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[193422_s_at] Vacuolar ATP synthase subunit

Description R10E11.2 /REP_DB=WormBase Gene ID /WP=CE06290 /GEN=vha-2 /TR=SW:P34546 /GB=CAA82355.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Vacuolar ATP synthase subunit
Cluster 6grp_highest_10_10 > 33      6grp_high1_10_10 > 22      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 16      6grp_total > 22      4grp_total > 19      6grp_highest_sub > 02      6grp_cgc > 62      6grp_high1_sub > De      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2874
1 2 3 4 range
A 11597.3
(-2.6)
P 		13223
(3)
P 		11469.8
(-3)
P 		12610.3
(0.9)
P 		1753
B 12563
(2.2)
P 		11823.5
(-3)
P 		12493.8
(1.7)
P 		12676.3
(3)
P 		853
C 11209.6
(-2)
P 		11303.1
(-1.8)
P 		10727.1
(-3)
P 		13601.2
(3)
P 		2874
avr 11790
(-2) 		12116.5
(-0.6) 		11563.6
(-3) 		12962.6
(3) 		1399

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5657
1 2 3 4 5 6 range
A 9048.1
(1.2)
P 		10297.6
(3)
P 		8669.5
(0.7)
P 		7481.8
(-1.1)
P 		6133.7
(-3)
P 		6153.6
(-3)
P 		4164
B 7285.3
(0.3)
P 		9457.1
(3)
P 		8741.1
(2.1)
P 		7509.6
(0.6)
P 		6601.2
(-0.6)
P 		4640.3
(-3)
P 		4817
C 9170.7
(2.5)
P 		9454.6
(3)
P 		9365.9
(2.8)
P 		7620
(-0.3)
P 		6710
(-2)
P 		6155.4
(-3)
P 		3299
avr 8501.4
(1.2) 		9736.4
(3) 		8925.5
(1.8) 		7537.1
(-0.2) 		6481.6
(-1.8) 		5649.8
(-3) 		4087
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2377
1 2 3 4 range
A 4222.6
(3)
P 		2870.4
(-0.4)
P 		2998.4
(-0.1)
P 		1845.9
(-3)
P 		2377
B 4006.2
(3)
P 		2920.1
(-2)
P 		2895.1
(-2.1)
P 		2701.3
(-3)
P 		1305
C 3710.7
(2.9)
P 		3249.7
(1)
P 		3738.7
(3)
P 		2293.4
(-3)
P 		1445
avr 3979.8
(3) 		3013.4
(-0.4) 		3210.7
(0.3) 		2280.2
(-3) 		1700

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2164
1 2 3 4 5 6 range
A 1667.9
(-2.5)
P 		3662.3
(3)
P 		1888
(-1.9)
P 		1897.6
(-1.9)
P 		1850.9
(-2)
P 		1498.2
(-3)
P 		2164
B 2534.9
(0.4)
P 		3147.9
(3)
P 		2122.6
(-1.3)
P 		1989
(-1.9)
P 		2682
(1)
P 		1730.3
(-3)
P 		1418
C 3399.2
(3)
P 		2884.9
(1.3)
P 		2383.8
(-0.3)
P 		1532.4
(-3)
P 		2171.3
(-0.9)
P 		2060.6
(-1.3)
P 		1867
avr 2534
(0.1) 		3231.7
(3) 		2131.5
(-1.5) 		1806.3
(-2.8) 		2234.7
(-1.1) 		1763
(-3) 		1469
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193422_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7000
Sequence Type Exemplar sequence
Representative Public ID R10E11.2 NCBI
Target Description R10E11.2 /REP_DB=WormBase Gene ID /WP=CE06290 /GEN=vha-2 /TR=SW:P34546 /GB=CAA82355.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Vacuolar ATP synthase subunit
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_066765(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066765 NCBI Caenorhabditis elegans Vacuolar H ATPase family member (vha-2) (vha-2) mRNA, complete cds. 11/11 None
SNAP00000016241 ENSEMBL cdna:SNAP chromosome:CEL140:III:9782060:9782642:1 11/11 None
GENEFINDER00000016248 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9782060:9782642:1 11/11 None
R10E11.2.2 ENSEMBL cdna:known chromosome:CEL140:III:9782052:9783118:1 gene:R10E11.2 11/11 A 
R10E11.2.1 ENSEMBL cdna:known chromosome:CEL140:III:9782059:9783118:1 gene:R10E11.2 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
chrIII:9782055-9782638(+) 100.0 100.0
Public Domain and Genome References
Gene Title Vacuolar ATP synthase subunit
Gene Symbol vha-2
Ensembl R10E11.2
Entrez Gene 187779 Entrez gene
SwissProt P34546 EMBL-EBI
WormBase CE06290 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:16969_I_AT vacuolar ATP synthase 16 kDa proteolipid subunit 5 / V-ATPase 16 kDa proteolipid subunit 5 (AVAP5) at
ATH1-121501:263267_AT vacuolar ATP synthase 16 kDa proteolipid subunit 5 / V-ATPase 16 kDa proteolipid subunit 5 (AVAP5) at
DROSOPHILA_2:1624514_AT dm
YEAST_2:1773107_AT Vacuolar ATPase V0 domain subunit c', involved in proton transport activity; hydrophobic integral membrane protein (proteolipid) containing four transmembrane segments; N and C termini are in the vacuolar lumen 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
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_499166.1 4 15-37,58-78,98-120,133-155
R10E11.2.2 4 15-37,58-78,98-120,133-155
R10E11.2.1 4 15-37,58-78,98-120,133-155
SNAP00000016241 4 15-37,58-78,98-120,133-155
GENEFINDER00000016248 4 15-37,58-78,98-120,133-155
Sequence
Target Sequence 
>C. ELEGANS:193422_S_AT
ctacgctccattcttcggatacatgggagccgcttctgcccagatcttcaccgttttggg
agcagcttatggaactgccaagtccgccgtcggtatttgctcaatgggtgtgatgagacc
tgagctcatcatgaaatcggtcattccagttattatggctggtatcatcggtatctacgg
attggtcgtggctatggttctcaagggaaaggtcacatctgcttcagctggttatgacct
caacaagggattcgctcacttggcagctggacttacctgcggactttgcggacttggagc
tggatacgctatcggaattgtcggagacgccggagtccgtggaactgcccaacagccaag
actcttcgtcggaatgatccttatcctcattttctct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTACGCTCCATTCTTCGGATACATG 516 225 48 Antisense
GATCTTCACCGTTTTGGGAGCAGCT 658 417 90 Antisense
AGCTTATGGAACTGCCAAGTCCGCC 334 77 111 Antisense
CGCCGTCGGTATTTGCTCAATGGGT 59 239 132 Antisense
GATTGGTCGTGGCTATGGTTCTCAA 315 435 227 Antisense
AGGGAAAGGTCACATCTGCTTCAGC 460 53 251 Antisense
ATCTGCTTCAGCTGGTTATGACCTC 85 35 264 Antisense
ACTTGGCAGCTGGACTTACCTGCGG 219 105 305 Antisense
CGGACTTTGCGGACTTGGAGCTGGA 374 241 327 Antisense
AACAGCCAAGACTCTTCGTCGGAAT 280 133 398 Antisense
AATGATCCTTATCCTCATTTTCTCT 151 165 420 Antisense
Sequence Source Affymetrix Proprietary Database