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[177110_s_at]

Description Y38F2AL.C /REP_DB=WormBase Gene ID /WP=CE06290 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59473.1
Cluster 4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_total > 55      4grp_total > 59      6grp_cgc > 46      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2042
1 2 3 4 range
A 4101.5
(2.9)
P 		3906.4
(2.3)
P 		4121.9
(3)
P 		2336.4
(-3)
P 		1786
B 2804.6
(-1.7)
P 		3445.5
(3)
P 		3192.2
(1.1)
P 		2624.3
(-3)
P 		821
C 3408.3
(1.5)
P 		3849.7
(3)
P 		3695.8
(2.5)
P 		2079.8
(-3)
P 		1770
avr 3438.1
(1.7) 		3733.9
(3) 		3670
(2.7) 		2346.8
(-3) 		1387

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1327
1 2 3 4 5 6 range
A 994.1
(0.3)
P 		740
(-1)
A 		1510
(3)
P 		478
(-2.4)
A 		356.5
(-3)
A 		869.4
(-0.3)
P 		1154
B 1233.7
(1.4)
P 		454.9
(-2.1)
M 		964.2
(0.2)
P 		952.4
(0.1)
P 		256.7
(-3)
A 		1583.5
(3)
P 		1327
C 567
(-1)
M 		588.9
(-0.8)
M 		1063.2
(3)
P 		528.7
(-1.3)
A 		320.4
(-3)
A 		1058.7
(3)
P 		743
avr 931.6
(1.3) 		594.6
(-1) 		1179.1
(3) 		653
(-0.6) 		311.2
(-3) 		1170.5
(2.9) 		868
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1151
1 2 3 4 range
A 1493.3
(3)
P 		848
(-0.4)
P 		1077.5
(0.8)
P 		342
(-3)
P 		1151
B 894.4
(3)
P 		851
(2.2)
P 		739.7
(0.2)
P 		559.2
(-3)
P 		335
C 1128.3
(2)
P 		1106.8
(1.8)
P 		1288.1
(3)
P 		350.7
(-3)
P 		937
avr 1172
(3) 		935.3
(1.1) 		1035.1
(1.9) 		417.3
(-3) 		755

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 487
1 2 3 4 5 6 range
A 183.3
(-0.9)
P 		263.2
(1.2)
A 		328.8
(3)
P 		121.2
(-2.6)
A 		107.6
(-3)
A 		211.7
(-0.2)
P 		221
B 429.3
(1)
P 		151.4
(-2.4)
M 		234.1
(-1.4)
P 		252.3
(-1.2)
P 		104.3
(-3)
A 		590.5
(3)
P 		486
C 210.2
(-0.5)
M 		179.7
(-1.2)
M 		270.6
(1)
P 		106.3
(-2.9)
A 		103.7
(-3)
A 		354.4
(3)
P 		251
avr 274.3
(0.6) 		198.1
(-1) 		277.8
(0.7) 		159.9
(-1.8) 		105.2
(-3) 		385.5
(3) 		280
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 177110_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19324
Sequence Type Exemplar sequence
Representative Public ID Y38F2AL.C NCBI
Target Description Y38F2AL.C /REP_DB=WormBase Gene ID /WP=CE06290 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59473.1
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_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 
SNAP00000023928 ENSEMBL cdna:SNAP chromosome:CEL140:IV:2308245:2315944:-1 11/11 None
GENEFINDER00000023937 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:2315459:2317277:-1 11/11 None
Y38F2AL.4 ENSEMBL cdna:known chromosome:CEL140:IV:2315459:2315944:-1 gene:Y38F2AL.4 11/11 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
chrIV:2315464-2315950(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol vha-3
Ensembl Y38F2AL.4
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 NP_001023451 Vacuolar H ATPase family member (vha-11) [Caenorhabditis elegans] gb|AAF59474.3| Vacuolar h atpase protein 11, isoform a [Caenorhabditis elegans] sp|Q9XXU9|VATC_CAEEL Vacuolar ATP synthase subunit C (V-ATPase C subunit) (Vacuolar proton pump C subunit) dbj|BAA75067.1| Vha11 protein [Caenorhabditis elegans] 0.0
blast CAE70305 Hypothetical protein CBG16826 [Caenorhabditis briggsae] 0.0
blast AAH83532 Atp6v1c1l protein [Danio rerio] ref|XP_686493.1| PREDICTED: similar to Atp6v1c1l protein [Danio rerio] 1.0E-123
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 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] 8.0E-70
blast CAE70304 Hypothetical protein CBG16825 [Caenorhabditis briggsae] emb|CAE65134.1| Hypothetical protein CBG10000 [Caenorhabditis briggsae] 1.0E-68
blast CAE70304 Hypothetical protein CBG16825 [Caenorhabditis briggsae] emb|CAE65134.1| Hypothetical protein CBG10000 [Caenorhabditis briggsae] 4.0E-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
Pfam IPR004907 EMBL-EBI V-ATPase subunit C 1.0E-126
Pfam IPR002379 EMBL-EBI H+-transporting two-sector ATPase, C subunit 5.5E-22
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
Y38F2AL.4 4 15-37,58-78,98-120,133-155
SNAP00000023928 4 15-37,58-78,98-120,133-155
GENEFINDER00000023937 4 115-137,158-177,197-219,232-254
Sequence
Target Sequence 
>C. ELEGANS:177110_S_AT
cctacggaaccgccaaatctgccgtcggaatctgttcaatgggtgtcatgcgcccggagc
ttatcatgaagtctgtgattccggttattatggccggtatcatcggtatctacggtctcg
tcgtcgcgatggtcttgaagggaaaagtgacgtcggcaagtgctggttacgatttgaata
agggattcgctcacttggccgccggacttacgtgcggactttgtggattgggagccggat
atgctatcggaattgttggagacgccggagtccgtggaacagctcaacagccacgtcttt
tcgtcggaatgatccttatccttatcttctctgaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCTACGGAACCGCCAAATCTGCCGT 290 267 113 Antisense
ATCTGCCGTCGGAATCTGTTCAATG 550 33 129 Antisense
TTCAATGGGTGTCATGCGCCCGGAG 645 685 147 Antisense
GCGCCCGGAGCTTATCATGAAGTCT 455 287 162 Antisense
GATTCCGGTTATTATGGCCGGTATC 683 429 189 Antisense
CTCGTCGTCGCGATGGTCTTGAAGG 410 229 229 Antisense
GTGACGTCGGCAAGTGCTGGTTACG 532 481 259 Antisense
CGCCGGACTTACGTGCGGACTTTGT 582 257 312 Antisense
GGGAGCCGGATATGCTATCGGAATT 296 495 342 Antisense
GCCACGTCTTTTCGTCGGAATGATC 647 279 402 Antisense
TCCTTATCCTTATCTTCTCTGAAGT 46 593 425 Antisense
Sequence Source Affymetrix Proprietary Database