[Home] | [Total List]

[193638_s_at] Zinc finger, C4 type (two domains)

Description F43C1.4 /REP_DB=WormBase Gene ID /WP=CE28025 /GEN=nhr-20 /TR=SW:Q09565 /GB=CAA87058.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 18      6grp_highest_nonorm > 70      6grp_total > 28      4grp_total > 15      6grp_highest_sub > Cu      6grp_cgc > 03      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 393
1 2 3 4 range
A 401.4
(3)
P 		101.8
(-3)
A 		185.6
(-1.3)
A 		368.1
(2.3)
A 		300
B 487.5
(3)
P 		94.3
(-3)
P 		164
(-1.9)
P 		471.8
(2.8)
A 		393
C 361.8
(3)
P 		176.9
(-1.9)
P 		136.5
(-3)
P 		305.1
(1.5)
A 		225
avr 416.9
(3) 		124.3
(-3) 		162
(-2.2) 		381.7
(2.3) 		293

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 214
1 2 3 4 5 6 range
A 401.7
(3)
P 		305.3
(0.1)
P 		202.6
(-3)
P 		251.7
(-1.5)
P 		241.9
(-1.8)
P 		302.2
(0)
P 		199
B 413.9
(3)
P 		326.2
(0.5)
P 		199.9
(-3)
P 		241.8
(-1.8)
P 		310.2
(0.1)
P 		257.1
(-1.4)
P 		214
C 412.2
(3)
P 		352.5
(1.3)
P 		238.4
(-2)
P 		202
(-3)
P 		278.1
(-0.8)
P 		226.3
(-2.3)
P 		210
avr 409.3
(3) 		328
(0.5) 		213.6
(-3) 		231.8
(-2.4) 		276.7
(-1.1) 		261.9
(-1.5) 		196
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 133
1 2 3 4 range
A 146.1
(3)
P 		22.1
(-3)
A 		48.5
(-1.7)
A 		53.9
(-1.5)
A 		124
B 155.5
(3)
P 		23.3
(-3)
P 		38
(-2.3)
P 		100.6
(0.5)
A 		132
C 119.8
(3)
P 		50.8
(-2.7)
P 		47.6
(-3)
P 		51.5
(-2.7)
A 		72
avr 140.5
(3) 		32.1
(-3) 		44.7
(-2.3) 		68.7
(-1) 		108

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 112
1 2 3 4 5 6 range
A 74
(-0.2)
P 		108.6
(3)
P 		44.1
(-3)
P 		63.8
(-1.2)
P 		73
(-0.3)
P 		73.6
(-0.3)
P 		65
B 144
(3)
P 		108.6
(0.8)
P 		48.5
(-3)
P 		64
(-2)
P 		126
(1.9)
P 		95.9
(-0)
P 		96
C 152.8
(3)
P 		107.5
(0.6)
P 		60.7
(-1.9)
P 		40.6
(-3)
P 		90
(-0.4)
P 		75.7
(-1.1)
P 		112
avr 123.6
(3) 		108.2
(1.7) 		51.1
(-3) 		56.1
(-2.6) 		96.3
(0.7) 		81.7
(-0.5) 		73
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193638_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8043
Sequence Type Exemplar sequence
Representative Public ID F43C1.4 NCBI
Target Description F43C1.4 /REP_DB=WormBase Gene ID /WP=CE28025 /GEN=nhr-20 /TR=SW:Q09565 /GB=CAA87058.2 /SUBMIT=HINXTON /CHR=3 /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_065448(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065448 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-20) (nhr-20) mRNA, complete cds. 11/11 None
SNAP00000025134 ENSEMBL cdna:SNAP chromosome:CEL140:III:4230593:4232689:-1 11/11 None
GENEFINDER00000025141 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4230593:4232689:-1 11/11 None
F43C1.4 ENSEMBL cdna:known chromosome:CEL140:III:4165508:4233189:-1 gene:F43C1.4 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
chrIII:4230592-4233172(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-20
Ensembl F43C1.4
Entrez Gene 175546 Entrez gene
SwissProt Q09565 EMBL-EBI
WormBase CE28025 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 CAA87058 Hypothetical protein F43C1.4 [Caenorhabditis elegans] ref|NP_497849.1| Nuclear Hormone Receptor family member (nhr-20) [Caenorhabditis elegans] sp|Q09565|NHR20_CAEEL Nuclear hormone receptor family member nhr-20 0.0
blast AAG15120 nuclear receptor NHR-20 [Caenorhabditis elegans] 0.0
blast T22119 hypothetical protein F43C1.4 - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.1E-17
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.1E-20
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.1E-17
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 6.7E-6
Sequence
Target Sequence 
>C. ELEGANS:193638_S_AT
gataatctcctggcatttgacttttgtaaatgttgccccggattcgattttcttagtcga
gtggaaaaggcaatcttctttagaagttgttcattagcctactgcctgctggatatcgct
tggattactgtacaagcttacccagaagaagccgccgagccagttttaatgtatacggat
ggaagtgtgtgtacagttaataatttatcgtatggatgggatgatgaagaggatatttgt
gcgcatgataagaaaaagctatttcttggttttttgggtcgcttcaatgacgctatttgc
cggccgatccggaatttaaaaatgacacacgtggaatttgcagctcttaaagctttgtgc
atttggaaactgggttactgtgaatttactccaagtatgaaagtaatcgggaaggaacac
gaagaagcattgctcaacggattacacaattattatgatgatttgtacggaaatcctgat
gaaactggcatgaggataggaaatctcattttgttaatgggaactgtttttgaaatgaat
caattaataatggaaacctacaaatcggcggaacttttcgaactattca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATAATCTCCTGGCATTTGACTTTT 535 421 865 Antisense
TTTGTAAATGTTGCCCCGGATTCGA 654 653 887 Antisense
GCCCCGGATTCGATTTTCTTAGTCG 574 279 899 Antisense
GAAGTTGTTCATTAGCCTACTGCCT 452 337 947 Antisense
ACTGCCTGCTGGATATCGCTTGGAT 400 99 965 Antisense
AAGCTTACCCAGAAGAAGCCGCCGA 8 127 998 Antisense
GCCGCCGAGCCAGTTTTAATGTATA 599 285 1015 Antisense
TTGGTTTTTTGGGTCGCTTCAATGA 537 701 1130 Antisense
CGCTTCAATGACGCTATTTGCCGGC 240 255 1144 Antisense
GGGTTACTGTGAATTTACTCCAAGT 82 495 1236 Antisense
TCGGCGGAACTTTTCGAACTATTCA 511 271 1429 Antisense
Sequence Source Affymetrix Proprietary Database