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[194112_at] Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type

Description C28D4.1 /REP_DB=WormBase Gene ID /WP=CE25786 /TR=O17611 /GB=CAB05126.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors (2 domains), Zinc finger, C4 type (two domains) (2 domains)
Cluster 6grp_highest_10_10 > 63      6grp_high1_10_10 > 36      4grp_highest_8_8 > 39      4grp_high_8_8 > 12      6grp_highest_nonorm > 41      6grp_total > 36      4grp_total > 12      6grp_highest_sub > Cu      6grp_cgc > 15      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1452
1 2 3 4 range
A 1075.4
(-1.1)
P 		943.5
(-1.7)
P 		629
(-3)
P 		2045.9
(3)
P 		1417
B 1232.1
(0.2)
P 		1004.4
(-1)
P 		593.9
(-3)
P 		1803
(3)
P 		1209
C 1244.7
(-0.4)
P 		983.1
(-1.8)
P 		778.9
(-3)
P 		1834.5
(3)
P 		1056
avr 1184.1
(-0.5) 		977
(-1.5) 		667.3
(-3) 		1894.5
(3) 		1227

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 578
1 2 3 4 5 6 range
A 900.2
(3)
P 		844
(2.3)
P 		880
(2.8)
P 		707
(0.7)
P 		406.3
(-3)
P 		761
(1.3)
P 		494
B 922.2
(3)
P 		825
(1.4)
P 		622
(-1.9)
P 		558
(-3)
P 		593.4
(-2.4)
P 		830.7
(1.5)
P 		364
C 984.5
(3)
P 		867
(1.3)
P 		711
(-1.1)
P 		601.6
(-2.7)
P 		581.3
(-3)
P 		841.9
(0.9)
P 		403
avr 935.6
(3) 		845.3
(1.7) 		737.7
(0.1) 		622.2
(-1.6) 		527
(-3) 		811.2
(1.2) 		409
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 274
1 2 3 4 range
A 391.6
(3)
P 		204.8
(-1.9)
P 		164.4
(-3)
P 		299.5
(0.6)
P 		227
B 392.9
(3)
P 		248.1
(-0.4)
P 		137.6
(-3)
P 		384.2
(2.8)
P 		255
C 412
(3)
P 		282.6
(-2.5)
P 		271.5
(-3)
P 		309.3
(-1.4)
P 		141
avr 398.8
(3) 		245.2
(-1.4) 		191.2
(-3) 		331
(1) 		208

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 244
1 2 3 4 5 6 range
A 166
(-1.5)
P 		300.2
(3)
P 		191.6
(-0.7)
P 		179.3
(-1.1)
P 		122.6
(-3)
P 		185.3
(-0.9)
P 		178
B 320.9
(3)
P 		274.6
(1.4)
P 		151
(-2.9)
P 		147.8
(-3)
P 		241.1
(0.2)
P 		309.8
(2.6)
P 		173
C 364.9
(3)
P 		264.6
(0.5)
P 		181
(-1.5)
P 		121
(-3)
P 		188.1
(-1.3)
P 		281.8
(1)
P 		244
avr 283.9
(3) 		279.8
(2.8) 		174.5
(-1.9) 		149.4
(-3) 		183.9
(-1.5) 		259
(1.9) 		135
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194112_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9577
Sequence Type Exemplar sequence
Representative Public ID C28D4.1 NCBI
Target Description C28D4.1 /REP_DB=WormBase Gene ID /WP=CE25786 /TR=O17611 /GB=CAB05126.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors (2 domains), Zinc finger, C4 type (two domains) (2 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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_069330(11), AY305849(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069330 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-100) (nhr-100) mRNA, complete cds. 11/11 None
AY305849 NCBI Caenorhabditis elegans clone yk734h8 nuclear receptor NHR-100 mRNA, complete cds. 11/11 None
SNAP00000030225 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9728660:9730990:1 11/11 None
GENEFINDER00000030238 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9728660:9730990:1 11/11 None
C28D4.1.1 ENSEMBL cdna:known chromosome:CEL140:IV:9728486:9731050:1 gene:C28D4.1 11/11 None
C28D4.1.2 ENSEMBL cdna:known chromosome:CEL140:IV:9728651:9731050:1 gene:C28D4.1 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:9725851-9730996(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type
Gene Symbol nhr-100
Ensembl C28D4.1
Entrez Gene 177806 Entrez gene
SwissProt O17611 EMBL-EBI
WormBase CE28893 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 AAR11993 nuclear receptor NHR-100 [Caenorhabditis elegans] emb|CAB05126.3| Hypothetical protein C28D4.1 [Caenorhabditis elegans] ref|NP_501731.1| Nuclear Hormone Receptor family member (nhr-100) [Caenorhabditis elegans] 0.0
blast AAO39188 nuclear receptor NHR-100 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.3E-38
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 8.2E-36
Sequence
Target Sequence 
>C. ELEGANS:194112_AT
aattttcgttgatgccggttggttggttgtggtatgcatacaaatcatatgaataccgtt
gtgatggaattgtatttgtggatggaagctggttcccaagagataaaactattcaacaac
aagtttgtccgacatgtgtactgtattatggtcgtataacggaatcatttatggcagatg
ttgtgaattcaatgaaagaattagaaatggatgaaacagaaatggttctactaaaagcaa
tatgtcatcttcaaccggattatcgtctaacacgacgtggaaatgacgtcatctcaactg
gaagagagaaatacaagagagcactttgtgaatatattcgaatgaaatcaaatggattta
tggatgcttcatttcgattatgtaaattgatgcaaattttacctgttgtagatattctcg
gaaagtatgaagatgaaagtgcactactggtctcactcggtgaaacagaattcaatggct
caggaggtggacttccatatgacattcatgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATTTTCGTTGATGCCGGTTGGTTG 97 155 1916 Antisense
CCGGTTGGTTGGTTGTGGTATGCAT 555 265 1930 Antisense
GTGGATGGAAGCTGGTTCCCAAGAG 112 489 1993 Antisense
GTTTGTCCGACATGTGTACTGTATT 142 453 2038 Antisense
GTCATCTTCAACCGGATTATCGTCT 240 467 2159 Antisense
AATGACGTCATCTCAACTGGAAGAG 181 161 2197 Antisense
ATGGATGCTTCATTTCGATTATGTA 642 51 2275 Antisense
TTACCTGTTGTAGATATTCTCGGAA 444 681 2314 Antisense
GAAAGTGCACTACTGGTCTCACTCG 363 361 2350 Antisense
CAATGGCTCAGGAGGTGGACTTCCA 534 183 2388 Antisense
GTGGACTTCCATATGACATTCATGC 586 489 2402 Antisense
Sequence Source Affymetrix Proprietary Database