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[189961_at] zinc finger protein

Description ZK488.2 /REP_DB=WormBase Gene ID /WP=CE28191 /TR=O17025 /GB=AAB69950.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 6grp_highest_10_10 > 06      6grp_high1_10_10 > 60      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 81      6grp_total > 50      4grp_total > 39      6grp_highest_sub > 04      6grp_cgc > 94      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 349
1 2 3 4 range
A 356.4
(3)
P 		173.7
(-2.4)
P 		155
(-3)
P 		222.3
(-1)
P 		201
B 382.7
(3)
P 		225.3
(-0.6)
P 		119.2
(-3)
P 		267.3
(0.4)
P 		264
C 468.6
(3)
P 		189.8
(-3)
P 		215.7
(-2.4)
P 		285.3
(-0.9)
P 		279
avr 402.6
(3) 		196.3
(-2.2) 		163.3
(-3) 		258.3
(-0.6) 		239

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 117
1 2 3 4 5 6 range
A 252.3
(-1.5)
P 		291.3
(0.6)
P 		306.2
(1.4)
P 		335.8
(3)
P 		232.7
(-2.6)
P 		224.7
(-3)
P 		111
B 277.3
(2.1)
P 		285.4
(2.8)
P 		252.7
(-0.1)
P 		288
(3)
P 		221.5
(-2.8)
P 		219.3
(-3)
P 		69
C 315.4
(2.2)
P 		242.7
(-2.1)
P 		259.3
(-1.1)
P 		329.4
(3)
P 		226.6
(-3)
P 		232.8
(-2.6)
P 		103
avr 281.7
(0.7) 		273.1
(0.1) 		272.7
(0.1) 		317.7
(3) 		226.9
(-2.9) 		225.6
(-3) 		92
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 128
1 2 3 4 range
A 129.8
(3)
P 		37.7
(-2.7)
P 		40.5
(-2.5)
P 		32.5
(-3)
P 		97
B 122
(3)
P 		55.6
(-1.2)
P 		27.6
(-3)
P 		57
(-1.1)
P 		94
C 155.1
(3)
P 		54.6
(-2.6)
P 		75.2
(-1.5)
P 		48.1
(-3)
P 		107
avr 135.6
(3) 		49.3
(-2.8) 		47.8
(-2.9) 		45.9
(-3) 		90

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 70
1 2 3 4 5 6 range
A 46.5
(-3)
P 		103.6
(3)
P 		66.7
(-0.9)
P 		85.2
(1.1)
P 		70.2
(-0.5)
P 		54.7
(-2.1)
P 		57
B 96.5
(3)
P 		95
(2.7)
P 		61.4
(-3)
P 		76.3
(-0.5)
P 		90
(1.9)
P 		81.8
(0.5)
P 		35
C 116.9
(3)
P 		74.1
(-2)
P 		66
(-3)
P 		66.2
(-3)
P 		73.3
(-2.1)
P 		77.9
(-1.6)
P 		51
avr 86.6
(2) 		90.9
(3) 		64.7
(-3) 		75.9
(-0.4) 		77.8
(-0) 		71.5
(-1.4) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189961_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15420
Sequence Type Exemplar sequence
Representative Public ID ZK488.2 NCBI
Target Description ZK488.2 /REP_DB=WormBase Gene ID /WP=CE28191 /TR=O17025 /GB=AAB69950.2 /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_070862(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070862 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-90) (nhr-90) mRNA, complete cds. 11/11 None
GENEFINDER00000016997 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:610602:612312:1 11/11 None
ZK488.2 ENSEMBL cdna:known chromosome:CEL140:V:610299:612342:1 gene:ZK488.2 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
chrV:610379-612312(+) 100.0 100.0
Public Domain and Genome References
Gene Title zinc finger protein
Gene Symbol nhr-90
Ensembl ZK488.2
Entrez Gene 178577 Entrez gene
SwissProt O17025 EMBL-EBI
WormBase CE28191 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB69950 Nuclear hormone receptor family protein 90 [Caenorhabditis elegans] ref|NP_503263.1| Nuclear Hormone Receptor family member (nhr-90) [Caenorhabditis elegans] 0.0
blast AAG15180 nuclear receptor NHR-90 [Caenorhabditis elegans] 0.0
blast CAB60324 Hypothetical protein F57G8.6 [Caenorhabditis elegans] emb|CAB05534.2| Hypothetical protein F57G8.6 [Caenorhabditis elegans] ref|NP_507131.1| F57G8.6 [Caenorhabditis elegans] 1.0E-172
blast CAB60324 Hypothetical protein F57G8.6 [Caenorhabditis elegans] emb|CAB05534.2| Hypothetical protein F57G8.6 [Caenorhabditis elegans] ref|NP_507131.1| F57G8.6 [Caenorhabditis elegans] 1.0E-166
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0017
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-6
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 0.0017
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-6
Sequence
Target Sequence 
>C. ELEGANS:189961_AT
tgatgagtttcagcggattccagatgaaataaagataaaacttctcctatcattttggca
cgtttttgcaagactcgacaagctgatcacaactgcaaaagcccgaaaactaaaattatg
ctcgcagcagacatgggcaatgagtaatggattgattttggattttgataggacaaaggt
cgatttttcggatattagcaattaccccacggaagacctattctatttcctaaactcaat
caccgcattggatcttcagccacaagttttggaactcatggagctagaagtttcagatat
ggaattcaactttatgcttgctcagctaacattttcatatgcaggaaaacgatttcaagg
ggatattctgaagatttgtgataggtttcaagaagtcctgtcaaatgatttgcacgagta
ttatgtaaaagaaatgagaacgccgagatattctggaaggttaggcaaaattatgaagat
caataatgctatacagaacgacatttggaaaaaccgcccacgcggggagcttgccgcaat
tttcaatgttttcaaagtggagttctcccatcctgaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGATGAGTTTCAGCGGATTCCAGAT 268 567 630 Antisense
AAAACTTCTCCTATCATTTTGGCAC 170 131 666 Antisense
TTGGCACGTTTTTGCAAGACTCGAC 442 707 684 Antisense
GACTCGACAAGCTGATCACAACTGC 265 375 701 Antisense
TATGCTCGCAGCAGACATGGGCAAT 542 657 746 Antisense
AGCAATTACCCCACGGAAGACCTAT 76 77 826 Antisense
AGACCTATTCTATTTCCTAAACTCA 310 69 843 Antisense
AACTCAATCACCGCATTGGATCTTC 301 141 862 Antisense
TCAACTTTATGCTTGCTCAGCTAAC 296 631 935 Antisense
GAGCTTGCCGCAATTTTCAATGTTT 49 389 1156 Antisense
AAAGTGGAGTTCTCCCATCCTGAAA 476 119 1183 Antisense
Sequence Source Affymetrix Proprietary Database