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[190088_at] C4-type zinc finger

Description F44A2.4 /REP_DB=WormBase Gene ID /WP=CE04571 /TR=Q20379 /GB=AAA83445.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=C4-type zinc finger
Cluster 6grp_total > 45      4grp_total > 31      6grp_cgc > 35      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 67
1 2 3 4 range
A 50
(3)
A 		16.7
(-3)
A 		32.1
(-0.2)
A 		41.2
(1.4)
A 		33
B 71.4
(3)
P 		4.4
(-3)
A 		8.4
(-2.6)
A 		35.9
(-0.2)
A 		67
C 70.3
(3)
P 		21.4
(-2.2)
A 		14.2
(-3)
A 		38.5
(-0.4)
A 		56
avr 63.9
(3) 		14.2
(-3) 		18.2
(-2.5) 		38.5
(-0.1) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 36
1 2 3 4 5 6 range
A 7.8
(-2.2)
A 		21.1
(1.4)
A 		6.8
(-2.5)
A 		4.8
(-3)
A 		5.4
(-2.8)
A 		27.1
(3)
A 		22
B 24.2
(2.3)
A 		26.5
(3)
P 		11.9
(-1.3)
A 		17.7
(0.4)
A 		6.3
(-3)
A 		20.6
(1.2)
A 		20
C 25.1
(0.6)
A 		34.2
(2.2)
A 		39.3
(3)
A 		7.8
(-2.2)
A 		3.2
(-3)
A 		13.8
(-1.2)
A 		36
avr 19
(0.8) 		27.3
(3) 		19.3
(0.8) 		10.1
(-1.6) 		5
(-3) 		20.5
(1.2) 		22
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22
1 2 3 4 range
A 18.2
(3)
A 		3.6
(-3)
A 		8.4
(-1)
A 		6
(-2)
A 		15
B 22.8
(3)
P 		1.1
(-3)
A 		1.9
(-2.8)
A 		7.6
(-1.2)
A 		22
C 23.3
(3)
P 		6.1
(-2.6)
A 		5
(-3)
A 		6.5
(-2.5)
A 		18
avr 21.4
(3) 		3.6
(-3) 		5.1
(-2.5) 		6.7
(-2) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 1.4
(-2.8)
A 		7.5
(3)
A 		1.5
(-2.7)
A 		1.2
(-3)
A 		1.6
(-2.6)
A 		6.6
(2.1)
A 		6
B 8.4
(2.6)
A 		8.8
(3)
P 		2.9
(-2.7)
A 		4.7
(-1)
A 		2.6
(-3)
A 		7.7
(1.9)
A 		6
C 9.3
(2.3)
A 		10.4
(3)
A 		10
(2.7)
A 		1.6
(-2.6)
A 		1
(-3)
A 		4.6
(-0.7)
A 		9
avr 6.4
(0.9) 		8.9
(3) 		4.8
(-0.4) 		2.5
(-2.3) 		1.7
(-3) 		6.3
(0.8) 		7
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190088_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12515
Sequence Type Exemplar sequence
Representative Public ID F44A2.4 NCBI
Target Description F44A2.4 /REP_DB=WormBase Gene ID /WP=CE04571 /TR=Q20379 /GB=AAA83445.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=C4-type zinc finger
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_073004(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073004 NCBI Caenorhabditis elegans F44A2.4 (F44A2.4) mRNA, complete cds. 11/11 None
SNAP00000038850 ENSEMBL cdna:SNAP chromosome:CEL140:V:9306186:9307206:1 11/11 None
GENEFINDER00000038865 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9304743:9307206:1 11/11 None
F44A2.4 ENSEMBL cdna:known chromosome:CEL140:V:9305910:9307206:1 gene:F44A2.4 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:9305909-9307206(+) 100.0 100.0
Public Domain and Genome References
Gene Title C4-type zinc finger
Gene Symbol nhr-39
Ensembl F44A2.4
Entrez Gene 185720 Entrez gene
SwissProt Q20379 EMBL-EBI
WormBase CE04571 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 AAA83445 Hypothetical protein F44A2.4 [Caenorhabditis elegans] ref|NP_505405.1| F44A2.4 [Caenorhabditis elegans] 0.0
blast AAA83445 Hypothetical protein F44A2.4 [Caenorhabditis elegans] ref|NP_505405.1| F44A2.4 [Caenorhabditis elegans] 1.0E-175
blast CAB05759 Hypothetical protein K06B4.8 [Caenorhabditis elegans] ref|NP_506903.2| K06B4.8 [Caenorhabditis elegans] 3.0E-83
blast CAB05759 Hypothetical protein K06B4.8 [Caenorhabditis elegans] ref|NP_506903.2| K06B4.8 [Caenorhabditis elegans] 4.0E-83
blast CAB05761 Hypothetical protein K06B4.2 [Caenorhabditis elegans] ref|NP_506899.1| Nuclear Hormone Receptor family member (nhr-52) [Caenorhabditis elegans] gb|AAG15146.1| nuclear receptor NHR-52 [Caenorhabditis elegans] sp|O17928|NHR52_CAEEL Nuclear hormone receptor family member nhr-52 7.0E-81
blast CAB05761 Hypothetical protein K06B4.2 [Caenorhabditis elegans] ref|NP_506899.1| Nuclear Hormone Receptor family member (nhr-52) [Caenorhabditis elegans] gb|AAG15146.1| nuclear receptor NHR-52 [Caenorhabditis elegans] sp|O17928|NHR52_CAEEL Nuclear hormone receptor family member nhr-52 8.0E-81
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.6E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.8E-15
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.6E-46
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.6E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.8E-15
Sequence
Target Sequence 
>C. ELEGANS:190088_AT
ttgagaactggatcactctccggtgccatgcatgcttataaagcaaataaagagataatg
atgacaccatccggagaggactatgtatcagagaagattcatcagcttttcgtgaagtct
cctaatattattactcagatatcctcacttgtagtatctaagttcatagagttaaaggtt
acaaatgaagaatatgtactgctcgttatgttgtttttttgtaatccagcaatttcacac
aagttgtcggataaagctaaggagtctctagcaaaatatcaaaagatgtattgttctgca
ttgttcaattattgtcaaataaaatacaaaaaagcagctccagccagattagaagatctt
ttatcattatacagtgtcgccaatcaagctaatcaatgctttcatagcttgaccattttt
gttcatcttaataatcaaaattgtcaatttaagaagttgatagctgacacgtggatgagt
accctgaaaaacatgaacgattcttcactagctaccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGAGAACTGGATCACTCTCCGGTG 1 703 574 Antisense
TCTCCGGTGCCATGCATGCTTATAA 644 609 590 Antisense
GATGACACCATCCGGAGAGGACTAT 559 411 633 Antisense
CATCAGCTTTTCGTGAAGTCTCCTA 219 213 673 Antisense
TTATTACTCAGATATCCTCACTTGT 320 679 701 Antisense
GTAATCCAGCAATTTCACACAAGTT 233 463 794 Antisense
GCAGCTCCAGCCAGATTAGAAGATC 450 313 907 Antisense
TACAGTGTCGCCAATCAAGCTAATC 115 643 943 Antisense
TAGCTTGACCATTTTTGTTCATCTT 704 651 978 Antisense
GCTGACACGTGGATGAGTACCCTGA 496 295 1036 Antisense
ATGAACGATTCTTCACTAGCTACCC 178 45 1066 Antisense
Sequence Source Affymetrix Proprietary Database