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[172773_x_at]

Description K10B3.2 /REP_DB=WormBase Gene ID /WP=CE07365 /GB=AAB53871.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=TC3A transposable element
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 26      4grp_highest_8_8 > 23      4grp_high_8_8 > 05      6grp_highest_nonorm > 80      6grp_total > 26      4grp_total > 03      6grp_highest_sub > Cu      6grp_high1_sub > De      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1625
1 2 3 4 range
A 212.8
(-2.4)
P 		63.9
(-3)
P 		86.1
(-2.9)
P 		1521.1
(3)
P 		1457
B 241.4
(-2.4)
P 		139.5
(-2.8)
P 		97.9
(-3)
P 		1549.2
(3)
P 		1451
C 225.7
(-2.4)
P 		105.8
(-2.8)
P 		53.8
(-3)
P 		1678.4
(3)
P 		1625
avr 226.6
(-2.4) 		103.1
(-2.9) 		79.3
(-3) 		1582.9
(3) 		1504

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 284
1 2 3 4 5 6 range
A 385
(3)
P 		220.8
(-0.6)
P 		141.3
(-2.3)
P 		110.8
(-3)
P 		113.7
(-2.9)
P 		165.9
(-1.8)
P 		274
B 306.8
(3)
P 		283.8
(2.3)
P 		105.5
(-3)
P 		124.9
(-2.4)
P 		150.1
(-1.7)
P 		197.2
(-0.3)
P 		201
C 262.1
(2)
P 		293.4
(3)
P 		121.1
(-2.4)
P 		143.6
(-1.7)
P 		100.9
(-3)
P 		197.9
(0)
P 		193
avr 318
(3) 		266
(1.4) 		122.6
(-3) 		126.4
(-2.9) 		121.6
(-3) 		187
(-1) 		196
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 316
1 2 3 4 range
A 77.5
(-1.2)
P 		13.9
(-3)
P 		22.5
(-2.8)
P 		222.7
(3)
P 		209
B 77
(-1.9)
P 		34.4
(-2.8)
P 		22.7
(-3)
P 		330.1
(3)
P 		307
C 74.7
(-1.7)
P 		30.4
(-2.7)
P 		18.8
(-3)
P 		283
(3)
P 		264
avr 76.4
(-1.7) 		26.2
(-2.9) 		21.3
(-3) 		278.6
(3) 		257

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 71
(2.1)
P 		78.5
(3)
P 		30.8
(-2.7)
P 		28.1
(-3)
P 		34.3
(-2.3)
P 		40.4
(-1.5)
P 		50
B 106.7
(3)
P 		94.5
(2.1)
P 		25.6
(-3)
P 		33.1
(-2.4)
P 		61
(-0.4)
P 		73.5
(0.5)
P 		81
C 97.1
(3)
P 		89.5
(2.3)
P 		30.8
(-2.8)
P 		28.9
(-3)
P 		32.6
(-2.7)
P 		66.3
(0.3)
P 		68
avr 91.6
(3) 		87.5
(2.6) 		29.1
(-3) 		30
(-2.9) 		42.6
(-1.7) 		60.1
(-0) 		63
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172773_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18550
Sequence Type Exemplar sequence
Representative Public ID K10B3.2 NCBI
Target Description K10B3.2 /REP_DB=WormBase Gene ID /WP=CE07365 /GB=AAB53871.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=TC3A transposable element
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_001027065(9), AF273831(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027065 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-88) (nhr-88) mRNA, complete cds. 9/11 None
AF273831 NCBI Caenorhabditis elegans clone yk155h3 nuclear receptor NHR-88 (nhr-88) pseudogene, mRNA sequence. 11/11 None
SNAP00000010015 ENSEMBL cdna:SNAP chromosome:CEL140:I:13464813:13491947:1 9/11 None
GENEFINDER00000010022 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:13464813:13465850:1 9/11 None
SNAP00000043750 ENSEMBL cdna:SNAP chromosome:CEL140:I:13748728:13749765:-1 9/11 None
GENEFINDER00000043758 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:13748728:13749765:-1 9/11 None
SNAP00000032359 ENSEMBL cdna:SNAP chromosome:CEL140:I:597625:600381:-1 9/11 None
GENEFINDER00000032370 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:599344:600381:-1 9/11 None
SNAP00000036880 ENSEMBL cdna:SNAP chromosome:CEL140:I:11857979:11859016:-1 9/11 None
GENEFINDER00000036903 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11857979:11859016:-1 9/11 None
SNAP00000007172 ENSEMBL cdna:SNAP chromosome:CEL140:I:10248167:10249204:1 9/11 None
GENEFINDER00000007181 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10248167:10249204:1 9/11 None
SNAP00000002745 ENSEMBL cdna:SNAP chromosome:CEL140:II:479012:484352:1 9/11 None
GENEFINDER00000002751 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:479012:480049:1 9/11 None
SNAP00000014286 ENSEMBL cdna:SNAP chromosome:CEL140:II:7079604:7080641:1 9/11 None
GENEFINDER00000014305 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7079604:7080641:1 9/11 None
SNAP00000033727 ENSEMBL cdna:SNAP chromosome:CEL140:II:7502802:7503839:-1 9/11 None
GENEFINDER00000033729 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7502802:7503839:-1 9/11 None
SNAP00000036642 ENSEMBL cdna:SNAP chromosome:CEL140:II:2980998:2985921:1 9/11 None
GENEFINDER00000036648 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:2980998:2982035:1 9/11 None
SNAP00000038232 ENSEMBL cdna:SNAP chromosome:CEL140:II:3940033:3941070:1 9/11 None
GENEFINDER00000038235 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3940033:3941070:1 9/11 None
SNAP00000043176 ENSEMBL cdna:SNAP chromosome:CEL140:II:16602:17639:-1 9/11 None
GENEFINDER00000043188 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:16602:17639:-1 9/11 None
SNAP00000020821 ENSEMBL cdna:SNAP chromosome:CEL140:III:11605876:11606913:1 9/11 None
GENEFINDER00000020824 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11605876:11606913:1 9/11 None
SNAP00000042405 ENSEMBL cdna:SNAP chromosome:CEL140:III:8694986:8696023:1 9/11 None
GENEFINDER00000042423 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8694986:8696023:1 9/11 None
SNAP00000015167 ENSEMBL cdna:SNAP chromosome:CEL140:IV:12510519:12511556:1 9/11 None
GENEFINDER00000015178 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:12510519:12511556:1 9/11 None
SNAP00000025714 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13815739:13816776:1 9/11 None
GENEFINDER00000025734 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13815739:13816776:1 9/11 None
SNAP00000013662 ENSEMBL cdna:SNAP chromosome:CEL140:V:18430848:18431885:1 9/11 None
GENEFINDER00000013670 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:18430848:18431885:1 9/11 None
SNAP00000039943 ENSEMBL cdna:SNAP chromosome:CEL140:V:18767668:18768696:1 9/11 None
GENEFINDER00000039951 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:18764108:18768696:1 9/11 None
SNAP00000041061 ENSEMBL cdna:SNAP chromosome:CEL140:V:17098603:17099640:-1 9/11 None
GENEFINDER00000041072 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:17098603:17099640:-1 9/11 None
GENEFINDER00000032582 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3129295:3129952:1 11/11 None
SNAP00000032575 ENSEMBL cdna:SNAP chromosome:CEL140:X:3129490:3129952:1 9/11 None
K08A2.5b ENSEMBL cdna:known chromosome:CEL140:II:2978420:2982056:1 gene:K08A2.5 9/11 A 
ZC239.1 ENSEMBL cdna:pseudogene chromosome:CEL140:II:3227253:3228290:1 gene:ZC239.1 9/11 A 
T04A11.11 ENSEMBL cdna:pseudogene chromosome:CEL140:IV:12510519:12511556:1 gene:T04A11.11 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001027066 2/11 Cross Hyb Matching Probes None
SNAP00000024300 8/11 Cross Hyb Matching Probes None
GENEFINDER00000024311 7/11 Cross Hyb Matching Probes None
K08A2.5c 2/11 Cross Hyb Matching Probes A 
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
173641 3 1 NM_001027064 190898_at (11)
NM_001027065 172773_x_at (9), 173008_s_at (11), 189548_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Ensembl K08A2.5
ZC239.1
T04A11.11
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAO21381 Nuclear hormone receptor family protein 88, isoform b [Caenorhabditis elegans] ref|NP_001022236.1| Nuclear Hormone Receptor family member (nhr-88) [Caenorhabditis elegans] 0.0
blast AAA82401 Hypothetical protein T02G5.5 [Caenorhabditis elegans] 0.0
blast F87991 protein Y6B3B.8 [imported] - Caenorhabditis elegans 0.0
blast P34257 Transposable element Tc3 transposase 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 3.99999999927983E-23
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 4.99999984132761E-22
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 5.99999980959314E-22
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 6.99999977785866E-22
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 9.99999968265523E-22
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 1.99999993653105E-21
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 2.99999990479657E-21
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 3.99999987306209E-20
scop a.4.1.Recombinase DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Recombinase DNA-binding domain 4.99999998002099E-12
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 8.8E-48
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 6.4E-49
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 7.2E-31
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 9.3E-48
Pfam IPR001584 EMBL-EBI Integrase, catalytic domain 0.0027
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 1.3E-47
Pfam IPR001609 EMBL-EBI Myosin head (motor domain) 2.7E-24
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 1.4E-46
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 1.5E-47
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 7.7E-46
Pfam IPR005071 EMBL-EBI Protein of unknown function DUF274 2.0E-72
Pfam IPR002492 EMBL-EBI Transposase, Tc1/Tc3 7.7E-46
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.8E-27
Sequence
Target Sequence 
>C. ELEGANS:172773_X_AT
gaaggcttatcaggaatcaaatcgtttttctttgattacaaggttccatgggaccaatat
ttcaagttaaattgtccctcacagatgttatttactattttttgccaggataatgcgaca
atccatgtgagcaactcaacccgcgactatttcaagctcaagaagatcaaccttcttgat
tggccagctcgaagtcctgatctcaatccaatcgaaaatttgtgggggattcttgtccgt
atcgtgtatgctcagaacaagacttacccaacagttgcatcgttgaagcaaggaattctc
gacgcttggaagtctattccggacaaccagct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGGCTTATCAGGAATCAAATCGT 65 333 31 Antisense
GATTACAAGGTTCCATGGGACCAAT 308 431 64 Antisense
TCCATGTGAGCAACTCAACCCGCGA 615 587 152 Antisense
TCAACCCGCGACTATTTCAAGCTCA 594 631 166 Antisense
TGATTGGCCAGCTCGAAGTCCTGAT 430 435 207 Antisense
GAAGTCCTGATCTCAATCCAATCGA 535 335 221 Antisense
TTGTGGGGGATTCTTGTCCGTATCG 672 707 250 Antisense
TGTCCGTATCGTGTATGCTCAGAAC 432 557 264 Antisense
ACAAGACTTACCCAACAGTTGCATC 586 113 287 Antisense
GGAATTCTCGACGCTTGGAAGTCTA 632 531 322 Antisense
GGAAGTCTATTCCGGACAACCAGCT 643 529 338 Antisense
Sequence Source Affymetrix Proprietary Database