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[194120_at]

Description K10C3.6 /REP_DB=WormBase Gene ID /WP=CE12084 /GEN=nhr-49 /TR=SW:O45666 /GB=CAB05772.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Ligand-binding domain of nuclear hormone receptors, Zinc finger, C4 type (two domains)
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 47      4grp_highest_8_8 > 39      4grp_high_8_8 > 12      6grp_highest_nonorm > 77      6grp_total > 48      4grp_total > 05      6grp_highest_sub > Cu      6grp_cgc > 17      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2143
1 2 3 4 range
A 1819.7
(-0.8)
P 		1261.4
(-2.5)
P 		1088.8
(-3)
P 		3065
(3)
P 		1976
B 1880.7
(0)
P 		1208.7
(-2.1)
P 		922.1
(-3)
P 		2812.9
(3)
P 		1891
C 1649.4
(-1.2)
P 		1190.4
(-2.9)
P 		1149.2
(-3)
P 		2811.5
(3)
P 		1662
avr 1783.3
(-0.6) 		1220.2
(-2.5) 		1053.4
(-3) 		2896.5
(3) 		1843

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 960
1 2 3 4 5 6 range
A 1837.2
(3)
P 		1327.1
(-0.2)
P 		877.6
(-3)
P 		1067.5
(-1.8)
P 		1111.5
(-1.5)
P 		1660.8
(1.9)
P 		960
B 1662.4
(3)
P 		1267.9
(-0.3)
P 		951.8
(-3)
P 		1099.7
(-1.8)
P 		1011.7
(-2.5)
P 		1658.4
(3)
P 		711
C 1752.9
(2.8)
P 		1327.4
(-0.9)
P 		1322.1
(-0.9)
P 		1101.2
(-2.8)
P 		1080.1
(-3)
P 		1771.4
(3)
P 		691
avr 1750.8
(3) 		1307.5
(-0.8) 		1050.5
(-3) 		1089.5
(-2.7) 		1067.8
(-2.9) 		1696.9
(2.5) 		700
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 449
1 2 3 4 range
A 662.6
(3)
P 		273.8
(-3)
P 		284.6
(-2.8)
P 		448.7
(-0.3)
P 		389
B 599.7
(3)
P 		298.5
(-1.7)
P 		213.7
(-3)
P 		599.4
(3)
P 		386
C 546
(3)
P 		342.3
(-3)
P 		400.5
(-1.3)
P 		474.1
(0.9)
P 		204
avr 602.8
(3) 		304.9
(-2.9) 		299.6
(-3) 		507.4
(1.1) 		303

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 459
1 2 3 4 5 6 range
A 338.7
(0.2)
P 		472
(3)
P 		191.1
(-3)
P 		270.8
(-1.3)
P 		335.4
(0.1)
P 		404.4
(1.6)
P 		281
B 578.4
(2.4)
P 		422
(-0)
P 		231.1
(-3)
P 		291.3
(-2.1)
P 		411
(-0.2)
P 		618.4
(3)
P 		387
C 649.7
(3)
P 		405
(-0.4)
P 		336.5
(-1.4)
P 		221.5
(-3)
P 		349.5
(-1.2)
P 		593
(2.2)
P 		428
avr 522.3
(2.7) 		433
(0.8) 		252.9
(-3) 		261.2
(-2.8) 		365.3
(-0.6) 		538.6
(3) 		286
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194120_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1981
Sequence Type Exemplar sequence
Representative Public ID K10C3.6 NCBI
Target Description K10C3.6 /REP_DB=WormBase Gene ID /WP=CE12084 /GEN=nhr-49 /TR=SW:O45666 /GB=CAB05772.1 /SUBMIT=HINXTON /CHR=1 /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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_181998(11), NM_181999(11), NM_060212(11), NM_060211(11), AF273792(11), AF332206(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_181998 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-49) (nhr-49) mRNA, complete cds. 11/11 None
NM_181999 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-49) (nhr-49) mRNA, complete cds. 11/11 None
NM_060212 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-49) (nhr-49) mRNA, complete cds. 11/11 None
NM_060211 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-49) (nhr-49) mRNA, complete cds. 11/11 None
AF273792 NCBI Caenorhabditis elegans clone yk212f7 nuclear receptor NHR-49 mRNA, partial cds. 11/11 A 
AF332206 NCBI Caenorhabditis elegans clone yk598a1 nuclear receptor NHR-49 gene, partial cds. 11/11 None
SNAP00000018525 ENSEMBL cdna:SNAP chromosome:CEL140:I:9879351:9882245:1 11/11 None
GENEFINDER00000018528 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9879351:9882245:1 11/11 None
K10C3.6c.1 ENSEMBL cdna:known chromosome:CEL140:I:9877784:9882797:1 gene:K10C3.6 11/11 A 
K10C3.6c.2 ENSEMBL cdna:known chromosome:CEL140:I:9877807:9882894:1 gene:K10C3.6 11/11 A 
K10C3.6d ENSEMBL cdna:known chromosome:CEL140:I:9877823:9882245:1 gene:K10C3.6 11/11 None
K10C3.6b.2 ENSEMBL cdna:known chromosome:CEL140:I:9879318:9882749:1 gene:K10C3.6 11/11 A 
K10C3.6b.1 ENSEMBL cdna:known chromosome:CEL140:I:9879349:9882749:1 gene:K10C3.6 11/11 A 
K10C3.6a ENSEMBL cdna:known chromosome:CEL140:I:9879349:9882245:1 gene:K10C3.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
AF273794 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:9879281-9882176(+) 100.0 100.0
Public Domain and Genome References
Ensembl K10C3.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAD57702 Hypothetical protein K10C3.6c [Caenorhabditis elegans] ref|NP_871798.1| Nuclear Hormone Receptor family member (nhr-49) [Caenorhabditis elegans] sp|O45666|NHR49_CAEEL Nuclear hormone receptor family member nhr-49 0.0
blast CAD57703 Hypothetical protein K10C3.6d [Caenorhabditis elegans] ref|NP_871799.1| Nuclear Hormone Receptor family member (nhr-49) [Caenorhabditis elegans] 0.0
blast CAB05772 Hypothetical protein K10C3.6a [Caenorhabditis elegans] ref|NP_492612.1| Nuclear Hormone Receptor family member (nhr-49) [Caenorhabditis elegans] 0.0
blast CAD21653 Hypothetical protein K10C3.6b [Caenorhabditis elegans] ref|NP_492613.1| Nuclear Hormone Receptor family member (nhr-49) [Caenorhabditis elegans] 0.0
blast AAG15143 nuclear receptor NHR-49 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 4.4E-46
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 7.5E-48
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.4E-50
Sequence
Target Sequence 
>C. ELEGANS:194120_AT
tgcattcttgcacccagaagccaaaggactctcgaatagctcacagattatgattcgtga
tgctagaaatcgtgttttgaaagctctttatgcattcattctcgatcagatgccagatga
cgcacccacaagatatggaaatattttgttgttggcaccggctctcaaggctctgactca
gctgctcattgagaatatgacacttacaaagttcttcggattggcagaggtggattctct
gctctccgagttcattctcgacgacatcaatgatcattcgacggctccggtctctttaca
gcaacatctttcatctccgacaacgttaccgactaatggggtatctccgttaaatccagc
cggatcagtgggaagtgtttcgtctgtttctggaattacaccaactggaatgctctcagc
aactcttgcagctccattggcaattcatcctctccaatcacaagat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCATTCTTGCACCCAGAAGCCAAA 17 579 942 Antisense
GCCAAAGGACTCTCGAATAGCTCAC 215 277 961 Antisense
GATCAGATGCCAGATGACGCACCCA 394 421 1045 Antisense
ATATTTTGTTGTTGGCACCGGCTCT 602 19 1082 Antisense
GCTCTCCGAGTTCATTCTCGACGAC 708 299 1182 Antisense
TTACAGCAACATCTTTCATCTCCGA 527 683 1237 Antisense
ATCTCCGACAACGTTACCGACTAAT 204 33 1254 Antisense
GGGTATCTCCGTTAAATCCAGCCGG 389 497 1280 Antisense
GGAAGTGTTTCGTCTGTTTCTGGAA 499 531 1312 Antisense
TGCAGCTCCATTGGCAATTCATCCT 643 577 1368 Antisense
AATTCATCCTCTCCAATCACAAGAT 70 177 1383 Antisense
Sequence Source Affymetrix Proprietary Database