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[173440_at] synaptobrevin

Description g2196765-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g2196765 /5_PRIME_EXT_DB=GenBank Identifier /CHR=5 /FEA=Genomic Cluster /GEN=snb-1 /DEF=SNB-1
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 07      4grp_highest_8_8 > 47      4grp_high_8_8 > 12      6grp_highest_nonorm > 36      6grp_total > 08      4grp_total > 13      6grp_highest_sub > De      6grp_cgc > 11      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2579
1 2 3 4 range
A 4994.2
(-0.5)
P 		4258.9
(-2.4)
P 		4045.1
(-3)
P 		6285.7
(3)
P 		2241
B 5337.5
(1.2)
P 		4728.9
(-0.8)
P 		4090.9
(-3)
P 		5866.3
(3)
P 		1775
C 4574.5
(-0.7)
P 		4320.3
(-1.4)
P 		3707.2
(-3)
P 		6011.9
(3)
P 		2305
avr 4968.7
(-0.1) 		4436
(-1.6) 		3947.7
(-3) 		6054.6
(3) 		2107

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1782
1 2 3 4 5 6 range
A 5597.4
(3)
P 		4352.9
(-1.5)
P 		4518.3
(-0.9)
P 		3989.1
(-2.9)
P 		4087
(-2.5)
P 		3952.9
(-3)
P 		1645
B 5136.6
(3)
P 		4274.9
(-1)
P 		3839.4
(-3)
P 		5091.6
(2.8)
P 		3859.7
(-2.9)
P 		4447.2
(-0.2)
P 		1297
C 4682.4
(3)
P 		4305.1
(0.4)
P 		4132.3
(-0.8)
P 		4047.4
(-1.4)
P 		3815.7
(-3)
P 		3982.2
(-1.8)
P 		867
avr 5138.8
(3) 		4311
(-1.1) 		4163.3
(-1.8) 		4376
(-0.8) 		3920.8
(-3) 		4127.4
(-2) 		1218
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 898
1 2 3 4 range
A 1818.4
(3)
P 		924.5
(-3)
P 		1057.5
(-2.1)
P 		920.1
(-3)
P 		898
B 1702.1
(3)
P 		1167.9
(-1.2)
P 		947.9
(-3)
P 		1250.1
(-0.6)
P 		754
C 1514.3
(3)
P 		1242.1
(-0.3)
P 		1292.1
(0.3)
P 		1013.7
(-3)
P 		501
avr 1678.3
(3) 		1111.5
(-2.5) 		1099.2
(-2.6) 		1061.3
(-3) 		617

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 973
1 2 3 4 5 6 range
A 1031.8
(-2.3)
P 		1548.1
(3)
P 		984
(-2.8)
P 		1011.7
(-2.5)
P 		1233.3
(-0.2)
P 		962.4
(-3)
P 		586
B 1787.3
(3)
P 		1422.9
(0.4)
P 		932.3
(-3)
P 		1348.6
(-0.1)
P 		1568.1
(1.5)
P 		1658.3
(2.1)
P 		855
C 1735.6
(3)
P 		1313.6
(0.3)
P 		1051.7
(-1.5)
P 		813.9
(-3)
P 		1234.7
(-0.3)
P 		1333.1
(0.4)
P 		922
avr 1518.2
(3) 		1428.2
(2) 		989.3
(-3) 		1058.1
(-2.2) 		1345.4
(1) 		1317.9
(0.7) 		529
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173440_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25243
Sequence Type Exemplar sequence
Representative Public ID 2196765 NCBI
Target Description g2196765-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g2196765 /5_PRIME_EXT_DB=GenBank Identifier /CHR=5 /FEA=Genomic Cluster /GEN=snb-1 /DEF=SNB-1
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_072287(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072287 NCBI Caenorhabditis elegans T10H9.4 (synaptobrevin) mRNA, complete cds. 11/11 A 
T10H9.4.1 ENSEMBL cdna:known chromosome:CEL140:V:6658156:6659095:-1 gene:T10H9.4 11/11 None
T10H9.4.2 ENSEMBL cdna:known chromosome:CEL140:V:6658170:6659463:-1 gene:T10H9.4 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
chrV:6658153-6659103(-) 100.0 100.0
Public Domain and Genome References
Gene Title synaptobrevin
Gene Symbol snb-1
Ensembl T10H9.4
Entrez Gene 266648 Entrez gene
SwissProt O02495 EMBL-EBI
WormBase CE18252 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.23296.1.S1_AT similar to Vesicle-associated membrane protein 1 (VAMP-1) (Synaptobrevin 1) cfa
DROSOPHILA_2:1636838_A_AT n-synaptobrevin dm
DROSGENOME1:151978_AT n-synaptobrevin dm
HG-U95AV2:33779_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U95AV2:33780_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133_PLUS_2:207101_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A:207101_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A_2:207101_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133_PLUS_2:207100_S_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A:207100_S_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A_2:207100_S_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HU35KSUBB:RC_Z39585_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HUGENEFL:M36200_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
U133_X3P:G9257250_3P_A_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
U133_X3P:HS.20021.1.S1_3P_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A_2:213326_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-FOCUS:213326_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133_PLUS_2:213326_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U133A:213326_AT vesicle-associated membrane protein 1 (synaptobrevin 1) hs
HG-U95E:69723_AT Vesicle-associated membrane protein 1 (synaptobrevin 1) hs
MG-U74AV2:93652_I_AT vesicle-associated membrane protein 1 mm
MOUSE430_2:1453647_AT vesicle-associated membrane protein 1 mm
MOUSE430A_2:1453647_AT vesicle-associated membrane protein 1 mm
MOE430A:1453647_AT vesicle-associated membrane protein 1 mm
MU11KSUBB:MSA.2802.0_S_AT vesicle-associated membrane protein 1 mm
MG-U74AV2:93653_R_AT vesicle-associated membrane protein 1 mm
MG-U74BV2:114088_AT vesicle-associated membrane protein 1 mm
MOE430A:1421862_A_AT vesicle-associated membrane protein 1 mm
MOUSE430A_2:1421862_A_AT vesicle-associated membrane protein 1 mm
MOUSE430_2:1421862_A_AT vesicle-associated membrane protein 1 mm
MOE430A:1421863_AT vesicle-associated membrane protein 1 mm
MOUSE430A_2:1421863_AT vesicle-associated membrane protein 1 mm
MOUSE430_2:1421863_AT vesicle-associated membrane protein 1 mm
MU19KSUBB:TC28990_AT Vesicle-associated membrane protein 1 (Vamp1), mRNA mm
RG-U34A:M24104_G_AT vesicle-associated membrane protein 1 rn
RG-U34A:M24104_AT vesicle-associated membrane protein 1 rn
RG-U34C:RC_AI229196_G_AT vesicle-associated membrane protein 1 rn
RG-U34C:RC_AI229196_AT vesicle-associated membrane protein 1 rn
RG-U34C:RC_AI171731_S_AT vesicle-associated membrane protein 1 rn
RAE230A:1373510_AT vesicle-associated membrane protein 1 rn
RAT230_2:1373510_AT vesicle-associated membrane protein 1 rn
RAE230A:1370556_AT vesicle-associated membrane protein 1 rn
RAT230_2:1370556_AT vesicle-associated membrane protein 1 rn
RAE230A:1387519_AT vesicle-associated membrane protein 1 rn
RAT230_2:1387519_AT vesicle-associated membrane protein 1 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7271 synaptic transmission, cholinergic inferred from direct assay QuickGO AmiGO
43051 regulation of pharyngeal pumping inferred from direct assay QuickGO AmiGO
16079 synaptic vesicle exocytosis inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
8021 synaptic vesicle inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5485 v-SNARE activity inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAE71923 Hypothetical protein CBG18986 [Caenorhabditis briggsae] 6.0E-34
blast NP_504688 T10H9.4 [Caenorhabditis elegans] gb|AAC19234.1| Synaptobrevin related protein 1 [Caenorhabditis elegans] gb|AAB61235.1| SNB-1; synaptobrevin [Caenorhabditis elegans] gb|AAB61234.1| SNB-1; synaptobrevin [Caenorhabditis elegans] 6.0E-34
blast AAP05935 similar to GenBank Accession Number U00997 synaptobrevin in Aplysia californica [Schistosoma japonicum] 4.0E-26
Protein Domains
Database ID Description E-Value
Pfam IPR001388 EMBL-EBI Synaptobrevin 2.7E-44
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504688.1 1 85-107
T10H9.4.1 1 85-107
T10H9.4.2 1 85-107
Sequence
Target Sequence 
>C. ELEGANS:173440_AT
ttcacattttgcccattttcatctgttttcattttctaaaacatagaagctgagtattct
attcttattttgaacttcttctcttcattgtactatagttgaattatacgtttcccccca
catccccatccaatctgtcaattttcttaatattctttttctggttgatcgcaaatcatc
catttctgaaattaatttatttaggcggcgcgataagctgcgtgatcccacatccacatg
agcttatccgcggattccgtcgagctcgtgtgtgtatgtttttctagaattttcctattc
tcagactaacaacatgccttctcattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCACATTTTGCCCATTTTCATCTG 430 687 451 Antisense
GAAGCTGAGTATTCTATTCTTATTT 538 343 496 Antisense
GAACTTCTTCTCTTCATTGTACTAT 129 351 522 Antisense
CCCCATCCAATCTGTCAATTTTCTT 360 261 574 Antisense
TTCTTTTTCTGGTTGATCGCAAATC 41 689 603 Antisense
GATCGCAAATCATCCATTTCTGAAA 271 417 617 Antisense
AGGCGGCGCGATAAGCTGCGTGATC 90 43 653 Antisense
ACATCCACATGAGCTTATCCGCGGA 374 107 680 Antisense
CGTCGAGCTCGTGTGTGTATGTTTT 127 247 708 Antisense
GAATTTTCCTATTCTCAGACTAACA 163 325 737 Antisense
AGACTAACAACATGCCTTCTCATTC 606 71 753 Antisense
Sequence Source GenBank