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[192231_at]

Description F44C8.6 /REP_DB=WormBase Gene ID /WP=CE27385 /GEN=nhr-56 /TR=O16357 /GB=AAB65893.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 6grp_high1_10_10 > 17      4grp_high_8_8 > 25      6grp_total > 17      4grp_total > 38      6grp_cgc > 11      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 171
1 2 3 4 range
A 106.9
(2.9)
P 		73.1
(-0.2)
P 		43.6
(-3)
P 		107.5
(3)
P 		64
B 215
(3)
P 		83.7
(-2)
P 		57.1
(-3)
P 		61.4
(-2.8)
P 		158
C 117.5
(3)
P 		95.3
(0.5)
P 		63.6
(-3)
P 		86
(-0.5)
A 		54
avr 146.5
(3) 		84
(-1.1) 		54.8
(-3) 		85
(-1) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 142
1 2 3 4 5 6 range
A 186.3
(3)
P 		77.9
(-1.6)
P 		81.4
(-1.4)
P 		44
(-3)
A 		85.2
(-1.3)
P 		87.9
(-1.1)
P 		142
B 100.4
(3)
P 		64.6
(-1.3)
P 		57.9
(-2)
P 		82.8
(0.9)
P 		49.9
(-3)
P 		61.1
(-1.7)
P 		51
C 91.8
(2.7)
P 		89.3
(2.4)
P 		94.2
(3)
P 		56
(-1.9)
P 		66.2
(-0.6)
P 		47.7
(-3)
P 		47
avr 126.2
(3) 		77.3
(-1.5) 		77.8
(-1.4) 		60.9
(-3) 		67.1
(-2.4) 		65.6
(-2.6) 		65
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 57
1 2 3 4 range
A 38.9
(3)
P 		15.9
(-2)
P 		11.4
(-3)
P 		15.7
(-2.1)
P 		28
B 68.6
(3)
P 		20.7
(-2.2)
P 		13.2
(-3)
P 		13.1
(-3)
P 		56
C 38.9
(3)
P 		27.4
(0.2)
P 		22.2
(-1.1)
P 		14.5
(-3)
A 		24
avr 48.8
(3) 		21.3
(-1.8) 		15.6
(-2.8) 		14.4
(-3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 34.3
(3)
P 		27.7
(1.3)
P 		17.7
(-1.3)
P 		11.2
(-3)
A 		25.7
(0.8)
P 		21.4
(-0.4)
P 		23
B 34.9
(3)
P 		21.5
(-0.9)
P 		14.1
(-3)
P 		21.9
(-0.8)
P 		20.3
(-1.2)
P 		22.8
(-0.5)
P 		21
C 34
(3)
P 		27.3
(1.2)
P 		24
(0.4)
P 		11.3
(-3)
P 		21.4
(-0.3)
P 		16
(-1.8)
P 		23
avr 34.4
(3) 		25.5
(0.3) 		18.6
(-1.8) 		14.8
(-3) 		22.5
(-0.6) 		20.1
(-1.4) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192231_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15620
Sequence Type Exemplar sequence
Representative Public ID F44C8.6 NCBI
Target Description F44C8.6 /REP_DB=WormBase Gene ID /WP=CE27385 /GEN=nhr-56 /TR=O16357 /GB=AAB65893.1 /SUBMIT=ST.LOUIS /CHR=5 /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_071204(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071204 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-56) (nhr-56) mRNA, complete cds. 11/11 None
SNAP00000011142 ENSEMBL cdna:SNAP chromosome:CEL140:V:2219221:2224405:1 11/11 None
GENEFINDER00000011148 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:2218963:2221048:1 11/11 None
F44C8.6 ENSEMBL cdna:known chromosome:CEL140:V:2218892:2221126:1 gene:F44C8.6 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:2218962-2221048(+) 96.08 100.0
Public Domain and Genome References
Ensembl F44C8.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB65893 Nuclear hormone receptor family protein 56, isoform a [Caenorhabditis elegans] ref|NP_503605.3| Nuclear Hormone Receptor family member (nhr-56) [Caenorhabditis elegans] 0.0
blast AAG15152 nuclear receptor NHR-56 [Caenorhabditis elegans] 0.0
blast AAQ62454 Nuclear hormone receptor family protein 128, isoform b [Caenorhabditis elegans] ref|NP_001023923.1| Nuclear Hormone Receptor family member (nhr-128) [Caenorhabditis elegans] 0.0
blast AAB65893 Nuclear hormone receptor family protein 56, isoform a [Caenorhabditis elegans] ref|NP_503605.3| Nuclear Hormone Receptor family member (nhr-56) [Caenorhabditis elegans] 1.0E-164
blast AAG15152 nuclear receptor NHR-56 [Caenorhabditis elegans] 1.0E-164
blast AAZ32805 Nuclear hormone receptor family protein 56, isoform b [Caenorhabditis elegans] 1.0E-153
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0064
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.2E-16
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0064
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.7E-4
Sequence
Target Sequence 
>C. ELEGANS:192231_AT
ttctgcgaactgctaggtggctgagccatttcgatgagtttcaggagctcccgttgagca
tcaggatgcaaatcttaaaggtggcatggatcctttggggaagactggacaaacttgtga
aaactgcaaatgagcggaaaaatcaacagcttaatcaaaatttctatatgattggcaagg
atgtgggaatagatattggaaacttcgaagtagatgtttcctggtgcacgaattatagca
aggagcaactggcctactacctcgactgccaccacgacgaaccattcaacataatcgtcg
acgcaatctccgacctgaagcccagtgacatggaattgaactttatgctcctggagctct
gcctggcacatgctggaaagcagcatcagggggatgtcttgatgttcactgatcggcttc
tagaagttgtatccaatgagcttcacgactattatcaatcggaacaaatatctaactact
catctagaatcacaaaaatgatgaaaatcaacaatttgattaggagaaacttgttcgaac
ggctggaacgacaggcggtggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTGCGAACTGCTAGGTGGCTGAG 60 689 584 Antisense
GTGGCTGAGCCATTTCGATGAGTTT 482 491 600 Antisense
GTTTCAGGAGCTCCCGTTGAGCATC 466 449 621 Antisense
GTAGATGTTTCCTGGTGCACGAATT 128 457 793 Antisense
AGCAAGGAGCAACTGGCCTACTACC 625 75 820 Antisense
AACCATTCAACATAATCGTCGACGC 695 147 863 Antisense
GAATTGAACTTTATGCTCCTGGAGC 659 323 916 Antisense
CTCTGCCTGGCACATGCTGGAAAGC 455 231 940 Antisense
GATGTTCACTGATCGGCTTCTAGAA 576 409 984 Antisense
GTTGTATCCAATGAGCTTCACGACT 470 437 1009 Antisense
AACGGCTGGAACGACAGGCGGTGGC 576 139 1121 Antisense
Sequence Source Affymetrix Proprietary Database