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[193679_s_at] Zinc finger, C4 type (two domains)

Description H01A20.1 /REP_DB=WormBase Gene ID /WP=CE18798 /GEN=nhr-3 /TR=SW:Q9XTJ4 /GB=CAA16168.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 29      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 40      6grp_total > 28      4grp_total > 21      6grp_highest_sub > Cu      6grp_cgc > 02      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 343
1 2 3 4 range
A 352.7
(0.6)
P 		275.2
(-1.7)
P 		232.8
(-3)
P 		431.5
(3)
P 		199
B 457.3
(1.6)
P 		234.6
(-2.6)
P 		212.8
(-3)
P 		529.2
(3)
P 		316
C 415.5
(0.7)
P 		271.4
(-1.8)
P 		202.2
(-3)
P 		544.9
(3)
P 		343
avr 408.5
(1) 		260.4
(-2.1) 		215.9
(-3) 		501.9
(3) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 721
1 2 3 4 5 6 range
A 1112.8
(3)
P 		704.8
(-0.4)
P 		391.8
(-3)
P 		493
(-2.2)
P 		693.9
(-0.5)
P 		665.5
(-0.7)
P 		721
B 886.5
(3)
P 		716.5
(0.3)
P 		514.8
(-3)
P 		523.5
(-2.9)
P 		639.5
(-1)
P 		571.9
(-2.1)
P 		372
C 902.6
(3)
P 		689.3
(-0.1)
P 		483.6
(-3)
P 		626
(-1)
P 		598.4
(-1.4)
P 		646.4
(-0.7)
P 		419
avr 967.3
(3) 		703.5
(-0.1) 		463.4
(-3) 		547.5
(-2) 		643.9
(-0.9) 		627.9
(-1) 		504
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 97
1 2 3 4 range
A 128.4
(3)
P 		59.7
(-3)
P 		60.9
(-2.9)
P 		63.2
(-2.7)
P 		69
B 145.8
(3)
P 		57.9
(-2.5)
P 		49.3
(-3)
P 		112.8
(0.9)
P 		97
C 137.6
(3)
P 		78
(-2.3)
P 		70.5
(-3)
P 		91.9
(-1.1)
P 		67
avr 137.3
(3) 		65.2
(-2.6) 		60.2
(-3) 		89.3
(-0.7) 		77

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 249
1 2 3 4 5 6 range
A 205.1
(1.3)
P 		250.7
(3)
P 		85.3
(-3)
P 		125
(-1.6)
P 		209.4
(1.5)
P 		162
(-0.2)
P 		165
B 308.5
(3)
P 		238.5
(0.7)
P 		125
(-3)
P 		138.7
(-2.6)
P 		259.8
(1.4)
P 		213.2
(-0.1)
P 		184
C 334.6
(3)
P 		210.3
(-0.5)
P 		123.1
(-3)
P 		125.9
(-2.9)
P 		193.6
(-1)
P 		216.4
(-0.4)
P 		212
avr 282.7
(3) 		233.2
(1.3) 		111.1
(-3) 		129.9
(-2.3) 		220.9
(0.8) 		197.2
(0) 		172
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193679_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18030
Sequence Type Exemplar sequence
Representative Public ID H01A20.1 NCBI
Target Description H01A20.1 /REP_DB=WormBase Gene ID /WP=CE18798 /GEN=nhr-3 /TR=SW:Q9XTJ4 /GB=CAA16168.1 /SUBMIT=HINXTON /CHR=X /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_078022(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078022 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-3) (nhr-3) mRNA, complete cds. 11/11 A 
GENEFINDER00000013678 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:14558425:14561001:1 11/11 None
H01A20.1.2 ENSEMBL cdna:known chromosome:CEL140:X:14558421:14561001:1 gene:H01A20.1 11/11 None
H01A20.1.1 ENSEMBL cdna:known chromosome:CEL140:X:14558423:14561346:1 gene:H01A20.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000013675 6/11 Cross Hyb Matching Probes None
SNAP00000013676 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:14558424-14561001(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-3
Ensembl H01A20.1
Entrez Gene 181551 Entrez gene
SwissProt Q9XTJ4 EMBL-EBI
WormBase CE18798 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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
4879 ligand-dependent nuclear receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA16168 Hypothetical protein H01A20.1 [Caenorhabditis elegans] ref|NP_510423.1| Nuclear Hormone Receptor family member (nhr-3) [Caenorhabditis elegans] gb|AAG15118.1| nuclear receptor NHR-3 [Caenorhabditis elegans] gb|AAD03680.1| nuclear receptor NHR-3 [Caenorhabditis elegans] sp|Q9XTJ4|NHR3_CAEEL Nuclear hormone receptor family member nhr-3 0.0
blast CAE63197 Hypothetical protein CBG07552 [Caenorhabditis briggsae] 0.0
blast AAF39914 Nuclear hormone receptor family protein 88, isoform a [Caenorhabditis elegans] ref|NP_001022235.1| Nuclear Hormone Receptor family member (nhr-88) [Caenorhabditis elegans] 5.0E-44
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.2E-30
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 9.9E-40
Sequence
Target Sequence 
>C. ELEGANS:193679_S_AT
gatcgttttcacttttgactacatcaatacgttacgtccaattgctgatttgcatccatc
ggaaaagctggtcattgccagaagcatcatttccccgttctgtatcttgttctgtggtta
ccagtcggtagcgatcgaggcaccagaacacgacagtatttatctcccatcaggacacaa
gctacccgccagccagctgctatttacaaaagactcggaccaaaagaagtacatactgtt
ggaaaacaaagccgacaatgtccgacgaaacatgactgaaatgattatccaacagctccg
tcgcctcaatgtaacaaagactgaaatggttgcactgaaagcgattatggcattggatca
caacgtgaaaggattatccgccgaatcttgcgagcttctcgtagttgcaagagaatcggt
gcaaaatgctctgttctcccatttaattgcaacatttggaactgcggaggcaacatcgcg
atttgcacacctccttcttttaattgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCGTTTTCACTTTTGACTACATC 165 417 786 Antisense
ATTGCCAGAAGCATCATTTCCCCGT 512 7 859 Antisense
CCCGTTCTGTATCTTGTTCTGTGGT 219 261 879 Antisense
CAGTCGGTAGCGATCGAGGCACCAG 291 59 907 Antisense
AACACGACAGTATTTATCTCCCATC 580 135 932 Antisense
TCTCCCATCAGGACACAAGCTACCC 106 611 948 Antisense
GAAATGATTATCCAACAGCTCCGTC 624 361 1063 Antisense
TTATCCGCCGAATCTTGCGAGCTTC 542 679 1159 Antisense
TGCTCTGTTCTCCCATTTAATTGCA 204 581 1212 Antisense
GAGGCAACATCGCGATTTGCACACC 525 405 1252 Antisense
TGCACACCTCCTTCTTTTAATTGCT 646 577 1269 Antisense
Sequence Source Affymetrix Proprietary Database