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[173356_s_at]

Description AV176340_rc /REP_DB=TREMBL Accession /GB=AV176340 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk512a1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 0      6grp_high1_10_10 > 08      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 56      6grp_total > 09      4grp_total > 58      6grp_cgc > 0      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2151
1 2 3 4 range
A 2050
(-0.4)
P 		3283.4
(3)
P 		3247
(2.9)
P 		1132.5
(-3)
P 		2151
B 2369.3
(-0.2)
P 		3264.9
(3)
P 		3135.7
(2.5)
P 		1572.9
(-3)
P 		1692
C 2053.7
(-0.7)
P 		3072.1
(2.4)
P 		3258.6
(3)
P 		1308.5
(-3)
P 		1950
avr 2157.7
(-0.4) 		3206.8
(3) 		3213.8
(3) 		1338
(-3) 		1876

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1156
1 2 3 4 5 6 range
A 2284
(1.7)
P 		2389.6
(3)
P 		1937.6
(-2.4)
P 		2301.1
(1.9)
P 		1887.4
(-3)
P 		1943.1
(-2.3)
P 		502
B 2350.4
(2.5)
P 		2027.3
(0.2)
P 		1562.5
(-3)
P 		2427.9
(3)
P 		1907.6
(-0.6)
P 		2081.3
(0.6)
P 		865
C 2718.5
(3)
P 		1822.1
(-1.9)
P 		2241.8
(0.4)
P 		1878
(-1.6)
P 		2371.7
(1.1)
P 		1620.3
(-3)
P 		1098
avr 2451
(3) 		2079.7
(-0.9) 		1914
(-2.7) 		2202.3
(0.4) 		2055.6
(-1.2) 		1881.6
(-3) 		569
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 970
1 2 3 4 range
A 746.4
(2.1)
P 		712.7
(1.8)
P 		848.8
(3)
P 		165.8
(-3)
P 		683
B 755.6
(2.4)
P 		806.3
(3)
P 		726.6
(2)
P 		335.2
(-3)
P 		471
C 679.8
(0)
P 		883.2
(1.3)
P 		1135.7
(3)
P 		220.6
(-3)
P 		915
avr 727.3
(1.4) 		800.7
(2.1) 		903.7
(3) 		240.5
(-3) 		663

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 630
1 2 3 4 5 6 range
A 421
(-3)
P 		849.9
(3)
P 		422
(-3)
P 		583.6
(-0.7)
P 		569.5
(-0.9)
P 		473.1
(-2.3)
P 		429
B 817.8
(3)
P 		674.8
(1)
P 		379.4
(-3)
P 		643.1
(0.6)
P 		775
(2.4)
P 		776.1
(2.4)
P 		438
C 1007.6
(3)
P 		556
(-1.3)
P 		570.6
(-1.2)
P 		377.7
(-3)
P 		767.5
(0.7)
P 		542.4
(-1.4)
P 		630
avr 748.8
(3) 		693.6
(1.9) 		457.3
(-3) 		534.8
(-1.4) 		704
(2.1) 		597.2
(-0.1) 		292
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173356_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27933
Sequence Type Exemplar sequence
Representative Public ID AV176340 NCBI
Target Description AV176340_rc /REP_DB=TREMBL Accession /GB=AV176340 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk512a1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_075476(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075476 NCBI Caenorhabditis elegans yeast SEC homolog family member (sec-23) (sec-23) mRNA, complete cds. 11/11 A 
GENEFINDER00000016732 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:20094470:20103562:1 11/11 None
Y113G7A.3.2 ENSEMBL cdna:known chromosome:CEL140:V:20089258:20103661:1 gene:Y113G7A.3 11/11 A 
Y113G7A.3.1 ENSEMBL cdna:known chromosome:CEL140:V:20089260:20103665:1 gene:Y113G7A.3 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
chrV:20102115-20103562(+) 76.45 76.45
Public Domain and Genome References
Gene Title
Gene Symbol sec-23
Ensembl Y113G7A.3
Entrez Gene 180317 Entrez gene
SwissProt Q9U2Z1 EMBL-EBI
WormBase CE27230 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:258097_AT transport protein, putative at
CANINE:1605537_AT similar to Protein transport protein Sec23A (SEC23-related protein A) cfa
CANINE_2:CFA.555.1.S1_AT similar to Protein transport protein Sec23A (SEC23-related protein A) cfa
CANINE_2:CFAAFFX.21365.1.S1_S_AT similar to Protein transport protein Sec23A (SEC23-related protein A) cfa
DROSGENOME1:151775_AT dm
DROSOPHILA_2:1628598_S_AT dm
CHICKEN:GGA.3599.1.S1_AT similar to Sec23a protein gga
CHICKEN:GGA.3599.2.S1_A_AT similar to Sec23a protein gga
CHICKEN:GGA.3599.2.S1_S_AT similar to Sec23a protein gga
CHICKEN:GGA.3599.3.S1_A_AT similar to Sec23a protein gga
CHICKEN:GGA.3599.3.S1_AT similar to Sec23a protein gga
HG-U133_PLUS_2:212887_AT Sec23 homolog A (S. cerevisiae) hs
HG-U133A_2:212887_AT Sec23 homolog A (S. cerevisiae) hs
HG-U133A:212887_AT Sec23 homolog A (S. cerevisiae) hs
HG-U133_PLUS_2:204344_S_AT Sec23 homolog A (S. cerevisiae) hs
HG-U133A_2:204344_S_AT Sec23 homolog A (S. cerevisiae) hs
HG-U133A:204344_S_AT Sec23 homolog A (S. cerevisiae) hs
HG-FOCUS:204344_S_AT Sec23 homolog A (S. cerevisiae) hs
HU35KSUBA:D57823_AT Sec23 homolog A (S. cerevisiae) hs
HUGENEFL:X97064_AT Sec23 homolog A (S. cerevisiae) hs
U133_X3P:G5454041_3P_S_AT Sec23 homolog A (S. cerevisiae) hs
U133_X3P:HS.321403.0.S1_3P_AT Sec23 homolog A (S. cerevisiae) hs
HG-U95AV2:39099_AT Sec23 homolog A (S. cerevisiae) hs
HG-U95D:85014_I_AT Sec23 homolog A (S. cerevisiae) hs
HG-U95D:85017_R_AT Sec23 homolog A (S. cerevisiae) hs
RG-U34C:RC_AI179139_AT SEC23A (S. cerevisiae) (predicted) rn
RAE230A:1388755_AT SEC23A (S. cerevisiae) (predicted) rn
RAT230_2:1388755_AT SEC23A (S. cerevisiae) (predicted) rn
YEAST_2:1771120_AT GTPase-activating protein; component of the Sec23p-Sec24p heterodimeric complex of the COPII vesicle coat, involved in ER to Golgi transport and autophagy; stimulates the GDP-bound form of Sar1p 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
30127 COPII vesicle coat inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5515 protein binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB60476 Hypothetical protein Y113G7A.3 [Caenorhabditis elegans] ref|NP_507877.1| yeast SEC homolog family member (sec-23) [Caenorhabditis elegans] 0.0
blast CAE67428 Hypothetical protein CBG12918 [Caenorhabditis briggsae] 0.0
blast AAL91101 ABC protein [Acanthocheilonema viteae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006895 EMBL-EBI Sec23/Sec24 zinc finger 1.6E-21
Pfam IPR007123 EMBL-EBI Gelsolin region 2.7E-27
Pfam IPR006900 EMBL-EBI Sec23/Sec24 helical domain 5.1E-48
Pfam IPR006896 EMBL-EBI Sec23/Sec24 trunk domain 1.0E-126
Pfam IPR007123 EMBL-EBI Gelsolin region 2.7E-27
Pfam IPR006900 EMBL-EBI Sec23/Sec24 helical domain 5.1E-48
Pfam IPR006896 EMBL-EBI Sec23/Sec24 trunk domain 7.1E-97
Sequence
Target Sequence 
>C. ELEGANS:173356_S_AT
acgttacattgtgacagagcacgagggttcacaagcccggttcttgttgtcgaaagtcaa
tccatcactgacgcataataatccatatgctaatgaagccggttccgctgtattcaccga
tgacgtgtcacttcaagnnnnnatggaacatttgaagaagctctcctcc

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGTTACATTGTGACAGAGCACGAG 660 93 87 Antisense
AGAGCACGAGGGTTCACAAGCCCGG 655 69 102 Antisense
GTTCACAAGCCCGGTTCTTGTTGTC 331 445 113 Antisense
GCCCGGTTCTTGTTGTCGAAAGTCA 117 285 121 Antisense
GAAAGTCAATCCATCACTGACGCAT 118 361 138 Antisense
ATCACTGACGCATAATAATCCATAT 168 29 150 Antisense
TATGCTAATGAAGCCGGTTCCGCTG 708 655 172 Antisense
TAATGAAGCCGGTTCCGCTGTATTC 619 635 177 Antisense
TGTATTCACCGATGACGTGTCACTT 662 559 195 Antisense
TTCACCGATGACGTGTCACTTCAAG 558 685 199 Antisense
GGAACATTTGAAGAAGCTCTCCTCC 392 529 231 Antisense
Sequence Source Affymetrix Proprietary Database