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[175234_at]

Description AU116488_rc /REP_DB=TREMBL Accession /GB=AU116488 /CHR=X /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk745c4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 30      6grp_high1_10_10 > 05      4grp_highest_8_8 > 51      4grp_high_8_8 > 32      6grp_highest_nonorm > 71      6grp_total > 06      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 21      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 438
1 2 3 4 range
A 593.3
(3)
P 		262.3
(-3)
P 		342.1
(-1.6)
P 		370.8
(-1)
P 		331
B 674.7
(3)
P 		377.9
(-2)
P 		318.1
(-3)
P 		402
(-1.6)
P 		357
C 700
(3)
P 		429.7
(-1.6)
P 		366.8
(-2.7)
P 		346.5
(-3)
P 		354
avr 656
(3) 		356.6
(-2.7) 		342.3
(-3) 		373.1
(-2.4) 		314

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 319
1 2 3 4 5 6 range
A 302.1
(-1.9)
P 		381.2
(0.9)
P 		439.4
(3)
P 		271.4
(-3)
P 		355.7
(0)
P 		287.2
(-2.4)
P 		168
B 590.6
(3)
P 		383
(-1.6)
P 		368.9
(-1.9)
P 		369.6
(-1.8)
P 		327.9
(-2.8)
P 		317
(-3)
P 		274
C 509.1
(3)
P 		422.5
(0.8)
P 		343.9
(-1.3)
P 		384.1
(-0.2)
P 		314.5
(-2)
P 		276.6
(-3)
P 		233
avr 467.3
(3) 		395.6
(0.5) 		384.1
(0.1) 		341.7
(-1.3) 		332.7
(-1.6) 		293.6
(-3) 		174
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 177
1 2 3 4 range
A 216
(3)
P 		56.9
(-2.9)
P 		89.4
(-1.7)
P 		54.3
(-3)
P 		162
B 215.1
(3)
P 		93.3
(-2.2)
P 		73.7
(-3)
P 		85.7
(-2.5)
P 		141
C 231.7
(3)
P 		123.5
(-0.7)
P 		127.9
(-0.6)
P 		58.4
(-3)
P 		173
avr 220.9
(3) 		91.2
(-2) 		97
(-1.8) 		66.1
(-3) 		155

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 150
1 2 3 4 5 6 range
A 55.7
(-3)
P 		135.6
(3)
P 		95.7
(0)
P 		68.8
(-2)
P 		107.3
(0.9)
P 		69.9
(-1.9)
P 		80
B 205.5
(3)
P 		127.5
(-1)
P 		89.6
(-3)
P 		97.9
(-2.6)
P 		133.2
(-0.7)
P 		118.2
(-1.5)
P 		116
C 188.7
(3)
P 		128.9
(-0.2)
P 		87.5
(-2.5)
P 		77.3
(-3)
P 		101.8
(-1.7)
P 		92.6
(-2.2)
P 		111
avr 150
(3) 		130.7
(1.3) 		90.9
(-2.2) 		81.3
(-3) 		114.1
(-0.1) 		93.6
(-1.9) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175234_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22220
Sequence Type Exemplar sequence
Representative Public ID AU116488 NCBI
Target Description AU116488_rc /REP_DB=TREMBL Accession /GB=AU116488 /CHR=X /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk745c4 : 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_076508(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076508 NCBI Caenorhabditis elegans SYNtaxin family member (syn-1) (syn-1) mRNA, complete cds. 11/11 None
F35C8.4 ENSEMBL cdna:known chromosome:CEL140:X:5349063:5352358:1 gene:F35C8.4 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
chrX:5351993-5352273(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol syn-1
Ensembl F35C8.4
Entrez Gene 3565871 Entrez gene
SwissProt Q20024 EMBL-EBI
WormBase CE30968 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6886 intracellular protein transport inferred from electronic annotation QuickGO AmiGO
6944 membrane fusion inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
5886 plasma membrane inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8565 protein transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA81707 Syntaxin protein 1 [Caenorhabditis elegans] ref|NP_508909.2| SYNtaxin family member (syn-1) [Caenorhabditis elegans] sp|Q20024|STX1_CAEEL Putative syntaxin syn-1 1.0E-161
blast T16252 hypothetical protein F35C8.4 - Caenorhabditis elegans 1.0E-154
blast CAE68740 Hypothetical protein CBG14670 [Caenorhabditis briggsae] 1.0E-114
Protein Domains
Database ID Description E-Value
Pfam IPR006011 EMBL-EBI Syntaxin, N-terminal 8.9E-20
Pfam IPR000727 EMBL-EBI Target SNARE coiled-coil domain 5.1E-20
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508909.2 1 278-300
F35C8.4 1 278-300
Sequence
Target Sequence 
>C. ELEGANS:175234_AT
attgcggcaactctgattacactgtatttcactgtatctttattgcacatccctcatcat
cacgaccagtcactaatttgatcgctttaagatctttctcactttttgattcgtttctaa
tttttaatttggcagattttccaactgataatatggagttcacttatccgtttcatcgtt
ctcagcttttctgccgtttattgtgtgtttta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTGCGGCAACTCTGATTACACTGT 364 7 33 Antisense
GATTACACTGTATTTCACTGTATCT 114 431 47 Antisense
ACTGTATCTTTATTGCACATCCCTC 349 97 63 Antisense
CCTCATCATCACGACCAGTCACTAA 573 267 84 Antisense
GACCAGTCACTAATTTGATCGCTTT 674 383 96 Antisense
ATCGCTTTAAGATCTTTCTCACTTT 374 37 113 Antisense
CTCACTTTTTGATTCGTTTCTAATT 114 229 130 Antisense
GGCAGATTTTCCAACTGATAATATG 281 537 163 Antisense
TGGAGTTCACTTATCCGTTTCATCG 455 549 186 Antisense
TCTCAGCTTTTCTGCCGTTTATTGT 197 613 212 Antisense
TTTCTGCCGTTTATTGTGTGTTTTA 621 671 220 Antisense
Sequence Source Affymetrix Proprietary Database