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[174802_at] S. cerevisiae vacuolar sorting protein

Description CEK016G4R_rc /REP_DB=TREMBL Accession /GB=D32445 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk16g4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 36      4grp_highest_8_8 > 42      4grp_high_8_8 > 48      6grp_highest_nonorm > 77      6grp_total > 37      4grp_total > 62      6grp_highest_sub > Cu      6grp_cgc > 15      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 768
1 2 3 4 range
A 1570.3
(3)
P 		1070.2
(-0.9)
P 		1298.3
(0.9)
P 		802.6
(-3)
P 		768
B 1516.6
(3)
P 		1058.6
(-3)
P 		1178.5
(-1.4)
P 		1077.6
(-2.8)
P 		458
C 1418.7
(3)
P 		993.7
(-1.3)
P 		1228.7
(1.1)
P 		825.8
(-3)
P 		593
avr 1501.9
(3) 		1040.8
(-1.6) 		1235.2
(0.3) 		902
(-3) 		600

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 715
1 2 3 4 5 6 range
A 1652.3
(3)
P 		1391.7
(0.5)
P 		1054
(-2.7)
P 		1024.6
(-3)
P 		1309.9
(-0.3)
P 		1189.7
(-1.4)
P 		628
B 1601.6
(3)
P 		1399.7
(1.2)
P 		1031.8
(-2.1)
P 		1193.8
(-0.7)
P 		937.6
(-3)
P 		1357.5
(0.8)
P 		664
C 1226.7
(0.3)
P 		1331.3
(2.2)
P 		1193.5
(-0.3)
P 		1311.3
(1.8)
P 		1048.9
(-3)
P 		1375.9
(3)
P 		327
avr 1493.5
(3) 		1374.2
(1.2) 		1093.1
(-3) 		1176.6
(-1.7) 		1098.8
(-2.9) 		1307.7
(0.2) 		400
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 454
1 2 3 4 range
A 571.7
(3)
P 		232.3
(-1.5)
P 		339.4
(-0.1)
P 		117.5
(-3)
P 		454
B 483.6
(3)
P 		261.4
(-2.2)
P 		273.1
(-2)
P 		229.6
(-3)
P 		254
C 469.6
(3)
P 		285.7
(-0.3)
P 		428.2
(2.2)
P 		139.2
(-3)
P 		330
avr 508.3
(3) 		259.8
(-1.3) 		346.9
(0.2) 		162.1
(-3) 		346

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 328
1 2 3 4 5 6 range
A 304.6
(-1.3)
P 		495
(3)
P 		229.5
(-3)
P 		259.9
(-2.3)
P 		395.3
(0.7)
P 		289.6
(-1.6)
P 		266
B 557.3
(3)
P 		465.9
(1.2)
P 		250.5
(-3)
P 		316.2
(-1.7)
P 		380.9
(-0.4)
P 		506.2
(2)
P 		307
C 454.7
(2.8)
P 		406.2
(1.3)
P 		303.8
(-1.8)
P 		263.7
(-3)
P 		339.4
(-0.7)
P 		460.6
(3)
P 		197
avr 438.9
(2.5) 		455.7
(3) 		261.3
(-3) 		279.9
(-2.4) 		371.9
(0.4) 		418.8
(1.9) 		194
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174802_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20828
Sequence Type Exemplar sequence
Representative Public ID CEK016G4R NCBI
Target Description CEK016G4R_rc /REP_DB=TREMBL Accession /GB=D32445 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk16g4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_062779(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062779 NCBI Caenorhabditis elegans related to yeast Vacuolar Protein Sorting factor family member (vps-35) (vps-35) mRNA, complete cds. 11/11 None
F59G1.3 ENSEMBL cdna:known chromosome:CEL140:II:5907779:5911168:1 gene:F59G1.3 11/11 A 
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
chrII:5910770-5911155(+) 100.0 100.0
Public Domain and Genome References
Gene Title S. cerevisiae vacuolar sorting protein
Gene Symbol vps-35
Ensembl F59G1.3
Entrez Gene 174000 Entrez gene
SwissProt Q21053 EMBL-EBI
WormBase CE26372 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:262695_AT vacuolar protein sorting-associated protein 35 family protein / VPS35 family protein at
CANINE:1585854_AT similar to vacuolar protein sorting 35 cfa
CANINE:1585271_AT similar to vacuolar protein sorting 35 cfa
CANINE_2:CFA.13099.1.S1_S_AT similar to vacuolar protein sorting 35 cfa
CANINE_2:CFA.9366.1.A1_AT similar to vacuolar protein sorting 35 cfa
CANINE_2:CFA.9366.1.A1_S_AT similar to vacuolar protein sorting 35 cfa
DROSOPHILA_2:1625656_S_AT dm
DROSGENOME1:153904_AT dm
CHICKEN:GGAAFFX.11986.1.S1_S_AT vacuolar protein sorting 35 (yeast) gga
HG-U133_PLUS_2:233864_S_AT vacuolar protein sorting 35 (yeast) hs
HG-U133B:233864_S_AT vacuolar protein sorting 35 (yeast) hs
HG-U133B:222388_S_AT vacuolar protein sorting 35 (yeast) hs
HG-U133_PLUS_2:222388_S_AT vacuolar protein sorting 35 (yeast) hs
HG-U133_PLUS_2:217727_X_AT vacuolar protein sorting 35 (yeast) hs
HG-U133A:217727_X_AT vacuolar protein sorting 35 (yeast) hs
HG-U133A_2:217727_X_AT vacuolar protein sorting 35 (yeast) hs
HU35KSUBB:RC_W19227_AT vacuolar protein sorting 35 (yeast) hs
HG-U133_PLUS_2:222387_S_AT vacuolar protein sorting 35 (yeast) hs
HG-U133B:222387_S_AT vacuolar protein sorting 35 (yeast) hs
U133_X3P:G8922645_3P_A_AT vacuolar protein sorting 35 (yeast) hs
U133_X3P:G11875332_3P_A_AT vacuolar protein sorting 35 (yeast) hs
U133_X3P:HS2.384625.1.S1_3P_AT vacuolar protein sorting 35 (yeast) hs
U133_X3P:HS.264190.0.S1_3P_A_AT vacuolar protein sorting 35 (yeast) hs
HG-U133_PLUS_2:1561146_AT vacuolar protein sorting 35 (yeast) hs
HG-U95B:56344_AT vacuolar protein sorting 35 (yeast) hs
HG-U95E:90785_AT vacuolar protein sorting 35 (yeast) hs
HG-U95E:90787_G_AT vacuolar protein sorting 35 (yeast) hs
HG-U95B:55885_AT Vacuolar protein sorting 35 (yeast) hs
HG-U95D:77910_AT Hypothetical protein MGC34800 hs
HG-U95E:90789_AT Hypothetical protein MGC34800 hs
HU35KSUBC:RC_Z40752_AT Vacuolar protein sorting 35 (yeast) hs
MOUSE430A_2:1415784_AT vacuolar protein sorting 35 mm
MOUSE430_2:1415784_AT vacuolar protein sorting 35 mm
MOE430A:1415784_AT vacuolar protein sorting 35 mm
MOUSE430A_2:1415783_AT vacuolar protein sorting 35 mm
MOUSE430_2:1415783_AT vacuolar protein sorting 35 mm
MOE430A:1415783_AT vacuolar protein sorting 35 mm
MU11KSUBA:U47024_S_AT vacuolar protein sorting 35 mm
MG-U74AV2:92640_AT vacuolar protein sorting 35 mm
RG-U34B:RC_AA926047_AT vacuolar protein sorting 35 rn
RAE230A:1372806_AT vacuolar protein sorting 35 rn
RAT230_2:1372806_AT vacuolar protein sorting 35 rn
YEAST_2:1772684_AT Endosomal protein that is a subunit of the membrane-associated retromer complex essential for endosome-to-Golgi retrograde transport; forms a subcomplex with Vps26p and Vps29p that selects cargo proteins for endosome-to-Golgi retrieval Sc
Protein Similarities
Method ID Description E-Value
blast AAK31535 Related to yeast vacuolar protein sorting factor protein 35 [Caenorhabditis elegans] ref|NP_495180.1| related to yeast Vacuolar Protein Sorting factor family member (vps-35) [Caenorhabditis elegans] 0.0
blast T34314 hypothetical protein F59G1.3 - Caenorhabditis elegans 0.0
blast CAE59218 Hypothetical protein CBG02534 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005378 EMBL-EBI Vacuolar protein sorting-associated protein 35 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:174802_AT
accgcccattctaaatttgtgatagatttcctttattgaagatgtctctaaatatgcaat
tgtgatcagagccccccacctttcccgtcagaatattacccaaattttccggtttctcaa
atatttaaatatatactatacattgtgtgcatccaccttgccatatctctcatccatcat
accccgttctataatattttgaattttccttacaattattcgacgattttgagtttttaa
tggcgctataacttgggttctcatcaccactttgtgcacttatgttgaatgattaccctt
ccaaaacatga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCGCCCATTCTAAATTTGTGATAG 469 89 13 Antisense
GATTTCCTTTATTGAAGATGTCTCT 112 429 37 Antisense
TATGCAATTGTGATCAGAGCCCCCC 412 657 65 Antisense
TTCCCGTCAGAATATTACCCAAATT 301 695 94 Antisense
TATACATTGTGTGCATCCACCTTGC 118 661 149 Antisense
TCCATCATACCCCGTTCTATAATAT 291 591 185 Antisense
GACGATTTTGAGTTTTTAATGGCGC 524 377 234 Antisense
AATGGCGCTATAACTTGGGTTCTCA 577 161 251 Antisense
TAACTTGGGTTCTCATCACCACTTT 168 639 261 Antisense
CACCACTTTGTGCACTTATGTTGAA 143 203 277 Antisense
GAATGATTACCCTTCCAAAACATGA 391 331 299 Antisense
Sequence Source Affymetrix Proprietary Database