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[173874_s_at] epimorphin protein

Description AV198372 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F55A11.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198372 /WB_GENE_ID=F55A11.2 /WP=CE05944 /CHR=5 /FEA=Genomic Cluster /DEF=epimorphin protein; Caenorhabditis elegans cDNA clone:yk678c2 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 49      6grp_high1_10_10 > 83      4grp_highest_8_8 > 28      4grp_high_8_8 > 31      6grp_highest_nonorm > 74      6grp_total > 80      4grp_total > 32      6grp_highest_sub > 04_05_06      6grp_cgc > 95      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 395
1 2 3 4 range
A 492.1
(-1.3)
P 		384
(-3)
P 		553.4
(-0.4)
P 		771.2
(3)
P 		387
B 520
(-1.3)
P 		503.2
(-2.3)
P 		592.8
(3)
P 		491.5
(-3)
P 		101
C 461.1
(0.2)
P 		491
(1.4)
P 		534.4
(3)
P 		375.8
(-3)
P 		159
avr 491.1
(-1.1) 		459.4
(-3) 		560.2
(3) 		546.2
(2.2) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 315
1 2 3 4 5 6 range
A 684.4
(1.5)
P 		560.9
(-2.9)
P 		559.1
(-3)
P 		726
(3)
P 		679.7
(1.3)
P 		640.2
(-0.1)
P 		167
B 634.3
(-1)
P 		603.5
(-2.2)
P 		649.9
(-0.3)
P 		732.3
(3)
P 		583.5
(-3)
P 		689.6
(1.3)
P 		149
C 488.7
(-2.5)
P 		642.1
(0.5)
P 		555.1
(-1.2)
P 		774.9
(3)
P 		459.9
(-3)
P 		725.6
(2.1)
P 		315
avr 602.5
(-2) 		602.2
(-2) 		588
(-2.5) 		744.4
(3) 		574.4
(-3) 		685.1
(0.9) 		170
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 123
1 2 3 4 range
A 179.2
(3)
P 		83.4
(-3)
P 		144.7
(0.8)
P 		112.9
(-1.2)
P 		96
B 165.8
(3)
P 		124.3
(-1.1)
P 		137.4
(0.2)
P 		104.7
(-3)
P 		61
C 152.6
(1.4)
P 		141.2
(0.8)
P 		186.3
(3)
P 		63.4
(-3)
P 		123
avr 165.9
(3) 		116.3
(-1.1) 		156.1
(2.2) 		93.7
(-3) 		72

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 135
1 2 3 4 5 6 range
A 126.2
(-2.7)
P 		199.5
(2.6)
P 		121.8
(-3)
P 		184.1
(1.5)
P 		205.1
(3)
P 		155.9
(-0.5)
P 		83
B 220.7
(0.8)
P 		200.9
(-0.4)
P 		157.8
(-3)
P 		194
(-0.8)
P 		237.1
(1.8)
P 		257.1
(3)
P 		99
C 181.1
(-0.6)
P 		195.9
(0.2)
P 		141.3
(-3)
P 		155.8
(-2.1)
P 		148.8
(-2.6)
P 		242.9
(3)
P 		102
avr 176
(-0.3) 		198.8
(1.5) 		140.3
(-3) 		178
(-0.1) 		197
(1.3) 		218.6
(3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173874_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25431
Sequence Type Exemplar sequence
Representative Public ID AV198372 NCBI
Target Description AV198372 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F55A11.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198372 /WB_GENE_ID=F55A11.2 /WP=CE05944 /CHR=5 /FEA=Genomic Cluster /DEF=epimorphin protein; Caenorhabditis elegans cDNA clone:yk678c2 : 5prime 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_073567(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073567 NCBI Caenorhabditis elegans SYNtaxin family member (syn-3) (syn-3) mRNA, complete cds. 11/11 None
SNAP00000030954 ENSEMBL cdna:SNAP chromosome:CEL140:V:11767508:11769566:1 11/11 None
GENEFINDER00000030966 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11767508:11772256:1 10/11 None
F55A11.2 ENSEMBL cdna:known chromosome:CEL140:V:11767493:11769802:1 gene:F55A11.2 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:11767508-11769567(+) 100.0 100.0
Public Domain and Genome References
Gene Title epimorphin protein
Gene Symbol syn-3
Ensembl F55A11.2
Entrez Gene 179611 Entrez gene
SwissProt Q20797 EMBL-EBI
WormBase CE05944 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257157_AT syntaxin, putative (SYP32) at
CANINE:1599765_X_AT similar to Syntaxin-5 cfa
CANINE_2:CFA.652.1.A1_AT similar to Syntaxin-5 cfa
CANINE_2:CFAAFFX.23837.1.S1_S_AT similar to Syntaxin-5 cfa
CANINE_2:CFAAFFX.23842.1.S1_AT similar to Syntaxin-5 cfa
DROSOPHILA_2:1625607_S_AT Syntaxin 5 dm
DROSGENOME1:141717_AT Syntaxin 5 dm
HG-U133A:203330_S_AT syntaxin 5A hs
HG-U133_PLUS_2:203330_S_AT syntaxin 5A hs
HG-FOCUS:203330_S_AT syntaxin 5A hs
HG-U133A_2:203330_S_AT syntaxin 5A hs
HUGENEFL:U26648_AT syntaxin 5A hs
U133_X3P:G4507292_3P_S_AT syntaxin 5A hs
HG-U95AV2:40068_AT syntaxin 5A hs
HG-U95E:70425_AT Syntaxin 5A hs
HG-U95D:75762_R_AT Syntaxin 5A hs
MG-U74AV2:96076_AT syntaxin 5A mm
MOE430A:1449679_S_AT syntaxin 5A mm
MOUSE430A_2:1449679_S_AT syntaxin 5A mm
MOUSE430_2:1449679_S_AT syntaxin 5A mm
MOE430A:1448267_AT syntaxin 5A mm
MOUSE430A_2:1448267_AT syntaxin 5A mm
MOUSE430_2:1448267_AT syntaxin 5A mm
MOE430A:1419952_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOUSE430A_2:1419952_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOUSE430_2:1419952_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOE430B:1442185_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOUSE430_2:1442185_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOE430B:1444514_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MOUSE430_2:1444514_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MU19KSUBB:TC27133_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
MU19KSUBC:TC38860_AT Syntaxin 5A, mRNA (cDNA clone MGC:25518 IMAGE:3487476) mm
RN-U34:U87971_G_AT syntaxin 5a rn
RG-U34A:U87971_G_AT syntaxin 5a rn
RN-U34:L20822_AT syntaxin 5a rn
RG-U34A:L20822_AT syntaxin 5a rn
RG-U34A:U87971_AT syntaxin 5a rn
RAE230A:1367878_AT syntaxin 5a rn
RAT230_2:1367878_AT syntaxin 5a rn
RAE230B:1386853_S_AT syntaxin 5a rn
RAT230_2:1386853_S_AT syntaxin 5a rn
RAE230B:1380639_AT syntaxin 5a rn
RAT230_2:1380639_AT syntaxin 5a rn
YEAST_2:1770684_AT cis-Golgi t-SNARE syntaxin required for vesicular transport between the ER and the Golgi complex, binds at least 9 SNARE proteins Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6886 intracellular protein transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation 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 CAA96656 Hypothetical protein F55A11.2 [Caenorhabditis elegans] ref|NP_505968.1| SYNtaxin family member (syn-3) [Caenorhabditis elegans] sp|Q20797|STX3_CAEEL Putative syntaxin syn-3 0.0
blast CAE75302 Hypothetical protein CBG23272 [Caenorhabditis briggsae] 0.0
blast CAA96657 Hypothetical protein F55A11.3 [Caenorhabditis elegans] ref|NP_505969.1| F55A11.3 [Caenorhabditis elegans] 0.0
blast CAE75301 Hypothetical protein CBG23271 [Caenorhabditis briggsae] 0.0
blast AAH76467 Syntaxin 5A [Danio rerio] ref|NP_001002333.1| syntaxin 5A [Danio rerio] 4.0E-60
Protein Domains
Database ID Description E-Value
scop a.4.5.MarR-like transcriptional regulators All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; MarR-like transcriptional regulators 2.20000004768372
Pfam IPR006011 EMBL-EBI Syntaxin, N-terminal 2.8E-17
Pfam IPR000727 EMBL-EBI Target SNARE coiled-coil domain 1.3E-19
Pfam IPR000727 EMBL-EBI Target SNARE coiled-coil domain 3.1E-18
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.9E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505968.1 1 392-412
F55A11.2 1 392-412
SNAP00000030954 1 392-412
GENEFINDER00000030966 6 385-407,420-442,482-501,522-544,549-571,592-614
Sequence
Target Sequence 
>C. ELEGANS:173874_S_AT
aaattctcgagtggtgcagcagttccaatgggacttccttcctcctcttccggagctaat
ggtcgttcaaagcttcttcaagatgatgagcagcatggctcctcaagcatagctctggat
atgggtgctctgtcaaacatgcaatcacaacagactatggaacaaagagattcatcattg
gaatatgcgcaagcccgtagcaacaccatggcgacaattgaaggatccatctccgaactt
ggccaaattttctctcaactggcttcactcgtcagtgagcaaggagagatgataacaaga
atcgattcaaatgttgaagatacagctcttaatattgatatggcacattcagagcttgtg
agatatcttcaaaatattagcaaaaatcgatggttaatgattcaagtttttggagttctc
atggttttct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATTCTCGAGTGGTGCAGCAGTTC 63 117 795 Antisense
AGCAGTTCCAATGGGACTTCCTTCC 409 77 812 Antisense
GATGAGCAGCATGGCTCCTCAAGCA 123 411 879 Antisense
GGCTCCTCAAGCATAGCTCTGGATA 172 539 891 Antisense
GCTCTGGATATGGGTGCTCTGTCAA 285 299 906 Antisense
GGAATATGCGCAAGCCCGTAGCAAC 442 533 974 Antisense
CCGTAGCAACACCATGGCGACAATT 273 265 989 Antisense
TGAAGGATCCATCTCCGAACTTGGC 492 575 1013 Antisense
GAACTTGGCCAAATTTTCTCTCAAC 655 349 1029 Antisense
AACTGGCTTCACTCGTCAGTGAGCA 577 143 1051 Antisense
GTTTTTGGAGTTCTCATGGTTTTCT 486 447 1200 Antisense
Sequence Source Affymetrix Proprietary Database