[Home] | [Total List]

[187698_at]

Description C05D11.2 /REP_DB=WormBase Gene ID /WP=CE24785 /TR=SW:Q11182 /GB=AAB53823.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 09      4grp_total > 60      6grp_cgc > 0      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 123
1 2 3 4 range
A 369.6
(3)
P 		351.5
(0.5)
A 		363.8
(2.2)
A 		327
(-3)
A 		43
B 353.7
(3)
P 		316.1
(0.7)
A 		344.4
(2.4)
A 		253.5
(-3)
A 		100
C 288.8
(-1.7)
M 		354.2
(1.8)
A 		376.9
(3)
A 		264.8
(-3)
A 		112
avr 337.4
(1.2) 		340.6
(1.4) 		361.7
(3) 		281.8
(-3) 		80

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 150
1 2 3 4 5 6 range
A 431
(3)
A 		338.7
(-2.3)
A 		336.7
(-2.4)
A 		416.8
(2.2)
A 		375.8
(-0.2)
A 		326.1
(-3)
A 		105
B 376.3
(0.2)
M 		305.5
(-3)
A 		365.8
(-0.3)
A 		440.1
(3)
P 		370.7
(-0.1)
A 		356.7
(-0.7)
P 		135
C 348.9
(0.1)
A 		305.5
(-2.2)
M 		403.2
(3)
A 		290.5
(-3)
A 		308.1
(-2.1)
A 		356.4
(0.5)
M 		113
avr 385.4
(3) 		316.6
(-3) 		368.6
(1.5) 		382.5
(2.7) 		351.5
(0) 		346.4
(-0.4) 		69
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 90
1 2 3 4 range
A 134.6
(3)
P 		76.3
(-1)
A 		95.1
(0.3)
A 		47.9
(-3)
A 		87
B 112.8
(3)
P 		78.1
(-0.5)
A 		79.8
(-0.4)
A 		54
(-3)
A 		59
C 95.6
(0.5)
M 		101.8
(1)
A 		131.4
(3)
A 		44.6
(-3)
A 		87
avr 114.3
(3) 		85.4
(0.4) 		102.1
(1.9) 		48.8
(-3) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 92
1 2 3 4 5 6 range
A 79.5
(-2.2)
A 		120.5
(3)
A 		73.3
(-3)
A 		105.7
(1.1)
A 		113.4
(2.1)
A 		79.4
(-2.2)
A 		47
B 130.9
(1.1)
M 		101.7
(-1.7)
A 		88.8
(-3)
A 		116.6
(-0.3)
P 		150.6
(3)
A 		133
(1.3)
P 		62
C 129.3
(3)
A 		93.2
(-0.1)
M 		102.6
(0.7)
A 		58.4
(-3)
A 		99.7
(0.5)
A 		119.3
(2.2)
M 		71
avr 113.2
(1.5) 		105.1
(0.1) 		88.2
(-3) 		93.6
(-2) 		121.2
(3) 		110.6
(1.1) 		33
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187698_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7397
Sequence Type Exemplar sequence
Representative Public ID C05D11.2 NCBI
Target Description C05D11.2 /REP_DB=WormBase Gene ID /WP=CE24785 /TR=SW:Q11182 /GB=AAB53823.1 /SUBMIT=ST.LOUIS /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_066010(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066010 NCBI Caenorhabditis elegans related to yeast Vacuolar Protein Sorting factor family member (vps-16) (vps-16) mRNA, complete cds. 11/11 None
SNAP00000019456 ENSEMBL cdna:SNAP chromosome:CEL140:III:6433178:6436281:1 11/11 None
GENEFINDER00000019473 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6433178:6436281:1 11/11 None
C05D11.2.1 ENSEMBL cdna:known chromosome:CEL140:III:6433175:6436426:1 gene:C05D11.2 11/11 None
C05D11.2.2 ENSEMBL cdna:known chromosome:CEL140:III:6433176:6436377:1 gene:C05D11.2 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:6433176-6436280(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol vps-16
Ensembl C05D11.2
Entrez Gene 175913 Entrez gene
SwissProt Q11182 EMBL-EBI
WormBase CE24785 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6886 intracellular protein transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB53823 Related to yeast vacuolar protein sorting factor protein 16 [Caenorhabditis elegans] ref|NP_498411.1| related to yeast Vacuolar Protein Sorting factor family member (vps-16) [Caenorhabditis elegans] sp|Q11182|YPD2_CAEEL Hypothetical protein C05D11.2 in chromosome III 0.0
blast H88482 protein C05D11.2 [imported] - Caenorhabditis elegans 0.0
blast CAE72492 Hypothetical protein CBG19671 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006925 EMBL-EBI Vps16, C-terminal 1.0E-126
Pfam IPR006926 EMBL-EBI Vps16, N-terminal 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:187698_AT
tggaacaagccagcgacttcgagagacaaactttattccattttgatgttgcagaaactg
aaagaaatcccgatgaacgtttaaatgctctccgacgtgccaaggatgctgcaaaaagta
tgggtgacaaggcaatcgaagagattctgaatgacgtcagcgcatttgctccactacaaa
ttcaacggggacaagcagacatgtcagtgagggatacggtaattgagatggcacacgaca
ctgcaaaggttgcacagttgaaacagcaagcaagattgactgataaacaagttttgttat
ggacaatcgaaggattggctaaaaaaggaaaaatggagcagctgtttgatttggctcaaa
aaagatctccaattggatatgctccattcgtcaaagcctgtgttcgatataaaagacttg
acgagatcaagaagtattttgcaaaagttaatggatatccagatctggtggctgctcatc
ttgcaatgaaaaactacgtggaagctgccaagctggcctacgatcgccgagaccgtgatg
tcttgcacgcagttcacatgaaatctcacgaagatcccacacaatgtccgagagtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAACAAGCCAGCGACTTCGAGAG 371 547 1943 Antisense
GATGAACGTTTAAATGCTCTCCGAC 85 413 2014 Antisense
TGAATGACGTCAGCGCATTTGCTCC 464 575 2090 Antisense
TTGCTCCACTACAAATTCAACGGGG 77 701 2108 Antisense
GGCACACGACACTGCAAAGGTTGCA 597 535 2172 Antisense
GATATGCTCCATTCGTCAAAGCCTG 343 425 2318 Antisense
GGATATCCAGATCTGGTGGCTGCTC 170 511 2395 Antisense
CGTGGAAGCTGCCAAGCTGGCCTAC 444 245 2439 Antisense
CTACGATCGCCGAGACCGTGATGTC 548 223 2460 Antisense
TGATGTCTTGCACGCAGTTCACATG 471 565 2478 Antisense
AGATCCCACACAATGTCCGAGAGTC 292 67 2514 Antisense
Sequence Source Affymetrix Proprietary Database