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[176156_at]

Description Y34D9A.A /REP_DB=WormBase Gene ID /WP=CE26059 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_total > 58      4grp_total > 30      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 138.5
(3)
A 		93.1
(0.9)
A 		9.7
(-3)
A 		47.4
(-1.2)
A 		129
B 122.4
(3)
A 		66.6
(0.2)
A 		4.5
(-3)
A 		90.3
(1.4)
A 		118
C 96.8
(2.4)
A 		32.1
(-3)
A 		61.8
(-0.5)
A 		103.8
(3)
A 		72
avr 119.2
(3) 		63.9
(-0.5) 		25.3
(-3) 		80.5
(0.5) 		94

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 91
1 2 3 4 5 6 range
A 61.1
(3)
A 		3.4
(-3)
A 		8.8
(-2.4)
A 		34.7
(0.3)
A 		3.2
(-3)
A 		49.1
(1.8)
A 		58
B 50.5
(0.3)
A 		6.1
(-2.8)
A 		7.6
(-2.7)
A 		3.7
(-2.9)
A 		2.6
(-3)
A 		90.1
(3)
A 		88
C 29.9
(-1.2)
A 		28.8
(-1.3)
A 		3.3
(-3)
A 		18.7
(-2)
A 		4.8
(-2.9)
A 		93.9
(3)
A 		91
avr 47.2
(0.5) 		12.8
(-2.2) 		6.6
(-2.7) 		19
(-1.7) 		3.5
(-3) 		77.7
(3) 		74
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 50.4
(3)
A 		20.2
(-0.8)
A 		2.5
(-3)
A 		6.9
(-2.4)
A 		48
B 39
(3)
A 		16.4
(-0.6)
A 		1
(-3)
A 		19.2
(-0.1)
A 		38
C 32.1
(3)
A 		9.2
(-3)
A 		21.5
(0.2)
A 		17.5
(-0.8)
A 		23
avr 40.5
(3) 		15.3
(-1.7) 		8.3
(-3) 		14.5
(-1.8) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 33
1 2 3 4 5 6 range
A 11.3
(2.7)
A 		1.2
(-2.9)
A 		1.9
(-2.5)
A 		8.8
(1.3)
A 		1
(-3)
A 		11.9
(3)
A 		11
B 17.6
(0.1)
A 		2
(-2.8)
A 		1.8
(-2.9)
A 		1
(-3)
A 		1.1
(-3)
A 		33.6
(3)
A 		33
C 11.1
(-1)
A 		8.8
(-1.4)
A 		0.8
(-3)
A 		3.8
(-2.4)
A 		1.6
(-2.8)
A 		31.4
(3)
A 		31
avr 13.3
(-0) 		4
(-2.3) 		1.5
(-2.9) 		4.5
(-2.2) 		1.2
(-3) 		25.6
(3) 		24
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176156_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18632
Sequence Type Exemplar sequence
Representative Public ID Y34D9A.A NCBI
Target Description Y34D9A.A /REP_DB=WormBase Gene ID /WP=CE26059 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster Evidence This cluster is supported by a 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_058415(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058415 NCBI Caenorhabditis elegans Y34D9A.10 (Y34D9A.10) mRNA, complete cds. 10/11 A 
SNAP00000009173 ENSEMBL cdna:SNAP chromosome:CEL140:I:1063796:1066770:-1 11/11 None
GENEFINDER00000009198 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:1065980:1067220:-1 10/11 None
Y34D9A.10.2 ENSEMBL cdna:known chromosome:CEL140:I:1053923:1066903:-1 gene:Y34D9A.10 10/11 None
Y34D9A.10.1 ENSEMBL cdna:known chromosome:CEL140:I:1053923:1066901:-1 gene:Y34D9A.10 10/11 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
chrI:1065979-1066871(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y34D9A.10
Entrez Gene 189590 Entrez gene
SwissProt Q9BL83 EMBL-EBI
WormBase CE39043 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.1079.1.S1_AT similar to vacuolar protein sorting factor 4B cfa
DROSOPHILA_2:1624050_AT dm
DROSGENOME1:151868_AT dm
CHICKEN:GGA.8210.1.S1_S_AT vacuolar protein sorting 4B (yeast) gga
CHICKEN:GGAAFFX.21211.1.S1_S_AT vacuolar protein sorting 4B (yeast) gga
HG-U95AV2:37804_AT vacuolar protein sorting 4B (yeast) hs
HU35KSUBA:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HU35KSUBB:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HU35KSUBC:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HU35KSUBD:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HUGENEFL:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HC-G110:HUM_ALU_AT vacuolar protein sorting 4B (yeast) hs
HU35KSUBC:RC_AA357927_AT vacuolar protein sorting 4B (yeast) hs
HG-U133A:218171_AT vacuolar protein sorting 4B (yeast) hs
HG-U133_PLUS_2:218171_AT vacuolar protein sorting 4B (yeast) hs
HG-FOCUS:218171_AT vacuolar protein sorting 4B (yeast) hs
HG-U133A_2:218171_AT vacuolar protein sorting 4B (yeast) hs
U133_X3P:G11225484_3P_AT vacuolar protein sorting 4B (yeast) hs
HG-U95B:54107_AT vacuolar protein sorting 4B (yeast) hs
MU11KSUBA:U10119_S_AT vacuolar protein sorting 4b (yeast) mm
MG-U74AV2:93337_AT vacuolar protein sorting 4b (yeast) mm
MOE430A:1417007_A_AT vacuolar protein sorting 4b (yeast) mm
MOUSE430A_2:1417007_A_AT vacuolar protein sorting 4b (yeast) mm
MOUSE430_2:1417007_A_AT vacuolar protein sorting 4b (yeast) mm
MOE430B:1460104_AT vacuolar protein sorting 4b (yeast) mm
MOUSE430_2:1460104_AT vacuolar protein sorting 4b (yeast) mm
RG-U34C:AA848378_AT vacuolar protein sorting 4b (yeast) (predicted) rn
RAE230A:1372834_AT vacuolar protein sorting 4b (yeast) (predicted) rn
RAT230_2:1372834_AT vacuolar protein sorting 4b (yeast) (predicted) rn
YEAST_2:1778299_AT AAA-type ATPase required for efficient late endosome to vacuole transport; catalyzes the release of an endosomal membrane-associated class E VPS protein complex; cytoplasmic protein that is also associated with an endosomal compartment Sc
Protein Similarities
Method ID Description E-Value
blast NP_490816 Y34D9A.10 [Caenorhabditis elegans] gb|AAK29883.3| Hypothetical protein Y34D9A.10 [Caenorhabditis elegans] 0.0
blast XP_857162 PREDICTED: similar to vacuolar protein sorting factor 4B isoform 3 [Canis familiaris] 1.0E-134
blast XP_393250 PREDICTED: similar to ENSANGP00000019192 [Apis mellifera] 1.0E-132
blast NP_490816 Y34D9A.10 [Caenorhabditis elegans] gb|AAK29883.3| Hypothetical protein Y34D9A.10 [Caenorhabditis elegans] 3.0E-63
Protein Domains
Database ID Description E-Value
Pfam IPR007330 EMBL-EBI MIT 7.2E-27
Pfam IPR007330 EMBL-EBI MIT 1.4E-30
Pfam IPR007330 EMBL-EBI MIT 1.4E-30
Pfam IPR003959 EMBL-EBI AAA ATPase, central region 8.1E-35
Pfam IPR003959 EMBL-EBI AAA ATPase, central region 1.3E-13
Sequence
Target Sequence 
>C. ELEGANS:176156_AT
aaagccaccgaggaggatacagccggcagatacgaccaagcgctgagattatacgatcag
gccattgaatacttccttcatgcgataaaatacgagtcacaaggcgataaacagcgtaat
gcgattcgtgacaaagtcgggcagtatttgaatcgcgccgagcagatcaaaacccatctg
aaagacggaaaaacgcagaaaaagccggtgaaagacgggaaagacgattccgacgaggat
gaggacaagaaaaagtttcaggacaaactgtcgggcgcaattgtgatggagaagccgaat
gtcaagtggaccgatattgcaggacttgagggagcgaaagaggcgctcaaggaggccgtc
attcttccaatcaaatttccacagcttttcactggtgag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAGCCACCGAGGAGGATACAGCCG 356 123 55 Antisense
TACAGCCGGCAGATACGACCAAGCG 361 641 72 Antisense
GGCCATTGAATACTTCCTTCATGCG 36 545 114 Antisense
AAACAGCGTAATGCGATTCGTGACA 202 129 163 Antisense
AAGTCGGGCAGTATTTGAATCGCGC 197 157 188 Antisense
GAATCGCGCCGAGCAGATCAAAACC 313 329 204 Antisense
ACTGTCGGGCGCAATTGTGATGGAG 510 95 321 Antisense
GGAGAAGCCGAATGTCAAGTGGACC 560 519 342 Antisense
GTGGACCGATATTGCAGGACTTGAG 692 489 360 Antisense
AGAGGCGCTCAAGGAGGCCGTCATT 663 67 393 Antisense
ATTTCCACAGCTTTTCACTGGTGAG 462 17 429 Antisense
Sequence Source Affymetrix Proprietary Database