[Home] | [Total List]

[188213_at]

Description Y39A1B.2 /REP_DB=WormBase Gene ID /WP=CE19144 /GEN=ptr-19 /TR=Q9XXR9 /GB=CAA16339.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 34      4grp_total > 01      6grp_cgc > 33      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 99
1 2 3 4 range
A 31
(-1.4)
A 		5
(-3)
A 		51.1
(-0.2)
A 		104.3
(3)
A 		99
B 52.3
(3)
A 		20.1
(-1.7)
A 		11
(-3)
A 		50.7
(2.8)
A 		41
C 7.8
(-3)
A 		66.3
(0.7)
A 		56.6
(0.1)
A 		102.9
(3)
A 		95
avr 30.4
(-3) 		30.5
(-3) 		39.6
(-2) 		86
(3) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 69
1 2 3 4 5 6 range
A 62.3
(3)
A 		13.7
(-2.2)
A 		62
(3)
A 		6.5
(-3)
A 		24.2
(-1.1)
A 		8.2
(-2.8)
A 		56
B 30.9
(0.6)
A 		49.1
(3)
A 		9.3
(-2.3)
A 		3.7
(-3)
A 		28.9
(0.3)
A 		5
(-2.8)
A 		45
C 30.1
(-0.7)
A 		72.9
(3)
A 		42.1
(0.3)
A 		13.9
(-2.1)
A 		3.5
(-3)
A 		19.3
(-1.6)
A 		69
avr 41.1
(2.3) 		45.2
(3) 		37.8
(1.8) 		8
(-3) 		18.9
(-1.2) 		10.8
(-2.5) 		37
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 11.3
(1.3)
A 		1.1
(-3)
A 		13.4
(2.2)
A 		15.3
(3)
A 		14
B 16.7
(3)
A 		5
(-1.9)
A 		2.5
(-3)
A 		10.8
(0.5)
A 		14
C 2.6
(-3)
A 		19.1
(2.8)
A 		19.7
(3)
A 		17.4
(2.2)
A 		17
avr 10.2
(-1.2) 		8.4
(-3) 		11.9
(0.4) 		14.5
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 21
1 2 3 4 5 6 range
A 11.5
(2)
A 		4.9
(-1.3)
A 		13.5
(3)
A 		1.6
(-3)
A 		7.3
(-0.1)
A 		2
(-2.8)
A 		12
B 10.7
(0.8)
A 		16.3
(3)
A 		2.3
(-2.5)
A 		1
(-3)
A 		11.8
(1.2)
A 		1.9
(-2.6)
A 		15
C 11.2
(-0.1)
A 		22.3
(3)
A 		10.7
(-0.3)
A 		2.8
(-2.5)
A 		1.1
(-3)
A 		6.5
(-1.5)
A 		21
avr 11.1
(1.4) 		14.5
(3) 		8.8
(0.3) 		1.8
(-3) 		6.7
(-0.7) 		3.5
(-2.2) 		13
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188213_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6786
Sequence Type Exemplar sequence
Representative Public ID Y39A1B.2 NCBI
Target Description Y39A1B.2 /REP_DB=WormBase Gene ID /WP=CE19144 /GEN=ptr-19 /TR=Q9XXR9 /GB=CAA16339.1 /SUBMIT=HINXTON /CHR=3 /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_066979(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066979 NCBI Caenorhabditis elegans PaTched Related family member (ptr-19) (ptr-19) mRNA, complete cds. 11/11 None
GENEFINDER00000005069 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10781758:10796381:1 11/11 None
SNAP00000005066 ENSEMBL cdna:SNAP chromosome:CEL140:III:10783757:10791053:1 11/11 None
Y39A1B.2 ENSEMBL cdna:known chromosome:CEL140:III:10781758:10791053:1 gene:Y39A1B.2 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
chrIII:10781753-10791049(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ptr-19
Ensembl Y39A1B.2
Entrez Gene 191751 Entrez gene
SwissProt Q9XXR9 EMBL-EBI
WormBase CE19144 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8158 hedgehog receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA16339 Hypothetical protein Y39A1B.2 [Caenorhabditis elegans] ref|NP_499380.1| PaTched Related family member (ptr-19) [Caenorhabditis elegans] 0.0
blast CAE71402 Hypothetical protein CBG18310 [Caenorhabditis briggsae] 0.0
blast CAA16338 Hypothetical protein Y39A1B.1 [Caenorhabditis elegans] ref|NP_499381.1| Y39A1B.1 [Caenorhabditis elegans] 0.0
blast AAB42325 Patched related family protein 2 [Caenorhabditis elegans] ref|NP_491221.1| PaTched Related family member (ptr-2) [Caenorhabditis elegans] 1.0E-106
Protein Domains
Database ID Description E-Value
Pfam IPR002035 EMBL-EBI von Willebrand factor, type A 5.9E-22
Pfam IPR003392 EMBL-EBI Patched family 3.1E-91
Pfam IPR003392 EMBL-EBI Patched family 6.5E-65
Pfam IPR003392 EMBL-EBI Patched family 3.1E-91
Pfam IPR003392 EMBL-EBI Patched family 6.5E-65
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499380.1 12 20-42,293-315,322-344,354-376,396-418,428-450,501-523,705-727,734-756,760-782,799-821,836-858
Y39A1B.2 12 20-42,293-315,322-344,354-376,396-418,428-450,501-523,705-727,734-756,760-782,799-821,836-858
GENEFINDER00000005069 12 20-42,293-315,322-344,354-376,396-418,428-450,501-523,705-727,734-756,760-782,799-821,836-858
SNAP00000005066 11 170-192,199-221,231-253,273-295,305-327,378-400,582-604,611-633,637-659,676-698,713-735
Sequence
Target Sequence 
>C. ELEGANS:188213_AT
tgagaaatgctctttacgctgtcggtgctccaatcctcatgtcggccacctcaacaatca
tcggagtgtcgtttatggcatcagccgagtcttacgttttccgaagtttcctgaaaacta
ttatgctcgttattctactcggagctttacatggactcgtaattctgccggttttattat
ccatgttttattgtggaggatcgtcgaaaaaggcaaaggagcatattgatgctgtggacc
aaaagctacaagcccagtacaacaacccagctcgaacagcttcaatacagttcctgagca
accctgatctctacacaatgccaccacctccaagcgttgaatactctctttcaacactgg
aattcaatcgaacccagtcgagacctctcggtgctccgccagcgctcaccggaagcccaa
aacgagaattatcggggctctcggggccgcccgaatacgaggaacacgatccgacggggc
tcagcacattcggtgtatcgcctgcagttgtcgcgaacactacgggaatgataccgatgc
gtgccaagttgaaatatccgagcagcatgacacagcgac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAGAAATGCTCTTTACGCTGTCGG 706 567 2399 Antisense
CGGAGTGTCGTTTATGGCATCAGCC 324 243 2460 Antisense
ATGGACTCGTAATTCTGCCGGTTTT 501 49 2549 Antisense
ACAACCCAGCTCGAACAGCTTCAAT 416 113 2660 Antisense
AATACAGTTCCTGAGCAACCCTGAT 438 171 2682 Antisense
AGCAACCCTGATCTCTACACAATGC 513 75 2695 Antisense
ACCACCTCCAAGCGTTGAATACTCT 461 83 2721 Antisense
GGCTCAGCACATTCGGTGTATCGCC 253 539 2876 Antisense
GTATCGCCTGCAGTTGTCGCGAACA 19 453 2893 Antisense
GAATGATACCGATGCGTGCCAAGTT 423 329 2924 Antisense
TATCCGAGCAGCATGACACAGCGAC 71 657 2953 Antisense
Sequence Source Affymetrix Proprietary Database