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[175182_at] Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors

Description AV177366_rc /REP_DB=TREMBL Accession /GB=AV177366 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk527g9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 18      4grp_highest_8_8 > 50      4grp_high_8_8 > 41      6grp_highest_nonorm > 40      6grp_total > 05      4grp_total > 46      6grp_highest_sub > De      6grp_cgc > 12      6grp_cgc_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 627
1 2 3 4 range
A 1023.8
(3)
P 		603.2
(-1)
P 		582.2
(-1.2)
P 		397.1
(-3)
P 		627
B 854.4
(3)
P 		545.7
(-2)
P 		485.3
(-3)
P 		528.8
(-2.3)
P 		369
C 906.2
(3)
P 		675.8
(-0.2)
P 		534.9
(-2.2)
P 		476.7
(-3)
P 		430
avr 928.1
(3) 		608.2
(-1.2) 		534.1
(-2.1) 		467.5
(-3) 		461

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 671
1 2 3 4 5 6 range
A 817.2
(3)
P 		617
(0.5)
P 		434.6
(-1.9)
P 		371.1
(-2.7)
P 		580.3
(-0)
P 		344.5
(-3)
P 		473
B 645
(2.8)
P 		618.5
(2)
P 		568.2
(0.6)
P 		653.7
(3)
P 		526.2
(-0.6)
P 		442.9
(-3)
P 		211
C 1015.4
(3)
P 		569.2
(-1.4)
P 		425.2
(-2.8)
P 		542.5
(-1.7)
P 		541.1
(-1.7)
P 		409.3
(-3)
P 		606
avr 825.9
(3) 		601.6
(-0.2) 		476
(-1.9) 		522.4
(-1.3) 		549.2
(-0.9) 		398.9
(-3) 		427
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 315
1 2 3 4 range
A 372.8
(3)
P 		130.9
(-1.6)
P 		152.2
(-1.2)
P 		58.1
(-3)
P 		315
B 272.5
(3)
P 		134.8
(-2.2)
P 		112.4
(-3)
P 		112.7
(-3)
P 		160
C 300
(3)
P 		194.3
(0.1)
P 		186.4
(-0.1)
P 		80.4
(-3)
P 		220
avr 315.1
(3) 		153.3
(-1.2) 		150.3
(-1.3) 		83.7
(-3) 		231

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 293
1 2 3 4 5 6 range
A 150.6
(-0)
P 		219.5
(3)
P 		94.6
(-2.5)
P 		94.1
(-2.5)
P 		175.1
(1)
P 		83.9
(-3)
P 		136
B 224.4
(3)
P 		205.9
(1.7)
P 		138
(-3)
P 		173.2
(-0.6)
P 		213.8
(2.3)
P 		165.2
(-1.1)
P 		86
C 376.4
(3)
P 		173.7
(-1.5)
P 		108.2
(-3)
P 		109.1
(-3)
P 		175.1
(-1.5)
P 		137
(-2.4)
P 		268
avr 250.5
(3) 		199.7
(0.8) 		113.6
(-3) 		125.5
(-2.5) 		188
(0.3) 		128.7
(-2.3) 		137
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175182_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21483
Sequence Type Exemplar sequence
Representative Public ID AV177366 NCBI
Target Description AV177366_rc /REP_DB=TREMBL Accession /GB=AV177366 /CHR=4 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk527g9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_069337(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069337 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-97) (nhr-97) mRNA, complete cds. 11/11 A 
H27C11.1 ENSEMBL cdna:known chromosome:CEL140:IV:9757622:9764468:1 gene:H27C11.1 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
chrIV:9764120-9764400(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C4 type (two domains) ; Ligand-binding domain of nuclear hormone receptors
Gene Symbol nhr-97
Ensembl H27C11.1
Entrez Gene 177810 Entrez gene
SwissProt Q9BJK5 EMBL-EBI
WormBase CE31027 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 CAD36480 Hypothetical protein H27C11.1 [Caenorhabditis elegans] emb|CAA18549.2| Hypothetical protein H27C11.1 [Caenorhabditis elegans] ref|NP_501738.2| Nuclear Hormone Receptor family member (nhr-97) [Caenorhabditis elegans] gb|AAK17982.1| nuclear receptor NHR-97 [Caenorhabditis elegans] sp|Q9BJK5|NHR97_CAEEL Nuclear hormone receptor family member nhr-97 0.0
blast T23126 hypothetical protein H27C11.1 - Caenorhabditis elegans 0.0
blast CAE69012 Hypothetical protein CBG15006 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 8.8E-20
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.5E-27
Sequence
Target Sequence 
>C. ELEGANS:175182_AT
gatctgttctatcaaacactcatttttctccccttccacctccaaattttccgtgttctg
ccttttttcagatattctcattttcattaatctcaattgctaaataaccaaccaatattt
tcttttgtattttaaattgcaacgtattttgaattggaactgcatattatctactgtttt
ttattcttctttctacttcccatccctctactatcagagacatattttcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCTGTTCTATCAAACACTCATTT 289 419 13 Antisense
CTATCAAACACTCATTTTTCTCCCC 90 225 21 Antisense
CCACCTCCAAATTTTCCGTGTTCTG 496 273 48 Antisense
TTCCGTGTTCTGCCTTTTTTCAGAT 282 699 61 Antisense
GATATTCTCATTTTCATTAATCTCA 398 427 83 Antisense
ATTAATCTCAATTGCTAAATAACCA 145 3 98 Antisense
ATTGCAACGTATTTTGAATTGGAAC 583 3 148 Antisense
ATTGGAACTGCATATTATCTACTGT 433 3 165 Antisense
TATCTACTGTTTTTTATTCTTCTTT 582 659 180 Antisense
TCCCATCCCTCTACTATCAGAGACA 699 597 210 Antisense
TCTACTATCAGAGACATATTTTCAA 71 615 219 Antisense
Sequence Source Affymetrix Proprietary Database