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[194035_s_at]

Description T03G6.2 /REP_DB=WormBase Gene ID /WP=CE28074 /GEN=nhr-40 /TR=SW:Q22127 /GB=AAA81704.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=steroid-thyroid-retinoic nuclear hormone receptor family
Cluster 6grp_highest_10_10 > 50      6grp_high1_10_10 > 03      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 70      6grp_total > 25      4grp_total > 46      6grp_highest_sub > De      6grp_cgc > 24      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 472
1 2 3 4 range
A 635.3
(3)
P 		324.7
(-1.8)
P 		275.3
(-2.6)
P 		250.3
(-3)
P 		385
B 722.1
(3)
P 		357.3
(-1.6)
P 		251.1
(-3)
P 		323.3
(-2.1)
P 		471
C 655.1
(3)
P 		351.3
(-2)
P 		297.3
(-2.9)
P 		290.4
(-3)
P 		365
avr 670.8
(3) 		344.4
(-1.9) 		274.6
(-3) 		288
(-2.8) 		396

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 407
1 2 3 4 5 6 range
A 385.8
(3)
P 		333.2
(1.8)
P 		321.7
(1.5)
P 		200.7
(-1.2)
P 		122.9
(-3)
P 		248.6
(-0.1)
P 		263
B 441.4
(3)
P 		367.6
(1.5)
P 		282.9
(-0.3)
P 		221.8
(-1.6)
P 		154
(-3)
P 		211.7
(-1.8)
P 		287
C 529.9
(3)
P 		351.6
(0.2)
P 		262.7
(-1.2)
P 		187.9
(-2.4)
P 		149.4
(-3)
P 		210.9
(-2)
P 		381
avr 452.4
(3) 		350.8
(1) 		289.1
(-0.2) 		203.5
(-1.8) 		142.1
(-3) 		223.7
(-1.4) 		310
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 195
1 2 3 4 range
A 231.3
(3)
P 		70.5
(-2)
P 		72
(-1.9)
P 		36.6
(-3)
P 		195
B 230.3
(3)
P 		88.2
(-2)
P 		58.2
(-3)
P 		68.9
(-2.6)
P 		172
C 216.9
(3)
P 		101
(-1.1)
P 		103.6
(-1)
P 		49
(-3)
P 		168
avr 226.2
(3) 		86.6
(-1.8) 		77.9
(-2.1) 		51.5
(-3) 		175

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 159
1 2 3 4 5 6 range
A 71.1
(-0.5)
P 		118.5
(3)
P 		70.1
(-0.6)
P 		50.9
(-2)
P 		37.1
(-3)
P 		60.5
(-1.3)
P 		81
B 153.6
(3)
P 		122.4
(1)
P 		68.7
(-2.4)
P 		58.7
(-3)
P 		62.6
(-2.8)
P 		78.9
(-1.7)
P 		95
C 196.4
(3)
P 		107.3
(-0.4)
P 		66.9
(-1.9)
P 		37.8
(-3)
P 		48.3
(-2.6)
P 		70.6
(-1.8)
P 		159
avr 140.4
(3) 		116.1
(1.4) 		68.6
(-1.7) 		49.1
(-3) 		49.3
(-3) 		70
(-1.6) 		91
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194035_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18361
Sequence Type Exemplar sequence
Representative Public ID T03G6.2 NCBI
Target Description T03G6.2 /REP_DB=WormBase Gene ID /WP=CE28074 /GEN=nhr-40 /TR=SW:Q22127 /GB=AAA81704.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=steroid-thyroid-retinoic nuclear hormone receptor family
Cluster Evidence This cluster is supported by a 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_171636(11), NM_001029702(11), NM_001029703(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171636 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-40) (nhr-40) mRNA, complete cds. 11/11 A 
NM_001029702 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-40) (nhr-40) mRNA, complete cds. 11/11 None
NM_001029703 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-40) (nhr-40) mRNA, complete cds. 11/11 None
GENEFINDER00000022498 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:2599422:2608143:1 11/11 None
SNAP00000022491 ENSEMBL cdna:SNAP chromosome:CEL140:X:2602623:2606267:1 11/11 None
T03G6.2b ENSEMBL cdna:known chromosome:CEL140:X:2593997:2606728:1 gene:T03G6.2 11/11 A 
T03G6.2a ENSEMBL cdna:known chromosome:CEL140:X:2593999:2606725:1 gene:T03G6.2 11/11 A 
T03G6.2c ENSEMBL cdna:known chromosome:CEL140:X:2599401:2606267:1 gene:T03G6.2 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
chrX:2599448-2604618(+) 100.0 100.0
Public Domain and Genome References
Ensembl T03G6.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM69089 Nuclear hormone receptor family protein 40, isoform a [Caenorhabditis elegans] ref|NP_741729.1| Nuclear Hormone Receptor family member (nhr-40) [Caenorhabditis elegans] gb|AAG15131.1| nuclear receptor NHR-40 [Caenorhabditis elegans] 0.0
blast AAN39667 Nuclear hormone receptor family protein 40, isoform c [Caenorhabditis elegans] ref|NP_001024874.1| Nuclear Hormone Receptor family member (nhr-40) [Caenorhabditis elegans] sp|Q22127|NHR40_CAEEL Nuclear hormone receptor family member nhr-40 0.0
blast AAM69090 Nuclear hormone receptor family protein 40, isoform b [Caenorhabditis elegans] ref|NP_001024873.1| Nuclear Hormone Receptor family member (nhr-40) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-20
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 5.9E-37
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-20
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-20
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 5.9E-37
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.8E-17
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 5.9E-37
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-20
Sequence
Target Sequence 
>C. ELEGANS:194035_S_AT
tcattcttatgatcccgaagcacagaacgatgtaaaagctgttatcgaagatttattacg
gttagagtcaagagtgaagtcacttaggaactcatatcgcttcgaatctcaagtgtctgc
cacatcttgcatgtactccagctgcttactggatgacatcacatatatggcagaaaacac
acatgaaaacgagggcacaattgaaccattcgagtgttctgtggagaagctgagggaatg
gtttgtgcgagatttgtcgttaatgctcgaatggggcaagtgcttaccgattatggaaag
gttactactcaacgacaagcttgccctgatgaaagctttcgcaccaatatttccattgat
tcaactagcattctacacgagaaacgaatttgaatgtgatattgtgataaaactcgaacc
ggattgtacgcctaaaccaattccagaacggctcaattatccagatggct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCATTCTTATGATCCCGAAGCACAG 621 619 372 Antisense
GAAGTCACTTAGGAACTCATATCGC 172 337 447 Antisense
GCTTCGAATCTCAAGTGTCTGCCAC 47 307 470 Antisense
TGTCTGCCACATCTTGCATGTACTC 314 557 485 Antisense
AGCTGCTTACTGGATGACATCACAT 189 81 511 Antisense
GGGGCAAGTGCTTACCGATTATGGA 150 497 644 Antisense
TCAACGACAAGCTTGCCCTGATGAA 264 629 680 Antisense
AAAGCTTTCGCACCAATATTTCCAT 166 125 703 Antisense
GATTCAACTAGCATTCTACACGAGA 139 431 729 Antisense
GTACGCCTAAACCAATTCCAGAACG 29 457 797 Antisense
GAACGGCTCAATTATCCAGATGGCT 98 349 817 Antisense
Sequence Source Affymetrix Proprietary Database