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[193665_s_at]

Description C11G6.4 /REP_DB=WormBase Gene ID /WP=CE27061 /GEN=nhr-28 /TR=SW:Q17905 /GB=CAA94114.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 63      6grp_high1_10_10 > 36      4grp_highest_8_8 > 46      4grp_high_8_8 > 02      6grp_highest_nonorm > 80      6grp_total > 36      4grp_total > 14      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 298
1 2 3 4 range
A 342.8
(2.1)
P 		189
(-1.5)
P 		127.5
(-3)
P 		379.3
(3)
P 		252
B 344.4
(1.5)
P 		120.4
(-3)
P 		141.1
(-2.6)
P 		418.7
(3)
P 		298
C 392.7
(2.8)
P 		167.4
(-3)
P 		208.4
(-1.9)
P 		401.5
(3)
P 		234
avr 360
(2) 		158.9
(-3) 		159
(-3) 		399.8
(3) 		241

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 220
1 2 3 4 5 6 range
A 224.7
(-0.1)
P 		314.3
(3)
P 		207.9
(-0.6)
P 		139.2
(-3)
P 		175.9
(-1.7)
P 		252.3
(0.9)
P 		175
B 359.1
(3)
P 		273.6
(0.4)
P 		235.5
(-0.8)
P 		163.1
(-3)
P 		196.9
(-2)
P 		247.3
(-0.4)
P 		196
C 330.8
(3)
P 		292.8
(1.4)
P 		217.1
(-1.8)
P 		209.1
(-2.1)
P 		188.7
(-3)
P 		284.5
(1)
P 		142
avr 304.9
(3) 		293.6
(2.5) 		220.2
(-0.8) 		170.5
(-3) 		187.2
(-2.3) 		261.4
(1.1) 		134
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 124.8
(3)
P 		41
(-2.5)
P 		33.3
(-3)
P 		55.5
(-1.5)
P 		92
B 109.8
(3)
P 		29.7
(-3)
P 		32.7
(-2.8)
P 		89.2
(1.5)
P 		80
C 130
(3)
P 		48.1
(-3)
P 		72.6
(-1.2)
P 		67.7
(-1.6)
P 		82
avr 121.5
(3) 		39.6
(-3) 		46.2
(-2.5) 		70.8
(-0.7) 		82

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 90
1 2 3 4 5 6 range
A 41.4
(-2.5)
P 		111.8
(3)
P 		45.3
(-2.2)
P 		35.3
(-3)
P 		53.1
(-1.6)
P 		61.4
(-1)
P 		77
B 124.9
(3)
P 		91.1
(0.5)
P 		57.2
(-2)
P 		43.2
(-3)
P 		80
(-0.3)
P 		92.2
(0.6)
P 		82
C 122.6
(3)
P 		89.4
(0.5)
P 		55.3
(-2)
P 		42
(-3)
P 		61.1
(-1.6)
P 		95.2
(1)
P 		81
avr 96.3
(2.9) 		97.4
(3) 		52.6
(-1.7) 		40.2
(-3) 		64.7
(-0.4) 		82.9
(1.5) 		57
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193665_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17428
Sequence Type Exemplar sequence
Representative Public ID C11G6.4 NCBI
Target Description C11G6.4 /REP_DB=WormBase Gene ID /WP=CE27061 /GEN=nhr-28 /TR=SW:Q17905 /GB=CAA94114.2 /SUBMIT=HINXTON /CHR=X /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_001029217(10), NM_001029218(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029217 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-28) (nhr-28) mRNA, complete cds. 10/11 None
NM_001029218 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-28) (nhr-28) mRNA, complete cds. 10/11 None
GENEFINDER00000002971 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:16354903:16359214:1 10/11 None
SNAP00000002970 ENSEMBL cdna:SNAP chromosome:CEL140:X:16358079:16359214:1 10/11 None
C11G6.4b.2 ENSEMBL cdna:known chromosome:CEL140:X:16354890:16359471:1 gene:C11G6.4 10/11 None
C11G6.4a ENSEMBL cdna:known chromosome:CEL140:X:16354890:16359568:1 gene:C11G6.4 10/11 None
C11G6.4b.1 ENSEMBL cdna:known chromosome:CEL140:X:16355535:16359214:1 gene:C11G6.4 10/11 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
chrX:16354902-16359214(+) 100.0 100.0
Public Domain and Genome References
Ensembl C11G6.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAR11977 nuclear receptor NHR-28 [Caenorhabditis elegans] gb|AAR11976.1| nuclear receptor NHR-28 [Caenorhabditis elegans] emb|CAA94114.2| Hypothetical protein C11G6.4a [Caenorhabditis elegans] ref|NP_001024388.1| Nuclear Hormone Receptor family member (nhr-28) [Caenorhabditis elegans] sp|Q17905|NHR28_CAEEL Nuclear hormone receptor family member nhr-28 0.0
blast AAG15123 nuclear receptor NHR-28 [Caenorhabditis elegans] 0.0
blast T19202 hypothetical protein C11G6.4 - Caenorhabditis elegans 0.0
blast CAI46566 Hypothetical protein C11G6.4b [Caenorhabditis elegans] ref|NP_001024389.1| Nuclear Hormone Receptor family member (nhr-28) [Caenorhabditis elegans] 0.0
blast AAG15124 nuclear receptor NHR-28 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.2E-34
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.4E-10
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.2E-34
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.4E-29
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 2.9E-18
Sequence
Target Sequence 
>C. ELEGANS:193665_S_AT
gaaatctaccgaaggaatgtcctcgatccaatgcgacgagaaaacgtcgataatttcgaa
ttcttcactctttgctcattagtcttatgggatcatggtctagagggtcaaacagaggaa
tgtgtccagatggctagatgcaatagagagagaattcttcgagaagttttatactactac
agaagggtgaaacaaattagcgatccatcgatgcggcttgccaatttgctcgtgctactt
ccagccctacagagatcagtaagaaggtttcaagaggatgtagagataactcatgtattt
aatgtatactcagtggaggaaacattttacgagttggtcagtggaagactatccgatagc
tttttccaaactacccagttgacaacaagtgtggaagaggaaaaagttatcaaaacagag
gagattgacagtaagaactttgtggaaattttaaaatgcgagtttaattcgaaaaggcta
taccattatatttcggaaattgaaaaaatgttcaccttttttagtattcgggatctcaac
aaagggca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAATCTACCGAAGGAATGTCCTCG 281 361 793 Antisense
AATGTCCTCGATCCAATGCGACGAG 396 163 808 Antisense
AATTTCGAATTCTTCACTCTTTGCT 299 175 844 Antisense
CACTCTTTGCTCATTAGTCTTATGG 667 197 858 Antisense
GATCATGGTCTAGAGGGTCAAACAG 708 419 883 Antisense
GAATGTGTCCAGATGGCTAGATGCA 469 331 910 Antisense
ATTAGCGATCCATCGATGCGGCTTG 401 11 988 Antisense
CGATGCGGCTTGCCAATTTGCTCGT 549 249 1001 Antisense
GACTATCCGATAGCTTTTTCCAAAC 255 371 1139 Antisense
TAGCTTTTTCCAAACTACCCAGTTG 255 647 1149 Antisense
GTATTCGGGATCTCAACAAAGGGCA 213 451 1316 Antisense
Sequence Source Affymetrix Proprietary Database