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[193559_s_at] Zinc finger, C4 type (two domains)

Description F36D3.2 /REP_DB=WormBase Gene ID /WP=CE15966 /GEN=nhr-54 /TR=O45460 /GB=CAB04316.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 53      6grp_high1_10_10 > 34      6grp_highest_nonorm > 90      6grp_total > 03      4grp_total > 14      6grp_highest_sub > 02      6grp_cgc > 40      6grp_high1_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 150
1 2 3 4 range
A 129
(2.2)
P 		62.5
(-1.1)
A 		23.5
(-3)
A 		144.9
(3)
P 		121
B 107.4
(0.3)
P 		24.2
(-3)
A 		63.1
(-1.4)
A 		173.4
(3)
P 		149
C 145.6
(1.9)
P 		32.7
(-3)
A 		41
(-2.6)
P 		172.1
(3)
P 		139
avr 127.3
(1.2) 		39.8
(-3) 		42.5
(-2.9) 		163.5
(3) 		124

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 64
1 2 3 4 5 6 range
A 78.4
(-1.7)
P 		126.3
(3)
P 		87.8
(-0.8)
P 		83.6
(-1.2)
P 		65.7
(-3)
P 		73
(-2.3)
P 		61
B 103
(3)
P 		99.1
(2.3)
P 		73.1
(-2.1)
P 		86.3
(0.1)
P 		67.9
(-3)
P 		94.8
(1.6)
P 		35
C 115.9
(1.8)
P 		113.1
(1.5)
P 		71.4
(-2.4)
P 		128.7
(3)
P 		68.2
(-2.7)
P 		65.2
(-3)
P 		64
avr 99.1
(1.2) 		112.8
(3) 		77.4
(-1.7) 		99.5
(1.2) 		67.3
(-3) 		77.7
(-1.6) 		46
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 42
1 2 3 4 range
A 47
(3)
P 		13.6
(-1.9)
A 		6.1
(-3)
A 		21.2
(-0.8)
P 		41
B 34.2
(2.5)
P 		6
(-3)
A 		14.6
(-1.3)
A 		37
(3)
P 		31
C 48.2
(3)
P 		9.4
(-3)
A 		14.3
(-2.2)
P 		29
(0)
P 		39
avr 43.1
(3) 		9.7
(-3) 		11.7
(-2.6) 		29.1
(0.5) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 14.5
(-3)
P 		44.9
(3)
P 		19.1
(-2.1)
P 		21.2
(-1.7)
P 		19.8
(-2)
P 		17.8
(-2.3)
P 		30
B 35.8
(3)
P 		33
(2.1)
P 		17.7
(-3)
P 		22.9
(-1.3)
P 		27.6
(0.3)
P 		35.4
(2.9)
P 		18
C 43
(3)
P 		34.5
(0.9)
P 		18.2
(-3)
P 		25.9
(-1.1)
P 		22.1
(-2.1)
P 		21.8
(-2.1)
P 		25
avr 31.1
(1) 		37.5
(3) 		18.3
(-3) 		23.3
(-1.4) 		23.2
(-1.5) 		25
(-0.9) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193559_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13323
Sequence Type Exemplar sequence
Representative Public ID F36D3.2 NCBI
Target Description F36D3.2 /REP_DB=WormBase Gene ID /WP=CE15966 /GEN=nhr-54 /TR=O45460 /GB=CAB04316.1 /SUBMIT=HINXTON /CHR=5 /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_074778(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074778 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-54) (nhr-54) mRNA, complete cds. 11/11 None
SNAP00000025145 ENSEMBL cdna:SNAP chromosome:CEL140:V:16505529:16508499:-1 9/11 None
GENEFINDER00000025158 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16506611:16508499:-1 11/11 None
F36D3.2 ENSEMBL cdna:known chromosome:CEL140:V:16506529:16508499:-1 gene:F36D3.2 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:16506610-16508499(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains)
Gene Symbol nhr-54
Ensembl F36D3.2
Entrez Gene 180106 Entrez gene
SwissProt O45460 EMBL-EBI
WormBase CE15966 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 CAB04316 Hypothetical protein F36D3.2 [Caenorhabditis elegans] ref|NP_507179.3| Nuclear Hormone Receptor family member (nhr-54) [Caenorhabditis elegans] sp|O45460|NHR54_CAEEL Nuclear hormone receptor family member nhr-54 0.0
blast CAB03998 Hypothetical protein C54E10.5 [Caenorhabditis elegans] ref|NP_507673.2| C54E10.5 [Caenorhabditis elegans] 1.0E-169
blast CAB03998 Hypothetical protein C54E10.5 [Caenorhabditis elegans] ref|NP_507673.2| C54E10.5 [Caenorhabditis elegans] 1.0E-167
blast CAE73304 Hypothetical protein CBG20729 [Caenorhabditis briggsae] 1.0E-166
blast CAE73304 Hypothetical protein CBG20729 [Caenorhabditis briggsae] 1.0E-164
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.6E-16
Sequence
Target Sequence 
>C. ELEGANS:193559_S_AT
gtatgggcggtttggagaaggttggagaggtatacaatgacagcacaagtgtttgggcaa
aaatgttatgacgagcagattcttctacattcccatcaggatgctgctcgatttaccgat
tacgacgttgattactcgtacataactgatcaaggatttgagaaaataaatggacttttc
ggcggtaaaatgattcaatactttgatatcatcgtgaaaccatacctggaactcgagctc
tctgacacagaaatagcatatattctttgccaaattgtttggaattatgctggacgacgc
cttcagggacagacccaggcggccggagaacgatttttagaagtaatttccaataatttg
cacaaatattatgaagacaagtctggaaatcggaaaagagctgaagacaagcaaaattat
gtggcgaggttggcgaaaatgatgcaaattgtgaatcagatgttgaatgcccaactaaaa
atggaaaacacaatggatgtggcaatgcttttcaacacgttcaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTATGGGCGGTTTGGAGAAGGTTGG 702 431 721 Antisense
GACGAGCAGATTCTTCTACATTCCC 444 379 790 Antisense
CTACATTCCCATCAGGATGCTGCTC 140 227 805 Antisense
GATGCTGCTCGATTTACCGATTACG 695 413 820 Antisense
GACGTTGATTACTCGTACATAACTG 312 377 844 Antisense
ATATCATCGTGAAACCATACCTGGA 183 21 926 Antisense
AAACCATACCTGGAACTCGAGCTCT 349 125 937 Antisense
AACTCGAGCTCTCTGACACAGAAAT 568 141 950 Antisense
GAATTATGCTGGACGACGCCTTCAG 403 325 1002 Antisense
ACGCCTTCAGGGACAGACCCAGGCG 292 89 1017 Antisense
GGCAATGCTTTTCAACACGTTCAAC 270 535 1221 Antisense
Sequence Source Affymetrix Proprietary Database