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[190015_at] zinc finger protein

Description C38C3.9 /REP_DB=WormBase Gene ID /WP=CE08646 /TR=O17081 /GB=AAB70328.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=zinc finger protein
Cluster 4grp_highest_8_8 > 56      4grp_high_8_8 > 35      6grp_total > 37      4grp_total > 36      6grp_cgc > 07      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 178.4
(1.3)
P 		214.1
(3)
P 		90.6
(-3)
P 		187.2
(1.7)
P 		124
B 179.5
(2.8)
P 		183.4
(3)
P 		100.9
(-2)
P 		84.3
(-3)
P 		99
C 163.7
(0.4)
P 		184.5
(3)
P 		136.7
(-3)
P 		154
(-0.8)
P 		48
avr 173.9
(1.6) 		194
(3) 		109.4
(-3) 		141.8
(-0.7) 		85

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 97
1 2 3 4 5 6 range
A 131.5
(3)
A 		51.3
(-3)
A 		54.2
(-2.8)
A 		79
(-0.9)
A 		59.7
(-2.4)
A 		86.8
(-0.3)
M 		80
B 109
(3)
P 		102.9
(2.5)
A 		76.1
(0.4)
A 		34.4
(-3)
A 		81.1
(0.8)
A 		99.7
(2.3)
P 		75
C 72.6
(0.9)
P 		81.9
(2.2)
A 		67.3
(0.2)
P 		44.3
(-3)
A 		52.6
(-1.9)
A 		87.8
(3)
P 		44
avr 104.4
(3) 		78.7
(0) 		65.9
(-1.5) 		52.6
(-3) 		64.5
(-1.6) 		91.4
(1.5) 		52
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 64.9
(3)
P 		46.5
(0.3)
P 		23.7
(-3)
P 		27.4
(-2.5)
P 		41
B 57.2
(3)
P 		45.3
(1.2)
P 		23.4
(-2.2)
P 		18
(-3)
P 		39
C 54.2
(3)
P 		53
(2.7)
P 		47.6
(1.6)
P 		26
(-3)
P 		28
avr 58.8
(3) 		48.3
(1.2) 		31.6
(-1.7) 		23.8
(-3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 29
1 2 3 4 5 6 range
A 24.2
(3)
A 		18.3
(0.1)
A 		11.8
(-3)
A 		20
(1)
A 		18
(0)
A 		21.1
(1.5)
M 		12
B 37.9
(3)
P 		34.3
(2.3)
A 		18.5
(-1)
A 		9.1
(-3)
A 		33
(2)
A 		37.2
(2.9)
P 		29
C 26.9
(2.3)
P 		25
(1.7)
A 		17.1
(-0.6)
P 		8.9
(-3)
A 		17
(-0.6)
A 		29.4
(3)
P 		21
avr 29.7
(3) 		25.9
(1.7) 		15.8
(-1.9) 		12.7
(-3) 		22.7
(0.5) 		29.2
(2.8) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190015_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14856
Sequence Type Exemplar sequence
Representative Public ID C38C3.9 NCBI
Target Description C38C3.9 /REP_DB=WormBase Gene ID /WP=CE08646 /TR=O17081 /GB=AAB70328.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=zinc finger protein
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_071034(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071034 NCBI Caenorhabditis elegans C38C3.9 (C38C3.9) mRNA, complete cds. 11/11 None
SNAP00000029153 ENSEMBL cdna:SNAP chromosome:CEL140:V:1509965:1510511:-1 9/11 None
GENEFINDER00000029160 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:1509965:1511459:-1 10/11 None
C38C3.9 ENSEMBL cdna:known chromosome:CEL140:V:1509853:1511459:-1 gene:C38C3.9 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:1509852-1511459(-) 100.0 100.0
Public Domain and Genome References
Gene Title zinc finger protein
Gene Symbol nhr-260
Ensembl C38C3.9
Entrez Gene 183304 Entrez gene
SwissProt O17081 EMBL-EBI
WormBase CE08646 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 AAB70328 Hypothetical protein C38C3.9 [Caenorhabditis elegans] ref|NP_503435.1| C38C3.9 [Caenorhabditis elegans] 0.0
blast CAB04068 Hypothetical protein F09C6.8 [Caenorhabditis elegans] ref|NP_507272.1| F09C6.8 [Caenorhabditis elegans] 1.0E-160
blast CAB04068 Hypothetical protein F09C6.8 [Caenorhabditis elegans] ref|NP_507272.1| F09C6.8 [Caenorhabditis elegans] 1.0E-153
blast CAE62481 Hypothetical protein CBG06579 [Caenorhabditis briggsae] 1.0E-152
blast CAE62481 Hypothetical protein CBG06579 [Caenorhabditis briggsae] 1.0E-143
blast AAB70328 Hypothetical protein C38C3.9 [Caenorhabditis elegans] ref|NP_503435.1| C38C3.9 [Caenorhabditis elegans] 6.0E-80
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.9E-31
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.8E-27
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.1E-17
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.1E-25
Sequence
Target Sequence 
>C. ELEGANS:190015_AT
cgagtggggaagtcgtctcaagccttttaaaaaattgccggtagattcaaaaaagagtat
gatggctgaatattgtctcgcgttcaatttgatagatcagggatacaaaacttcgaagga
agctgatctggggatttggttgcttcaaaatggtagttttatgcatcccgactacttttt
tggattgaacgtgacaaatgttaacatggagagtatgaagctcaaaacacaacttcatca
caattttgttaccgaaatgataaactgcctgggtaccccattccgcaggcttcaaattga
cgatgtcgagtgtgccgcgttgaaaatcattcttctactgaccccttcatgcaccaagcg
agctatctatgctggtcaagaaggtgtgcttgcggggctttacacaaaatgtaccgaaga
gctcatggatcattgcatgagcaagtttcccgagagcggagccgaacgatttggggaaat
tctgctgttgttaggcgggattcgttgtggaattaaagccatgtataatcaaacacgtgt
ctcggatctcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGAGTGGGGAAGTCGTCTCAAGCCT 315 249 609 Antisense
GATGGCTGAATATTGTCTCGCGTTC 340 407 669 Antisense
ATGCATCCCGACTACTTTTTTGGAT 329 43 769 Antisense
GATAAACTGCCTGGGTACCCCATTC 346 419 867 Antisense
CCATTCCGCAGGCTTCAAATTGACG 46 271 886 Antisense
ATTGACGATGTCGAGTGTGCCGCGT 267 5 904 Antisense
TGAAAATCATTCTTCTACTGACCCC 444 573 929 Antisense
GCACCAAGCGAGCTATCTATGCTGG 551 313 959 Antisense
GTGTGCTTGCGGGGCTTTACACAAA 610 487 992 Antisense
GCATGAGCAAGTTTCCCGAGAGCGG 307 309 1043 Antisense
TCAAACACGTGTCTCGGATCTCTTC 336 629 1137 Antisense
Sequence Source Affymetrix Proprietary Database