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[179082_s_at]

Description T08G5.5 /REP_DB=WormBase Gene ID /WP=CE18946 /TR=Q9XUQ4 /GB=CAB04720.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 77      4grp_high_8_8 > 0      6grp_highest_nonorm > 95      6grp_total > 78      4grp_total > 15      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 212
1 2 3 4 range
A 587.8
(3)
P 		419.6
(-3)
P 		512.9
(0.3)
P 		551
(1.7)
P 		168
B 610.2
(3)
P 		398
(-3)
P 		428.2
(-2.1)
P 		511.9
(0.2)
P 		212
C 573.9
(3)
P 		412.4
(-3)
A 		491.7
(-0.1)
P 		573.8
(3)
P 		162
avr 590.6
(3) 		410
(-3) 		477.6
(-0.8) 		545.6
(1.5) 		181

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1161
1 2 3 4 5 6 range
A 551.5
(-2)
P 		440.1
(-2.5)
P 		349.8
(-3)
P 		563
(-1.9)
P 		688.9
(-1.2)
P 		1511.1
(3)
P 		1161
B 424.6
(-2.7)
P 		494.1
(-2.2)
P 		380.8
(-3)
P 		550.3
(-1.9)
P 		646.1
(-1.2)
P 		1285.8
(3)
P 		905
C 464.9
(-2.9)
P 		468.2
(-2.8)
P 		533.9
(-2.3)
P 		447.9
(-3)
P 		727.5
(-0.6)
P 		1141.9
(3)
P 		694
avr 480.3
(-2.6) 		467.5
(-2.7) 		421.5
(-3) 		520.4
(-2.3) 		687.5
(-1.2) 		1312.9
(3) 		891
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 133
1 2 3 4 range
A 214
(3)
P 		91.1
(-2.5)
P 		134.1
(-0.6)
P 		80.7
(-3)
P 		133
B 194.6
(3)
P 		98.3
(-3)
P 		99.2
(-2.9)
P 		109.1
(-2.3)
P 		96
C 190
(3)
P 		118.6
(-1.6)
A 		171.4
(1.8)
P 		96.7
(-3)
P 		93
avr 199.5
(3) 		102.7
(-2.6) 		134.9
(-0.7) 		95.5
(-3) 		104

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 403
1 2 3 4 5 6 range
A 101.7
(-2.5)
P 		156.5
(-1.3)
P 		76.2
(-3)
P 		142.8
(-1.6)
P 		207.9
(-0.3)
P 		367.9
(3)
P 		292
B 147.7
(-2.1)
P 		164.5
(-1.9)
P 		92.5
(-3)
P 		145.7
(-2.2)
P 		262.5
(-0.4)
P 		479.5
(3)
P 		387
C 172.3
(-1.3)
P 		142.8
(-1.9)
P 		135.9
(-2.1)
P 		90.1
(-3)
P 		235.4
(-0)
P 		382.3
(3)
P 		292
avr 140.6
(-2.2) 		154.6
(-2) 		101.5
(-3) 		126.2
(-2.5) 		235.3
(-0.4) 		409.9
(3) 		308
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 179082_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13627
Sequence Type Exemplar sequence
Representative Public ID T08G5.5 NCBI
Target Description T08G5.5 /REP_DB=WormBase Gene ID /WP=CE18946 /TR=Q9XUQ4 /GB=CAB04720.1 /SUBMIT=HINXTON /CHR=5 /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_074085(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074085 NCBI Caenorhabditis elegans T08G5.5 (T08G5.5) mRNA, complete cds. 11/11 None
SNAP00000009113 ENSEMBL cdna:SNAP chromosome:CEL140:V:14037181:14040937:-1 11/11 None
GENEFINDER00000009135 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:14037181:14041701:-1 11/11 None
T08G5.5 ENSEMBL cdna:known chromosome:CEL140:V:14036683:14040960:-1 gene:T08G5.5 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
chrV:14037180-14040937(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl T08G5.5
Entrez Gene 179902 Entrez gene
SwissProt Q9XUQ4 EMBL-EBI
WormBase CE18946 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:16239_AT expressed protein at
ATH1-121501:246232_AT expressed protein at
CANINE_2:CFAAFFX.15745.1.S1_AT similar to Vam6/Vps39-like protein (hVam6p) cfa
DROSGENOME1:152318_AT dm
DROSOPHILA_2:1637189_AT dm
CHICKEN:GGA.9875.1.S1_AT vacuolar protein sorting 39 (yeast) gga
CHICKEN:GGAAFFX.12603.1.S1_AT vacuolar protein sorting 39 (yeast) gga
CHICKEN:GGAAFFX.12603.1.S1_S_AT vacuolar protein sorting 39 (yeast) gga
CHICKEN:GGAAFFX.5674.1.S1_S_AT vacuolar protein sorting 39 (yeast) gga
HG-U133_PLUS_2:212156_AT vacuolar protein sorting 39 (yeast) hs
HG-U133A_2:212156_AT vacuolar protein sorting 39 (yeast) hs
HG-U133A:212156_AT vacuolar protein sorting 39 (yeast) hs
HU35KSUBA:RC_AA453761_AT vacuolar protein sorting 39 (yeast) hs
HU35KSUBB:RC_AA043115_AT vacuolar protein sorting 39 (yeast) hs
HU35KSUBD:RC_R49084_S_AT vacuolar protein sorting 39 (yeast) hs
U133_X3P:HS.9452.0.S1_3P_X_AT vacuolar protein sorting 39 (yeast) hs
U133_X3P:HS.9452.0.S1_3P_AT vacuolar protein sorting 39 (yeast) hs
HG-U95AV2:39130_AT vacuolar protein sorting 39 (yeast) hs
HG-U95C:54347_AT Vacuolar protein sorting 39 (yeast) hs
HU35KSUBC:RC_AA252815_AT Vacuolar protein sorting 39 (yeast) hs
MG-U74BV2:109747_AT vacuolar protein sorting 39 (yeast) mm
MOE430A:1451720_AT vacuolar protein sorting 39 (yeast) mm
MOUSE430A_2:1451720_AT vacuolar protein sorting 39 (yeast) mm
MOUSE430_2:1451720_AT vacuolar protein sorting 39 (yeast) mm
MOE430A:1425474_A_AT vacuolar protein sorting 39 (yeast) mm
MOUSE430A_2:1425474_A_AT vacuolar protein sorting 39 (yeast) mm
MOUSE430_2:1425474_A_AT vacuolar protein sorting 39 (yeast) mm
MU19KSUBB:TC31521_AT Vacuolar protein sorting 39 (yeast) (Vps39), transcript variant 1, mRNA mm
RG-U34A:RC_AI639080_AT vacuolar protein sorting 39 (yeast) (predicted) rn
RG-U34B:RC_AA998061_AT vacuolar protein sorting 39 (yeast) (predicted) rn
RG-U34C:RC_AA818856_AT vacuolar protein sorting 39 (yeast) (predicted) rn
RAE230A:1374068_AT vacuolar protein sorting 39 (yeast) (predicted) rn
RAT230_2:1374068_AT vacuolar protein sorting 39 (yeast) (predicted) rn
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5083 small GTPase regulator activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04720 Hypothetical protein T08G5.5 [Caenorhabditis elegans] ref|NP_506486.1| T08G5.5 [Caenorhabditis elegans] 0.0
blast CAE61026 Hypothetical protein CBG04769 [Caenorhabditis briggsae] 0.0
blast NP_849182 vacuolar protein sorting 39 isoform 2 [Mus musculus] gb|AAH07479.1| Vacuolar protein sorting 39, isoform 2 [Mus musculus] dbj|BAE42179.1| unnamed protein product [Mus musculus] dbj|BAC30140.1| unnamed protein product [Mus musculus] dbj|BAD88411.1| mVAM6 [Mus musculus] gb|AAL79767.1| VPS39 short isoform [Mus musculus] 1.0E-107
Sequence
Target Sequence 
>C. ELEGANS:179082_S_AT
tagactctactacaatgcacacgatgagaccaattcacaggtgtatctgatgctcttccg
aactctggtacatccaaatcagcaacaactgcactcgattccttatcacgccgattcgac
tccattcggatcatatcgtgatgatgtttctgaagcatcaacgttagtcaactctacatc
atcgtatcaaccagatgtcaatacagcaatcaagattctggcaaaacatgcagataaaat
cgatacagttggagcattgaatatgcttccagccaccactccgctcagagtcgtgttctc
ggcaattaacgcggtgattcaaactaccggacgacaagcgagcactcgaaaaatggaaaa
atctgtgtcccaatgtgcaatgtcaaagaagctggagcgcaaaaacaaggcgcaatctac
taaaatcatcgtcaatttctcaagtgaatgtgttgtttgtgagaagaaaatcgctgtaag
cgcatttgtccggtatccggatggtcgattggcacatctctactgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAGACTCTACTACAATGCACACGAT 461 651 2226 Antisense
ACAGGTGTATCTGATGCTCTTCCGA 653 107 2262 Antisense
CAGCAACAACTGCACTCGATTCCTT 55 205 2305 Antisense
GATTCGACTCCATTCGGATCATATC 182 433 2338 Antisense
GTCAACTCTACATCATCGTATCAAC 140 465 2392 Antisense
GCATTGAATATGCTTCCAGCCACCA 394 307 2479 Antisense
GTCGTGTTCTCGGCAATTAACGCGG 458 471 2515 Antisense
AAACTACCGGACGACAAGCGAGCAC 345 125 2546 Antisense
AATCTGTGTCCCAATGTGCAATGTC 319 167 2585 Antisense
TGTAAGCGCATTTGTCCGGTATCCG 427 557 2700 Antisense
TGGTCGATTGGCACATCTCTACTGC 60 553 2727 Antisense
Sequence Source Affymetrix Proprietary Database