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[192168_at]

Description R09G11.2 /REP_DB=WormBase Gene ID /WP=CE07444 /GEN=nhr-1 /TR=Q21878 /GB=AAC48174.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 15      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 60      6grp_total > 16      4grp_total > 39      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 382
1 2 3 4 range
A 609
(3)
P 		315.2
(-1.9)
P 		249.8
(-3)
P 		263
(-2.8)
P 		359
B 509.2
(3)
P 		254.4
(-2.4)
P 		227.1
(-3)
P 		477.8
(2.3)
P 		282
C 594.8
(3)
P 		262.6
(-2.5)
P 		231.7
(-3)
P 		369.2
(-0.7)
P 		363
avr 571
(3) 		277.4
(-2.3) 		236.2
(-3) 		370
(-0.6) 		335

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 688
1 2 3 4 5 6 range
A 473.2
(2.2)
P 		507.5
(3)
P 		320.8
(-1.1)
P 		234.4
(-3)
P 		250.6
(-2.6)
P 		238.2
(-2.9)
P 		273
B 622.1
(3)
P 		599.9
(2.7)
P 		230.2
(-3)
P 		232.9
(-3)
P 		310.3
(-1.8)
P 		275.9
(-2.3)
P 		392
C 872.3
(3)
P 		553.3
(0.2)
P 		224.3
(-2.7)
P 		220.9
(-2.7)
P 		308.1
(-1.9)
P 		184.3
(-3)
P 		688
avr 655.9
(3) 		553.6
(1.6) 		258.4
(-2.6) 		229.4
(-3) 		289.7
(-2.2) 		232.8
(-3) 		427
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 183
1 2 3 4 range
A 221.7
(3)
P 		68.4
(-2)
P 		65.3
(-2.1)
P 		38.5
(-3)
P 		183
B 162.4
(3)
P 		62.8
(-2.4)
P 		52.6
(-3)
P 		101.8
(-0.3)
P 		110
C 196.9
(3)
P 		75.5
(-2.4)
P 		80.8
(-2.2)
P 		62.3
(-3)
P 		135
avr 193.7
(3) 		68.9
(-2.9) 		66.2
(-3) 		67.5
(-2.9) 		128

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 279
1 2 3 4 5 6 range
A 87.2
(-1.6)
P 		180.5
(3)
P 		69.9
(-2.4)
P 		59.4
(-2.9)
P 		75.6
(-2.1)
P 		58
(-3)
P 		123
B 216.4
(3)
P 		199.7
(2.4)
P 		55.9
(-3)
P 		61.7
(-2.8)
P 		126.1
(-0.4)
P 		102.9
(-1.2)
P 		161
C 323.3
(3)
P 		168.8
(-0.3)
P 		57.1
(-2.7)
P 		44.4
(-3)
P 		99.7
(-1.8)
P 		61.7
(-2.6)
P 		279
avr 209
(3) 		183
(2) 		61
(-2.8) 		55.2
(-3) 		100.5
(-1.2) 		74.2
(-2.3) 		154
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192168_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17985
Sequence Type Exemplar sequence
Representative Public ID R09G11.2 NCBI
Target Description R09G11.2 /REP_DB=WormBase Gene ID /WP=CE07444 /GEN=nhr-1 /TR=Q21878 /GB=AAC48174.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=zinc finger protein
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_001029684(10), NM_001029682(10), NM_001029683(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029684 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-1) (nhr-1) mRNA, complete cds. 10/11 None
NM_001029682 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-1) (nhr-1) mRNA, complete cds. 10/11 None
NM_001029683 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-1) (nhr-1) mRNA, complete cds. 10/11 None
SNAP00000041296 ENSEMBL cdna:SNAP chromosome:CEL140:X:17519927:17527173:1 10/11 None
GENEFINDER00000041300 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:17519927:17527173:1 11/11 None
R09G11.2c ENSEMBL cdna:known chromosome:CEL140:X:17518353:17528111:1 gene:R09G11.2 10/11 A 
R09G11.2a.1 ENSEMBL cdna:known chromosome:CEL140:X:17518360:17528111:1 gene:R09G11.2 10/11 A 
R09G11.2a.2 ENSEMBL cdna:known chromosome:CEL140:X:17519761:17528111:1 gene:R09G11.2 10/11 A 
R09G11.2b ENSEMBL cdna:known chromosome:CEL140:X:17519984:17527173:1 gene:R09G11.2 10/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
181783 4 3 NM_001029682 174901_at (11), 192168_at (10)
NM_001029683 192168_at (10)
NM_001029684 174901_at (11), 192168_at (10)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:17519907-17527172(+) 100.0 100.0
Public Domain and Genome References
Ensembl R09G11.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_001024855 Nuclear Hormone Receptor family member (nhr-1) [Caenorhabditis elegans] gb|AAO39168.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAO39167.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAC48174.4| Nuclear hormone receptor family protein 1, isoform c [Caenorhabditis elegans] 0.0
blast NP_001024853 Nuclear Hormone Receptor family member (nhr-1) [Caenorhabditis elegans] gb|AAO39169.1| nuclear receptor NHR-1 [Caenorhabditis elegans] gb|AAP46277.1| Nuclear hormone receptor family protein 1, isoform a [Caenorhabditis elegans] sp|Q21878|NHR1_CAEEL Nuclear hormone receptor family member nhr-1 0.0
blast AAO39170 nuclear receptor NHR-1 [Caenorhabditis elegans] 0.0
blast NP_001024854 Nuclear Hormone Receptor family member (nhr-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.1E-39
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 8.7E-42
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.1E-39
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.9E-38
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.1E-39
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.9E-38
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.3E-4
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.3E-27
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.3E-27
Sequence
Target Sequence 
>C. ELEGANS:192168_AT
cagaacggacggattttagccctcgatttgccctcgtccgaaactttgccttcgcattta
atctgctcaacagagtgttctactcgccggaccatggaccagataagattgtcttccaaa
atggagccttcatcatgagacagccacaacaacaggtccaactctcgggatgccggccta
tctacactcgacaaatggacgagattatgattccattccgcaaattgcagttgagcgtgg
ccgagtttgccaccttcaaagccgctttgttttttaatccagacgctttggatttgtctc
cacaggcgaaacaggaagttttcgaggagagaaacaaatatttgggtggactttttacct
gtatcacac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGAACGGACGGATTTTAGCCCTCG 361 191 1151 Antisense
TTGCCTTCGCATTTAATCTGCTCAA 167 703 1196 Antisense
TCAACAGAGTGTTCTACTCGCCGGA 151 631 1217 Antisense
GGAGCCTTCATCATGAGACAGCCAC 532 521 1273 Antisense
CACAACAACAGGTCCAACTCTCGGG 550 193 1295 Antisense
GGCCTATCTACACTCGACAAATGGA 491 541 1325 Antisense
ATGATTCCATTCCGCAAATTGCAGT 416 47 1357 Antisense
GCAGTTGAGCGTGGCCGAGTTTGCC 552 311 1377 Antisense
GCCGCTTTGTTTTTTAATCCAGACG 38 285 1411 Antisense
GACGCTTTGGATTTGTCTCCACAGG 596 379 1432 Antisense
GGTGGACTTTTTACCTGTATCACAC 522 499 1495 Antisense
Sequence Source Affymetrix Proprietary Database