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[193577_at] Zinc finger, C4 type (two domains)

Description E03H4.13 /REP_DB=WormBase Gene ID /WP=CE09139 /GEN=nhr-89 /TR=O02235 /GB=CAB05470.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_total > 93      4grp_total > 32      6grp_cgc > 99      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 21.1
(-1.7)
A 		7.2
(-3)
A 		54.6
(1.6)
A 		69.7
(3)
A 		63
B 19.1
(-1.5)
A 		64.2
(3)
A 		42.4
(0.8)
A 		3.4
(-3)
A 		61
C 5.4
(-3)
A 		5.2
(-3)
A 		37.4
(-0.1)
A 		71.5
(3)
A 		66
avr 15.2
(-3) 		25.5
(-1.1) 		44.8
(2.4) 		48.2
(3) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 13.1
(-1.5)
A 		7.1
(-3)
A 		28
(2.2)
A 		11.3
(-2)
A 		31.1
(3)
A 		9.4
(-2.4)
A 		24
B 4
(-2.7)
A 		18.5
(3)
A 		3.2
(-3)
A 		11.3
(0.2)
A 		6.5
(-1.7)
A 		6.1
(-1.9)
A 		15
C 29.1
(0.4)
A 		44.1
(3)
A 		9.3
(-3)
A 		27.8
(0.2)
A 		37
(1.8)
A 		43.6
(2.9)
A 		35
avr 15.4
(-2) 		23.2
(2.1) 		13.5
(-3) 		16.8
(-1.3) 		24.9
(3) 		19.7
(0.3) 		11
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 7.7
(-0.1)
A 		1.6
(-3)
A 		14.3
(3)
A 		10.2
(1.1)
A 		13
B 6.1
(-0.9)
A 		15.9
(3)
A 		9.8
(0.6)
A 		0.7
(-3)
A 		15
C 1.8
(-2.8)
A 		1.5
(-3)
A 		13
(3)
A 		12.1
(2.5)
A 		12
avr 5.2
(-3) 		6.3
(-2.1) 		12.4
(3) 		7.7
(-0.9) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 2.4
(-2.9)
A 		2.5
(-2.8)
A 		6.1
(0.2)
A 		2.9
(-2.5)
A 		9.4
(3)
A 		2.3
(-3)
A 		7
B 1.4
(-2.3)
A 		6.1
(3)
A 		0.8
(-3)
A 		3
(-0.5)
A 		2.7
(-0.8)
A 		2.3
(-1.3)
A 		5
C 10.8
(1.1)
A 		13.5
(2.5)
A 		2.4
(-3)
A 		5.6
(-1.4)
A 		12
(1.7)
A 		14.6
(3)
A 		12
avr 4.9
(-0.8) 		7.4
(2.3) 		3.1
(-3) 		3.8
(-2.1) 		8
(3) 		6.4
(1) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193577_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2058
Sequence Type Exemplar sequence
Representative Public ID E03H4.13 NCBI
Target Description E03H4.13 /REP_DB=WormBase Gene ID /WP=CE09139 /GEN=nhr-89 /TR=O02235 /GB=CAB05470.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
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_060754(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060754 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-89) (nhr-89) mRNA, complete cds. 11/11 None
SNAP00000031047 ENSEMBL cdna:SNAP chromosome:CEL140:I:12448117:12449087:-1 11/11 None
E03H4.13 ENSEMBL cdna:known chromosome:CEL140:I:12448117:12449374:-1 gene:E03H4.13 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
chrI:12448047-12449305(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-89
Ensembl E03H4.13
Entrez Gene 184026 Entrez gene
SwissProt O02235 EMBL-EBI
WormBase CE09139 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
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
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
20037 heme binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB05470 Hypothetical protein E03H4.13 [Caenorhabditis elegans] emb|CAB04035.1| Hypothetical protein E03H4.13 [Caenorhabditis elegans] ref|NP_493155.1| Nuclear Hormone Receptor family member (nhr-89) [Caenorhabditis elegans] sp|O02235|NHR89_CAEEL Nuclear hormone receptor family member nhr-89 0.0
blast CAB05470 Hypothetical protein E03H4.13 [Caenorhabditis elegans] emb|CAB04035.1| Hypothetical protein E03H4.13 [Caenorhabditis elegans] ref|NP_493155.1| Nuclear Hormone Receptor family member (nhr-89) [Caenorhabditis elegans] sp|O02235|NHR89_CAEEL Nuclear hormone receptor family member nhr-89 1.0E-127
blast CAB04372 Hypothetical protein F41D3.1 [Caenorhabditis elegans] ref|NP_493090.1| Nuclear Hormone Receptor family member (nhr-82) [Caenorhabditis elegans] 5.0E-72
blast CAA15840 Hypothetical protein C47F8.8 [Caenorhabditis elegans] ref|NP_493118.2| Nuclear Hormone Receptor family member (nhr-81) [Caenorhabditis elegans] 3.0E-71
blast CAA15840 Hypothetical protein C47F8.8 [Caenorhabditis elegans] ref|NP_493118.2| Nuclear Hormone Receptor family member (nhr-81) [Caenorhabditis elegans] 1.0E-45
blast CAB04372 Hypothetical protein F41D3.1 [Caenorhabditis elegans] ref|NP_493090.1| Nuclear Hormone Receptor family member (nhr-82) [Caenorhabditis elegans] 5.0E-45
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-4
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-4
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.3E-11
Sequence
Target Sequence 
>C. ELEGANS:193577_AT
gcaaagccctttgaaaaacgcccatcaagttaaaacttcaaaggaactgcttgaaatctc
gaaatctgaagataaaacctcattggatgctgtcctgcattgctatggaacatatatctt
agacgatgaagacattacgactttgataagatacttcaaatttatgaacacttggattga
ctctgcattcgtttattcaaaatcgacatcaaatgaggaattgttggatggaaatgacat
ttgcaagttcgcctatcaaatcgatacatcaattggattgtctctcaaaaacctaaattt
aaacatctttgaatacgctgctctccgagcaatttgtatttggaatctgaaattttatga
gacgagtccaaagatgaagtcactggctttggaacattacaaaggaattactggtgcatt
aaggcagtactacgagaactacatgtctgatatggatattgctgtaagaataggtgaaat
caccatgcaaatcacgacgatttctgatctgttccacga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAAAGCCCTTTGAAAAACGCCCAT 194 313 387 Antisense
GGAACTGCTTGAAATCTCGAAATCT 74 531 429 Antisense
AAAACCTCATTGGATGCTGTCCTGC 307 131 460 Antisense
TGCTGTCCTGCATTGCTATGGAACA 147 583 474 Antisense
GGATTGACTCTGCATTCGTTTATTC 617 507 560 Antisense
TTGCAAGTTCGCCTATCAAATCGAT 513 701 627 Antisense
AACATCTTTGAATACGCTGCTCTCC 679 137 688 Antisense
TACGCTGCTCTCCGAGCAATTTGTA 302 649 700 Antisense
GAAGTCACTGGCTTTGGAACATTAC 288 337 762 Antisense
GAAATCACCATGCAAATCACGACGA 377 363 862 Antisense
CGACGATTTCTGATCTGTTCCACGA 439 251 881 Antisense
Sequence Source Affymetrix Proprietary Database