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[194101_at] Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)

Description C13C4.1 /REP_DB=WormBase Gene ID /WP=CE08126 /TR=O01929 /GB=CAB07313.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 11      6grp_high1_10_10 > 0      4grp_highest_8_8 > 54      4grp_high_8_8 > 18      6grp_highest_nonorm > 70      6grp_total > 23      4grp_total > 22      6grp_cgc > 20      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 274
1 2 3 4 range
A 427.5
(1.4)
P 		379.2
(0.3)
P 		228.2
(-3)
P 		502.6
(3)
P 		274
B 466.1
(2.4)
P 		368.9
(-0.3)
P 		268.8
(-3)
P 		489.7
(3)
P 		221
C 431.7
(3)
P 		273.5
(-3)
P 		319.6
(-1.3)
P 		339
(-0.5)
P 		158
avr 441.8
(2.9) 		340.5
(-0.6) 		272.2
(-3) 		443.8
(3) 		172

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 262
1 2 3 4 5 6 range
A 291.2
(3)
P 		220.2
(0.3)
P 		267
(2.1)
P 		264.6
(2)
P 		222.3
(0.4)
P 		131.6
(-3)
P 		160
B 338.8
(3)
P 		306.2
(1.8)
P 		295.6
(1.4)
P 		230.2
(-1)
P 		177.6
(-3)
P 		224.7
(-1.2)
P 		161
C 393.4
(3)
P 		264.6
(-0.6)
P 		265.6
(-0.6)
P 		390.7
(2.9)
P 		181.4
(-3)
P 		200.4
(-2.5)
P 		212
avr 341.1
(3) 		263.7
(0) 		276.1
(0.5) 		295.2
(1.2) 		193.8
(-2.7) 		185.6
(-3) 		156
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 99
1 2 3 4 range
A 155.7
(3)
P 		82.3
(-1.6)
P 		59.6
(-3)
P 		73.6
(-2.1)
P 		96
B 148.6
(3)
P 		91.1
(-1)
P 		62.3
(-3)
P 		104.3
(-0.1)
P 		86
C 142.9
(3)
P 		78.6
(-1.5)
P 		111.4
(0.8)
P 		57.2
(-3)
P 		86
avr 149.1
(3) 		84
(-2.5) 		77.8
(-3) 		78.4
(-2.9) 		71

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 114
1 2 3 4 5 6 range
A 53.7
(-0.2)
P 		78.3
(3)
P 		58.1
(0.4)
P 		67.1
(1.5)
P 		67.1
(1.5)
P 		32
(-3)
P 		46
B 117.9
(3)
P 		101.9
(1.3)
P 		71.8
(-1.9)
P 		61
(-3)
P 		72.2
(-1.8)
P 		83.8
(-0.6)
P 		57
C 145.8
(3)
P 		80.7
(-1.5)
P 		67.6
(-2.4)
P 		78.6
(-1.6)
P 		58.7
(-3)
P 		67.1
(-2.4)
P 		87
avr 105.8
(3) 		87
(0.5) 		65.8
(-2.4) 		68.9
(-1.9) 		66
(-2.3) 		61
(-3) 		45
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194101_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13865
Sequence Type Exemplar sequence
Representative Public ID C13C4.1 NCBI
Target Description C13C4.1 /REP_DB=WormBase Gene ID /WP=CE08126 /TR=O01929 /GB=CAB07313.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, 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_073637(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073637 NCBI Caenorhabditis elegans C13C4.1 (C13C4.1) mRNA, complete cds. 11/11 None
SNAP00000013560 ENSEMBL cdna:SNAP chromosome:CEL140:V:12107016:12109041:1 11/11 None
GENEFINDER00000013571 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12104521:12111725:1 10/11 None
C13C4.1 ENSEMBL cdna:known chromosome:CEL140:V:12107016:12109041:1 gene:C13C4.1 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
chrV:12107015-12109041(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Gene Symbol nhr-153
Ensembl C13C4.1
Entrez Gene 182564 Entrez gene
SwissProt O01929 EMBL-EBI
WormBase CE08126 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 CAB07313 Hypothetical protein C13C4.1 [Caenorhabditis elegans] ref|NP_506038.1| C13C4.1 [Caenorhabditis elegans] 0.0
blast CAB07314 Hypothetical protein C13C4.3 [Caenorhabditis elegans] ref|NP_506039.1| Nuclear Hormone Receptor family member (nhr-136) [Caenorhabditis elegans] sp|O01930|NH136_CAEEL Nuclear hormone receptor family member nhr-136 0.0
blast CAB00126 Hypothetical protein C13C4.2 [Caenorhabditis elegans] emb|CAB07316.1| Hypothetical protein C13C4.2 [Caenorhabditis elegans] ref|NP_506037.1| C13C4.2 [Caenorhabditis elegans] 0.0
blast CAE75393 Hypothetical protein CBG23381 [Caenorhabditis briggsae] 1.0E-131
blast CAE75392 Hypothetical protein CBG23380 [Caenorhabditis briggsae] 1.0E-116
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.7E-50
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-22
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 5.6E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 7.4E-39
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.4E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 3.3E-18
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-22
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 4.3E-29
Sequence
Target Sequence 
>C. ELEGANS:194101_AT
caagttgtcttgcatctatcgaatattccaaaacatttgacttttcaagtgcaattgaca
tttcaagtaaaataattctccttaaaaatactgcactatcttgtgcaaacttgacaaatg
cttatacaacattcagaaagctgaaatcagatacacttttatacccagatggtagtattt
atgggccaccacgacggaaaaatggtcctttgattgaaaaacaacgatcatttttacaaa
atacgttgatatcatttatgactaacaatgttgataaaactgaatatattttactaaaag
caatagtactatgtaatccagcaataatcgatctaccttatgccgattcaaaacatattc
aaagagagcgagaggtttacgctcagtgtttgttccgatattgtctactacaacatggta
cattacacgggcctgcaaggttttctgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGTTGTCTTGCATCTATCGAATA 365 185 659 Antisense
AATTCTCCTTAAAAATACTGCACTA 599 175 732 Antisense
AGATACACTTTTATACCCAGATGGT 696 59 807 Antisense
GTAGTATTTATGGGCCACCACGACG 609 453 830 Antisense
GACGGAAAAATGGTCCTTTGATTGA 47 369 851 Antisense
GTAATCCAGCAATAATCGATCTACC 599 461 971 Antisense
TCGATCTACCTTATGCCGATTCAAA 329 603 986 Antisense
GGTTTACGCTCAGTGTTTGTTCCGA 109 507 1032 Antisense
GTGTTTGTTCCGATATTGTCTACTA 142 485 1044 Antisense
AACATGGTACATTACACGGGCCTGC 67 137 1070 Antisense
TACACGGGCCTGCAAGGTTTTCTGC 27 643 1082 Antisense
Sequence Source Affymetrix Proprietary Database