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[188133_at]

Description K07A3.2 /REP_DB=WormBase Gene ID /WP=CE23854 /GEN=ptr-12 /TR=Q9N5J9 /GB=AAF39911.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 77      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 93      6grp_total > 68      4grp_total > 18      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 842
1 2 3 4 range
A 497.4
(-3)
P 		754.6
(-0.1)
P 		617.1
(-1.7)
P 		1037.8
(3)
P 		540
B 611.9
(-2.9)
P 		911.7
(-0.3)
P 		605.4
(-3)
P 		1273.8
(3)
P 		668
C 431.6
(-3)
P 		666.6
(-0.8)
P 		574.3
(-1.7)
P 		1078.8
(3)
P 		647
avr 513.6
(-3) 		777.6
(-0.4) 		598.9
(-2.2) 		1130.1
(3) 		617

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 800
1 2 3 4 5 6 range
A 311.3
(-2.4)
P 		339.8
(-2.2)
P 		293.8
(-2.6)
P 		235.7
(-3)
P 		413.8
(-1.7)
P 		1035.9
(3)
P 		800
B 456
(-0.9)
P 		345.5
(-2.2)
P 		347.1
(-2.2)
P 		282.7
(-3)
P 		340.9
(-2.3)
P 		776
(3)
P 		493
C 348
(-1.6)
P 		261.8
(-3)
P 		305
(-2.3)
P 		281.7
(-2.7)
P 		470.4
(0.3)
P 		642.7
(3)
P 		381
avr 371.8
(-1.9) 		315.7
(-2.5) 		315.3
(-2.5) 		266.7
(-3) 		408.4
(-1.5) 		818.2
(3) 		552
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 131
1 2 3 4 range
A 181.1
(3)
P 		163.8
(-0.6)
P 		161.3
(-1.1)
P 		151.9
(-3)
P 		29
B 195.1
(-0.5)
P 		225.2
(0.9)
P 		140.3
(-3)
P 		271.4
(3)
P 		131
C 142.9
(-3)
P 		191.7
(2.1)
P 		200.2
(3)
P 		181.9
(1.1)
P 		57
avr 173
(-2) 		193.6
(1.6) 		167.3
(-3) 		201.7
(3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 233
1 2 3 4 5 6 range
A 57.4
(-3)
P 		120.8
(-1)
P 		64
(-2.8)
P 		59.8
(-2.9)
P 		124.9
(-0.9)
P 		252.2
(3)
P 		195
B 158.7
(-0.7)
P 		115
(-1.9)
P 		84.3
(-2.7)
P 		74.9
(-3)
P 		138.5
(-1.2)
P 		289.4
(3)
P 		215
C 129
(-0.3)
P 		79.9
(-2.1)
P 		77.6
(-2.2)
P 		56.7
(-3)
P 		152.2
(0.6)
P 		215.1
(3)
P 		158
avr 115
(-1.4) 		105.2
(-1.7) 		75.3
(-2.6) 		63.8
(-3) 		138.5
(-0.6) 		252.2
(3) 		188
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188133_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.138
Sequence Type Exemplar sequence
Representative Public ID K07A3.2 NCBI
Target Description K07A3.2 /REP_DB=WormBase Gene ID /WP=CE23854 /GEN=ptr-12 /TR=Q9N5J9 /GB=AAF39911.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=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_001026388(10), NM_001026389(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001026388 NCBI Caenorhabditis elegans PaTched Related family member (ptr-12) (ptr-12) mRNA, complete cds. 10/11 None
NM_001026389 NCBI Caenorhabditis elegans PaTched Related family member (ptr-12) (ptr-12) mRNA, complete cds. 10/11 None
GENEFINDER00000015263 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:2587707:2597328:-1 11/11 None
K07A3.2a ENSEMBL cdna:known chromosome:CEL140:I:2587542:2595414:-1 gene:K07A3.2 10/11 None
K07A3.2b ENSEMBL cdna:known chromosome:CEL140:I:2587697:2592626:-1 gene:K07A3.2 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000015258 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:2588780-2595414(-) 88.84 100.0
Public Domain and Genome References
Ensembl K07A3.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAF39911 Patched related family protein 12, isoform a [Caenorhabditis elegans] ref|NP_001021559.1| PaTched Related family member (ptr-12) [Caenorhabditis elegans] 0.0
blast CAE60539 Hypothetical protein CBG04166 [Caenorhabditis briggsae] 0.0
blast AAU05563 Patched related family protein 12, isoform b [Caenorhabditis elegans] ref|NP_001021560.1| PaTched Related family member (ptr-12) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Pfam IPR003392 EMBL-EBI Patched family 1.3E-30
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Pfam IPR003392 EMBL-EBI Patched family 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001021559.1 13 13-35,92-114,340-362,372-394,399-421,453-475,482-504,567-589,792-809,813-835,842-864,884-906,919-941
NP_001021560.1 6 75-97,300-317,321-343,350-372,392-414,427-449
K07A3.2a 13 13-35,92-114,340-362,372-394,399-421,453-475,482-504,567-589,792-809,813-835,842-864,884-906,919-941
K07A3.2b 6 75-97,300-317,321-343,350-372,392-414,427-449
GENEFINDER00000015263 7 99-121,168-190,416-438,448-470,475-497,570-587,646-668
Sequence
Target Sequence 
>C. ELEGANS:188133_AT
tgccgactgacgcgtggcagtctgcggttgccacgttggcatgtatggcgtttatttgct
tcgttttcatgtatgatgtgccgacggttatggtggcaacttcgattattgcaagtatca
tgacagtagaaagtgtgctccaaagagcatatttgctcatggtgcatcaaaacttccgac
ccaatccaaattttgttgcaggaatccttggaatcctatctctcaccggcacagacctgg
acccgattgtaatgtctgcactgattatctcaattggtttctcagtggacatcccagcac
atatctcctatcattatcacacatctccgtcagataatggaattagacatcgactacaca
aaacactgtcatccgtcgggtttccagctttacaggcgacagtttccacgtcatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCCGACTGACGCGTGGCAGTCTGC 382 585 2762 Antisense
ATGGCGTTTATTTGCTTCGTTTTCA 427 51 2806 Antisense
TGGTGCATCAAAACTTCCGACCCAA 418 551 2921 Antisense
GAATCCTTGGAATCCTATCTCTCAC 4 331 2963 Antisense
CACAGACCTGGACCCGATTGTAATG 634 193 2991 Antisense
TTGGTTTCTCAGTGGACATCCCAGC 705 707 3035 Antisense
CCAGCACATATCTCCTATCATTATC 203 273 3055 Antisense
TCATTATCACACATCTCCGTCAGAT 649 619 3072 Antisense
CAAAACACTGTCATCCGTCGGGTTT 28 191 3120 Antisense
GGTTTCCAGCTTTACAGGCGACAGT 72 505 3140 Antisense
TACAGGCGACAGTTTCCACGTCATT 604 641 3152 Antisense
Sequence Source Affymetrix Proprietary Database