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[173421_at]

Description AV181201_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=g4579709 /5_PRIME_EXT_DB=GenBank Identifier /GB=AV181201 /CHR=4 /FEA=Genomic Cluster /PROTEIN_GB=BAA75066.1 /DEF=Vha3 protein; Caenorhabditis elegans cDNA clone:yk617c8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 26      4grp_high_8_8 > 59      6grp_highest_nonorm > 50      6grp_total > 05      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 983
1 2 3 4 range
A 1333.6
(3)
P 		429.7
(-3)
P 		976.6
(0.6)
P 		463.6
(-2.8)
P 		904
B 684.2
(-0.8)
P 		934.4
(0.9)
P 		1253.1
(3)
P 		350.9
(-3)
P 		902
C 890.6
(0.2)
P 		1282.3
(3)
P 		1099.9
(1.7)
P 		448.9
(-3)
P 		833
avr 969.5
(1.8) 		882.1
(1) 		1109.9
(3) 		421.1
(-3) 		689

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1440
1 2 3 4 5 6 range
A 497.3
(-1.4)
P 		1051
(3)
P 		384.1
(-2.3)
P 		300.4
(-3)
P 		353.9
(-2.6)
P 		328.2
(-2.8)
P 		751
B 634.8
(3)
P 		568.4
(2.1)
P 		317.3
(-1.3)
P 		418.9
(0)
P 		308.6
(-1.5)
P 		196
(-3)
P 		439
C 1636.2
(3)
P 		487.4
(-1.8)
P 		526.5
(-1.6)
P 		405.8
(-2.2)
P 		770.9
(-0.6)
P 		203.3
(-3)
P 		1433
avr 922.8
(3) 		702.3
(1.1) 		409.3
(-1.5) 		375
(-1.8) 		477.8
(-0.9) 		242.5
(-3) 		680
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 418
1 2 3 4 range
A 485.6
(3)
P 		93.3
(-2.6)
P 		255.3
(-0.3)
P 		67.9
(-3)
P 		418
B 218.2
(1)
P 		230.8
(1.3)
P 		290.4
(3)
P 		74.8
(-3)
P 		216
C 294.8
(1.3)
P 		368.7
(2.7)
P 		383.4
(3)
P 		75.7
(-3)
P 		308
avr 332.9
(3) 		230.9
(0.6) 		309.7
(2.5) 		72.8
(-3) 		260

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 539
1 2 3 4 5 6 range
A 91.7
(-2.7)
P 		373.8
(3)
P 		83.6
(-2.9)
P 		76.2
(-3)
P 		106.8
(-2.4)
P 		79.9
(-2.9)
P 		298
B 220.9
(3)
P 		189.2
(1.7)
P 		77.1
(-2.8)
P 		111
(-1.5)
P 		125.4
(-0.9)
P 		73.1
(-3)
P 		148
C 606.5
(3)
P 		148.7
(-2.1)
P 		134
(-2.3)
P 		81.6
(-2.8)
P 		249.5
(-1)
P 		68
(-3)
P 		539
avr 306.4
(3) 		237.2
(1.2) 		98.2
(-2.4) 		89.6
(-2.6) 		160.6
(-0.8) 		73.7
(-3) 		233
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173421_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24930
Sequence Type Exemplar sequence
Representative Public ID AV181201 NCBI
Target Description AV181201_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=g4579709 /5_PRIME_EXT_DB=GenBank Identifier /GB=AV181201 /CHR=4 /FEA=Genomic Cluster /PROTEIN_GB=BAA75066.1 /DEF=Vha3 protein; Caenorhabditis elegans cDNA clone:yk617c8 : 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_067787(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067787 NCBI Caenorhabditis elegans Vacuolar H ATPase family member (vha-3) (vha-3) mRNA, complete cds. 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
chrIV:2314594-2315996(-) 67.05 100.0
Public Domain and Genome References
Gene Title
Gene Symbol vha-3
Entrez Gene 177018 Entrez gene
SwissProt P34546 EMBL-EBI
WormBase CE06290 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:262924_S_AT vacuolar ATP synthase 16 kDa proteolipid subunit 2 / V-ATPase 16 kDa proteolipid subunit 2 (AVAP2) (AVA-P2) at
ATGENOME1:15584_S_AT vacuolar ATP synthase 16 kDa proteolipid subunit 2 / V-ATPase 16 kDa proteolipid subunit 2 (AVAP2) (AVA-P2) at
CANINE:1583550_S_AT similar to Vacuolar ATP synthase 16 kDa proteolipid subunit cfa
CANINE:1583549_AT similar to Vacuolar ATP synthase 16 kDa proteolipid subunit cfa
CANINE_2:CFAAFFX.29582.1.S1_S_AT similar to Vacuolar ATP synthase 16 kDa proteolipid subunit cfa
DROSOPHILA_2:1632117_S_AT Vacuolar H+ ATPase 16kD subunit dm
DROSGENOME1:141528_AT Vacuolar H+ ATPase 16kD subunit dm
HG-U133_PLUS_2:200954_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133A:200954_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133A_2:200954_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HUGENEFL:M62762_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:G4502312_3P_X_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:G4502312_3P_S_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:G4502312_3P_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:4901150C_3P_X_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:4901150C_3P_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:36994_3P_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:200954_3P_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133A_2:36994_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-FOCUS:36994_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133_PLUS_2:36994_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133A:36994_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U95AV2:36994_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U95D:75090_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:HS2.435455.1.S1_3P_S_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
U133_X3P:HS.315448.0.A1_3P_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HG-U133_PLUS_2:1557986_S_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
HU35KSUBD:RC_D20331_AT ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c hs
MG-U74AV2:96919_AT ATPase, H+ transporting, V0 subunit C mm
MOE430A:1416392_A_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430_2:1416392_A_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430A_2:1416392_A_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430_2:1435732_X_AT ATPase, H+ transporting, V0 subunit C mm
MOE430A:1435732_X_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430A_2:1435732_X_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430_2:1438925_X_AT ATPase, H+ transporting, V0 subunit C mm
MOE430A:1438925_X_AT ATPase, H+ transporting, V0 subunit C mm
MOUSE430A_2:1438925_X_AT ATPase, H+ transporting, V0 subunit C mm
MU11KSUBA:M64298_S_AT ATPase, H+ transporting, V0 subunit C mm
RG-U34A:D10874_G_AT ATPase, H+ transporting, V0 subunit C rn
RG-U34A:D10874_AT ATPase, H+ transporting, V0 subunit C rn
RG-U34C:RC_AI177126_S_AT ATPase, H+ transporting, V0 subunit C rn
RAE230A:1398755_AT ATPase, H+ transporting, V0 subunit C rn
RAT230_2:1398755_AT ATPase, H+ transporting, V0 subunit C rn
YEAST_2:1780211_AT Proteolipid subunit of the vacuolar H(+)-ATPase V0 sector (subunit c; dicyclohexylcarbodiimide binding subunit); required for vacuolar acidification and important for copper and iron metal ion homeostasis Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
15986 ATP synthesis coupled proton transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16469 proton-transporting two-sector ATPase complex inferred from electronic annotation QuickGO AmiGO
220 hydrogen-transporting ATPase V0 domain inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
46933 hydrogen-transporting ATP synthase activity, rotational mechanism inferred from electronic annotation QuickGO AmiGO
46961 hydrogen-transporting ATPase activity, rotational mechanism inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA82355 Hypothetical protein R10E11.2 [Caenorhabditis elegans] ref|NP_499166.1| Vacuolar H ATPase family member (vha-2) [Caenorhabditis elegans] ref|NP_500188.1| Vacuolar H ATPase family member (vha-3) [Caenorhabditis elegans] gb|AAF59473.1| Vacuolar h atpase protein 3 [Caenorhabditis elegans] sp|P34546|VATL2_CAEEL Vacuolar ATP synthase 16 kDa proteolipid subunit 2/3 dbj|BAA22596.1| VHA-2 [Caenorhabditis elegans] dbj|BAA75066.1| Vha3 protein [Caenorhabditis elegans] 3.0E-70
blast CAE70304 Hypothetical protein CBG16825 [Caenorhabditis briggsae] emb|CAE65134.1| Hypothetical protein CBG10000 [Caenorhabditis briggsae] 1.0E-68
blast Q17046 Vacuolar ATP synthase 16 kDa proteolipid subunit gb|AAA29372.1| gene-12 encoded protein 1.0E-66
Protein Domains
Database ID Description E-Value
Pfam IPR002379 EMBL-EBI H+-transporting two-sector ATPase, C subunit 2.7E-16
Pfam IPR002379 EMBL-EBI H+-transporting two-sector ATPase, C subunit 1.4E-25
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500188.1 4 15-37,58-78,98-120,133-155
Sequence
Target Sequence 
>C. ELEGANS:173421_AT
ttccaaactatccgtgaaaatcgataaaatacctgtttttccgttaaaaattaataaaaa
cctgatttttcctgtttttcatgaaaaattacaaaaaaatcgataaaattcgtggttttt
ttgttgatttttccgtaaaaatcgataaaattcgtggttttttttgtggattttttcgtg
aaaaatcgataaaatttgatcaaaactttttttttccaaattttctctgaaaatcgataa
aataccagtttttttctgttttttcgctgaaaattaccaaaaaatcacctaattaccgct
caaaaacccaaattttccaattttcccgcctaaaaatcgataattcactcaattttcccc
gatttttcaccgattttctccggaatttctcgtttttttccattttttctccaatttttc
agtctaaaccgctgtgattttttttctataacattcctatattctcctaggagtttctct
tttttttttaatctcacacaaaatttctatattttccctag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCCAAACTATCCGTGAAAATCGAT 76 611 793 Antisense
CGTGAAAATCGATAAAATACCTGTT 320 239 805 Antisense
CAAAAAATCACCTAATTACCGCTCA 53 191 1070 Antisense
TCACCGATTTTCTCCGGAATTTCTC 442 607 1159 Antisense
TCTCCAATTTTTCAGTCTAAACCGC 601 259 1200 Antisense
CAGTCTAAACCGCTGTGATTTTTTT 510 203 1212 Antisense
GTGATTTTTTTTCTATAACATTCCT 276 477 1226 Antisense
CTATAACATTCCTATATTCTCCTAG 177 225 1238 Antisense
TATTCTCCTAGGAGTTTCTCTTTTT 460 663 1252 Antisense
TTTAATCTCACACAAAATTTCTATA 564 673 1279 Antisense
CACAAAATTTCTATATTTTCCCTAG 52 195 1289 Antisense
Sequence Source Affymetrix Proprietary Database