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[176941_at]

Description Y34D9A.B /REP_DB=WormBase Gene ID /WP=CE25235 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59432.1
Cluster 6grp_total > 17      4grp_total > 22      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 129
1 2 3 4 range
A 138.4
(3)
A 		74.6
(-3)
A 		94.4
(-1.1)
A 		113.7
(0.7)
A 		64
B 67.4
(2.3)
A 		55.4
(-1)
A 		47.8
(-3)
A 		70.2
(3)
A 		22
C 73.9
(0.1)
A 		41.1
(-1.5)
A 		9.1
(-3)
A 		135.5
(3)
A 		126
avr 93.2
(1.6) 		57
(-2.3) 		50.4
(-3) 		106.5
(3) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 94
1 2 3 4 5 6 range
A 61.8
(1.5)
A 		75.4
(3)
A 		53.2
(0.6)
A 		32.3
(-1.7)
A 		20.8
(-3)
A 		56
(0.9)
A 		55
B 115
(3)
A 		41.9
(-2)
A 		63.3
(-0.5)
A 		53.7
(-1.2)
A 		27.1
(-3)
A 		58.5
(-0.9)
A 		88
C 110.5
(3)
P 		62.2
(-0.3)
A 		23.4
(-3)
A 		58.8
(-0.6)
A 		74.7
(0.5)
A 		39.7
(-1.9)
A 		87
avr 95.8
(3) 		59.8
(-0.9) 		46.6
(-2.4) 		48.3
(-2.2) 		40.9
(-3) 		51.4
(-1.9) 		55
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 50.4
(3)
A 		16.2
(-3)
A 		24.7
(-1.5)
A 		16.6
(-2.9)
A 		34
B 21.5
(3)
A 		13.7
(-1.5)
A 		11.1
(-3)
A 		15
(-0.8)
A 		10
C 24.5
(3)
A 		11.8
(-0.6)
A 		3.2
(-3)
A 		22.8
(2.5)
A 		21
avr 32.1
(3) 		13.9
(-2.7) 		13
(-3) 		18.1
(-1.4) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 35
1 2 3 4 5 6 range
A 11.4
(-1.5)
A 		26.8
(3)
A 		11.6
(-1.4)
A 		8.2
(-2.4)
A 		6.3
(-3)
A 		13.6
(-0.9)
A 		21
B 40
(3)
A 		13.9
(-2.4)
A 		15.4
(-2.1)
A 		14.2
(-2.3)
A 		11
(-3)
A 		21.8
(-0.8)
A 		29
C 41
(3)
P 		19
(-0.8)
A 		6
(-3)
A 		11.8
(-2)
A 		24.2
(0.1)
A 		13.3
(-1.7)
A 		35
avr 30.8
(3) 		19.9
(-0.3) 		11
(-3) 		11.4
(-2.9) 		13.8
(-2.2) 		16.2
(-1.4) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176941_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18643
Sequence Type Exemplar sequence
Representative Public ID Y34D9A.B NCBI
Target Description Y34D9A.B /REP_DB=WormBase Gene ID /WP=CE25235 /CHR=1 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59432.1
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 
SNAP00000009167 ENSEMBL cdna:SNAP chromosome:CEL140:I:1054364:1061761:-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
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000009192 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:1054363-1062411(-) 89.25 100.0
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 CAE74360 Hypothetical protein CBG22083 [Caenorhabditis briggsae] 1.0E-140
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
Protein Domains
Database ID Description E-Value
Pfam IPR003959 EMBL-EBI AAA ATPase, central region 3.7E-77
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:176941_AT
tcaagaatctgtttgcgttggcccgcgagcacaagccatcgattatttttattgatgagt
ttttgcctaattcctattcgaatttccgccaatcggctttgttcgatggagcgcgcttgc
accaattcaatacatatttttccaacaacagacgtttcgagaagcgaatctacattccac
tgcccgacattcacgctcgcaaagaaatgttccgaatcgacgttggcaagaactacaaca
cgctgacagatcaggatttcaaggtgctcgccgagcgatgtgaaggatattcgggttatg
atatcagtattcttgtcaaggatgcactcatgcaacccgtacgacgagtacaatcggcca
cacatttcaaacacgtcagcggtccatcaccaaaggatccaaatgtgattgcacatgatc
tactgacaccgtgcagtccaggagatccacacgcgattgcaatgaattggttggatgttc
caggggataagctggcgaatccaccactttccatgcaagacatttcgcgttcgctggcat
ccgtaaaaccgacagtcaacaacactgatctcgaccgtttggaggcgttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAAGAATCTGTTTGCGTTGGCCCG 1 629 488 Antisense
GAATTTCCGCCAATCGGCTTTGTTC 374 325 567 Antisense
TCAGGATTTCAAGGTGCTCGCCGAG 504 623 738 Antisense
GTACAATCGGCCACACATTTCAAAC 648 459 835 Antisense
TTTCAAACACGTCAGCGGTCCATCA 601 671 852 Antisense
ATTGCACATGATCTACTGACACCGT 122 7 895 Antisense
TGACACCGTGCAGTCCAGGAGATCC 62 571 911 Antisense
ATAAGCTGGCGAATCCACCACTTTC 277 25 974 Antisense
CATGCAAGACATTTCGCGTTCGCTG 339 207 999 Antisense
CGTTCGCTGGCATCCGTAAAACCGA 492 241 1015 Antisense
TGATCTCGACCGTTTGGAGGCGTTC 116 563 1053 Antisense
Sequence Source Affymetrix Proprietary Database