5 6 range
A 20
(-3)
P 		46.1
(1.1)
P 		35.4
(-0.6)
P 		58.3
(3)
P 		38.4
(-0.1)
P 		38.9
(-0)
P 		38
B 59.2
(2)
P 		51
(0.3)
P 		37.4
(-2.5)
P 		35
(-3)
P 		64.3
(3)
P 		60.4
(2.2)
P 		29
C 65.3
(3)
P 		51.6
(1.3)
P 		46.7
(0.7)
P 		17
(-3)
P 		44.7
(0.4)
P 		58.6
(2.2)
P 		48
avr 48.2
(1.3) 		49.6
(1.9) 		39.8
(-1.9) 		36.8
(-3) 		49.1
(1.7) 		52.6
(3) 		16
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175463_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20858
Sequence Type Exemplar sequence
Representative Public ID AU113761 NCBI
Target Description AU113761_rc /REP_DB=TREMBL Accession /GB=AU113761 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk711d10 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001027170(11), NM_001027169(11), AY204195(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027170 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-109) (nhr-109) mRNA, complete cds. 11/11 None
NM_001027169 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-109) (nhr-109) mRNA, complete cds. 11/11 None
AY204195 NCBI Caenorhabditis elegans clone yk711d10 nuclear receptor NHR-109 precursor RNA, partial cds. 11/11 A 
SNAP00000005695 ENSEMBL cdna:SNAP chromosome:CEL140:II:4433393:4435137:1 11/11 None
GENEFINDER00000005705 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:4433393:4435137:1 11/11 None
T12C9.5b ENSEMBL cdna:known chromosome:CEL140:II:4433382:4435159:1 gene:T12C9.5 11/11 A 
T12C9.5a ENSEMBL cdna:known chromosome:CEL140:II:4433394:4435137:1 gene:T12C9.5 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
chrII:4434807-4435087(+) 100.0 100.0
Public Domain and Genome References
Ensembl T12C9.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAR30202 Nuclear hormone receptor family protein 109, isoform b [Caenorhabditis elegans] ref|NP_001022341.1| Nuclear Hormone Receptor family member (nhr-109) [Caenorhabditis elegans] 0.0
blast AAO39198 nuclear receptor NHR-109 [Caenorhabditis elegans] 0.0
blast AAO39198 nuclear receptor NHR-109 [Caenorhabditis elegans] 1.0E-179
blast AAR30202 Nuclear hormone receptor family protein 109, isoform b [Caenorhabditis elegans] ref|NP_001022341.1| Nuclear Hormone Receptor family member (nhr-109) [Caenorhabditis elegans] 1.0E-179
blast AAR30202 Nuclear hormone receptor family protein 109, isoform b [Caenorhabditis elegans] ref|NP_001022341.1| Nuclear Hormone Receptor family member (nhr-109) [Caenorhabditis elegans] 1.0E-178
blast AAK18974 Nuclear hormone receptor family protein 109, isoform a [Caenorhabditis elegans] ref|NP_001022340.1| Nuclear Hormone Receptor family member (nhr-109) [Caenorhabditis elegans] 1.0E-176
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-16
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.1E-8
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-16
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.2E-26
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-16
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.5E-9
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-16
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.4E-9
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-16
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.1E-8
Sequence
Target Sequence 
>C. ELEGANS:175463_AT
atgaatcttcaagttgacatctatgaatttctcacactttttacacttctccactgggat
actggccttgttgagatcaccgatgaatgtctggaaattggcacaaaagtcaaagcagaa
gtattcaaggagctggatttctatttgacaaatgtgaagaaagtcgcagagccatcagtt
agaatagggacaattgtcaacttacttccagcagttcataaaagcgtacgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGAATCTTCAAGTTGACATCTATG 7 45 21 Antisense
GACATCTATGAATTTCTCACACTTT 205 371 36 Antisense
TTTTTACACTTCTCCACTGGGATAC 366 613 58 Antisense
TCCACTGGGATACTGGCCTTGTTGA 416 587 70 Antisense
TACTGGCCTTGTTGAGATCACCGAT 542 645 80 Antisense
AAGGAGCTGGATTTCTATTTGACAA 122 161 147 Antisense
GAAAGTCGCAGAGCCATCAGTTAGA 261 361 179 Antisense
GAGCCATCAGTTAGAATAGGGACAA 75 385 189 Antisense
GACAATTGTCAACTTACTTCCAGCA 96 365 209 Antisense
GTCAACTTACTTCCAGCAGTTCATA 29 465 216 Antisense
CCAGCAGTTCATAAAAGCGTACGGA 231 273 228 Antisense
Sequence Source Affymetrix Proprietary Database