[Home] | [Total List]

[179260_s_at]

Description K08E3.7 /REP_DB=WormBase Gene ID /WP=CE18873 /TR=Q9XUS3 /GB=CAB04599.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 66      6grp_high1_10_10 > 66      4grp_highest_8_8 > 37      4grp_high_8_8 > 01      6grp_highest_nonorm > 85      6grp_total > 66      4grp_total > 06      6grp_highest_sub > Da      6grp_cgc > 37      6grp_high1_sub > Da      6grp_cgc_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 378
1 2 3 4 range
A 656.3
(-0.6)
P 		565.2
(-3)
P 		610.8
(-1.8)
P 		792
(3)
P 		227
B 531.8
(-0.4)
P 		485.3
(-1.8)
P 		442.9
(-3)
P 		650.5
(3)
P 		208
C 691.1
(3)
P 		413.8
(-3)
P 		607.1
(1.2)
P 		611.9
(1.3)
P 		277
avr 626.4
(1.2) 		488.1
(-3) 		553.6
(-1) 		684.8
(3) 		197

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 585
1 2 3 4 5 6 range
A 626.5
(-2)
P 		666.3
(-0.8)
P 		676.6
(-0.4)
P 		603.1
(-2.7)
P 		593.5
(-3)
P 		788.7
(3)
P 		195
B 719
(-1.2)
P 		700.6
(-1.5)
P 		713.2
(-1.3)
P 		731.1
(-1)
P 		603.6
(-3)
P 		989.8
(3)
P 		386
C 563.3
(-3)
P 		683.7
(-1.8)
P 		626.8
(-2.3)
P 		751.2
(-1.1)
P 		578.4
(-2.8)
P 		1148.2
(3)
P 		585
avr 636.3
(-2.3) 		683.5
(-1.6) 		672.2
(-1.7) 		695.1
(-1.4) 		591.8
(-3) 		975.6
(3) 		384
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 136
1 2 3 4 range
A 239
(3)
P 		122.7
(-2.7)
P 		159.7
(-0.9)
P 		115.9
(-3)
P 		123
B 169.6
(3)
P 		119.9
(-1.5)
P 		102.6
(-3)
P 		138.6
(0.2)
P 		67
C 228.8
(3)
P 		119
(-2.2)
P 		211.6
(2.2)
P 		103.2
(-3)
P 		126
avr 212.5
(3) 		120.5
(-2.9) 		158
(-0.5) 		119.2
(-3) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 269
1 2 3 4 5 6 range
A 115.5
(-3)
P 		237
(3)
P 		147.3
(-1.4)
P 		153
(-1.1)
P 		179.1
(0.1)
P 		192
(0.8)
P 		122
B 250.2
(-0.6)
P 		233.2
(-1.2)
P 		173.2
(-3)
P 		193.6
(-2.4)
P 		245.2
(-0.8)
P 		369.1
(3)
P 		196
C 208.8
(-1.5)
P 		208.6
(-1.5)
P 		159.5
(-2.8)
P 		151.1
(-3)
P 		187.2
(-2.1)
P 		384.4
(3)
P 		233
avr 191.5
(-1.8) 		226.3
(-0.4) 		160
(-3) 		165.9
(-2.8) 		203.8
(-1.3) 		315.2
(3) 		155
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 179260_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6627
Sequence Type Exemplar sequence
Representative Public ID K08E3.7 NCBI
Target Description K08E3.7 /REP_DB=WormBase Gene ID /WP=CE18873 /TR=Q9XUS3 /GB=CAB04599.1 /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_067445(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067445 NCBI Caenorhabditis elegans Parkinson's Disease Related family member (pdr-1) (pdr-1) mRNA, complete cds. 11/11 A 
GENEFINDER00000031970 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13771047:13778175:1 11/11 None
SNAP00000031967 ENSEMBL cdna:SNAP chromosome:CEL140:III:13771278:13772766:1 9/11 None
K08E3.7.2 ENSEMBL cdna:known chromosome:CEL140:III:13770964:13772852:1 gene:K08E3.7 11/11 None
K08E3.7.1 ENSEMBL cdna:known chromosome:CEL140:III:13771035:13772852:1 gene:K08E3.7 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:13771042-13772762(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol pdr-1
Ensembl K08E3.7
Entrez Gene 176816 Entrez gene
SwissProt Q9XUS3 EMBL-EBI
WormBase CE31713 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1597895_AT similar to parkin isoform 1 cfa
CANINE_2:CFAAFFX.2074.1.S1_AT similar to parkin isoform 1 cfa
DROSOPHILA_2:1629967_S_AT Saccharomyces cerevisiae UAS construct a of Greene dm
DROSGENOME1:141474_AT Saccharomyces cerevisiae UAS construct a of Greene dm
CHICKEN:GGAAFFX.23587.1.S1_AT similar to Parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 3; parkin gga
CHICKEN:GGAAFFX.7323.1.S1_AT similar to Parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 3; parkin gga
HG-U133_PLUS_2:207058_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U133A_2:207058_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U133A:207058_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-FOCUS:207058_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
U133_X3P:G4758883_3P_A_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
U133_X3P:HS2.132954.6.S1_3P_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
U133_X3P:HS2.132954.4.S1_3P_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U133_PLUS_2:1554855_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U133_PLUS_2:1555668_A_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U95AV2:33019_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
U133_X3P:HS2.395630.1.S1_3P_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U133_PLUS_2:1569947_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U95B:42479_R_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U95C:61987_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U95D:69304_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HG-U95E:86935_R_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HU35KSUBB:RC_H68208_S_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
HU35KSUBD:RC_AA398227_AT Parkinson disease (autosomal recessive, juvenile) 2, parkin hs
MOE430A:1420755_A_AT parkin mm
MOUSE430A_2:1420755_A_AT parkin mm
MOUSE430_2:1420755_A_AT parkin mm
MOE430A:1449975_A_AT parkin mm
MOUSE430_2:1449975_A_AT parkin mm
MOUSE430A_2:1449975_A_AT parkin mm
MOUSE430_2:1426135_A_AT parkin mm
MOE430A:1426135_A_AT parkin mm
MOUSE430A_2:1426135_A_AT parkin mm
MG-U74AV2:102073_AT parkin mm
MG-U74CV2:140453_G_AT parkin mm
MG-U74CV2:140452_AT parkin mm
MG-U74CV2:135361_AT Parkin (Park2), mRNA mm
MOUSE430_2:1442361_AT Parkin (Park2), mRNA mm
MOE430B:1442361_AT Parkin (Park2), mRNA mm
RAE230A:1369138_A_AT parkin rn
RAT230_2:1369138_A_AT parkin rn
RAE230B:1398192_AT Parkin rn
RAT230_2:1398192_AT Parkin rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6512 ubiquitin cycle inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4842 ubiquitin-protein ligase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04599 Hypothetical protein K08E3.7 [Caenorhabditis elegans] ref|NP_499846.2| Parkinson's Disease Related family member (pdr-1) [Caenorhabditis elegans] 0.0
blast CAE71359 Hypothetical protein CBG18262 [Caenorhabditis briggsae] 0.0
blast CAB04600 Hypothetical protein K08E3.8 [Caenorhabditis elegans] ref|NP_499847.1| MeDiaTor family member (mdt-29) [Caenorhabditis elegans] 0.0
blast CAE71359 Hypothetical protein CBG18262 [Caenorhabditis briggsae] 1.0E-164
blast CAB04599 Hypothetical protein K08E3.7 [Caenorhabditis elegans] ref|NP_499846.2| Parkinson's Disease Related family member (pdr-1) [Caenorhabditis elegans] 1.0E-157
Sequence
Target Sequence 
>C. ELEGANS:179260_S_AT
gacgatggaagatcccagtgtccagattgttttttttcgttttgcagaaagtgcttcgaa
agaaattgtgtgtgccagagcgaagacgatctcacccgaactacaattgacgcgactaca
agaagatgcccaaaatgccacgtggcaaccgaacggaacggcggatgtgctcacattcac
tgtacctcgtgtggaatggattggtgtttcaagtgcaagaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGATGGAAGATCCCAGTGTCCAG 700 377 823 Antisense
CAGTGTCCAGATTGTTTTTTTTCGT 123 209 838 Antisense
AAGAAATTGTGTGTGCCAGAGCGAA 571 151 882 Antisense
GTGCCAGAGCGAAGACGATCTCACC 114 479 894 Antisense
CGATCTCACCCGAACTACAATTGAC 445 247 909 Antisense
CCCGAACTACAATTGACGCGACTAC 233 261 917 Antisense
GCCACGTGGCAACCGAACGGAACGG 262 279 959 Antisense
CGAACGGAACGGCGGATGTGCTCAC 444 251 972 Antisense
GATGTGCTCACATTCACTGTACCTC 306 409 986 Antisense
CTGTACCTCGTGTGGAATGGATTGG 495 229 1002 Antisense
GGATTGGTGTTTCAAGTGCAAGACA 656 507 1020 Antisense
Sequence Source Affymetrix Proprietary Database