[Home] | [Total List]

[173566_at]

Description CEC2302 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C13B9.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09230 /WB_GENE_ID=C13B9.3 /WP=CE01778 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk158f10 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 01      6grp_high1_10_10 > 08      4grp_highest_8_8 > 10      4grp_high_8_8 > 62      6grp_highest_nonorm > 66      6grp_total > 09      4grp_total > 56      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 952
1 2 3 4 range
A 1501.4
(-0.7)
P 		1372.4
(-2)
P 		1885.9
(3)
P 		1268.6
(-3)
P 		617
B 1066.9
(-3)
P 		1821.3
(2.9)
P 		1830.9
(3)
P 		1143.2
(-2.4)
P 		764
C 1499.7
(-0.9)
P 		1889.1
(2)
P 		2019
(3)
P 		1222.8
(-3)
P 		796
avr 1356
(-1.8) 		1694.3
(1.1) 		1911.9
(3) 		1211.5
(-3) 		700

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 986
1 2 3 4 5 6 range
A 1783.1
(3)
P 		1420.1
(0.2)
P 		1247.1
(-1.1)
P 		1334
(-0.4)
P 		1674.8
(2.2)
P 		1001.8
(-3)
P 		781
B 1834.6
(3)
P 		1057.5
(-3)
P 		1760.5
(2.4)
P 		1780.3
(2.6)
P 		1415.2
(-0.2)
P 		1179.3
(-2.1)
P 		777
C 1701.7
(3)
P 		1044.1
(-1.6)
P 		1346.2
(0.5)
P 		1435.6
(1.1)
P 		1264.3
(-0.1)
P 		848.4
(-3)
P 		853
avr 1773.1
(3) 		1173.9
(-1.7) 		1451.3
(0.5) 		1516.6
(1) 		1451.4
(0.5) 		1009.8
(-3) 		763
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 518
1 2 3 4 range
A 546.7
(3)
P 		297.9
(-1.1)
P 		493
(2.1)
P 		185.7
(-3)
P 		361
B 340.2
(-0.2)
P 		449.8
(3)
P 		424.3
(2.3)
P 		243.6
(-3)
P 		206
C 496.4
(0.5)
P 		543.1
(1.1)
P 		703.7
(3)
P 		206.2
(-3)
P 		498
avr 461.1
(1.6) 		430.3
(1) 		540.3
(3) 		211.8
(-3) 		329

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 394
1 2 3 4 5 6 range
A 328.7
(-1.1)
P 		505
(3)
P 		271.6
(-2.4)
P 		338.3
(-0.8)
P 		505.4
(3)
P 		243.9
(-3)
P 		262
B 638.3
(3)
P 		352
(-3)
P 		427.5
(-1.4)
P 		471.5
(-0.5)
P 		575
(1.7)
P 		439.8
(-1.2)
P 		286
C 630.8
(3)
P 		318.6
(-2.4)
P 		342.6
(-2)
P 		288.7
(-2.9)
P 		409.1
(-0.8)
P 		284
(-3)
P 		347
avr 532.6
(3) 		391.9
(-1) 		347.2
(-2.3) 		366.2
(-1.8) 		496.5
(2) 		322.6
(-3) 		210
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173566_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24288
Sequence Type Exemplar sequence
Representative Public ID CEC2302 NCBI
Target Description CEC2302 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C13B9.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09230 /WB_GENE_ID=C13B9.3 /WP=CE01778 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk158f10 : 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_066062(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066062 NCBI Caenorhabditis elegans C13B9.3 (C13B9.3) mRNA, complete cds. 11/11 None
C13B9.3.1 ENSEMBL cdna:known chromosome:CEL140:III:6622611:6624907:-1 gene:C13B9.3 11/11 None
C13B9.3.2 ENSEMBL cdna:known chromosome:CEL140:III:6622650:6624914:-1 gene:C13B9.3 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
chrIII:6622664-6624896(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl C13B9.3
Entrez Gene 175940 Entrez gene
SwissProt Q09236 EMBL-EBI
WormBase CE01778 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:250816_AT clathrin adaptor complexes medium subunit-related at
CANINE:1589644_AT similar to archain cfa
CANINE_2:CFA.20988.1.S1_S_AT similar to archain cfa
CANINE_2:CFAAFFX.19532.1.S1_S_AT similar to archain cfa
DROSOPHILA_2:1628472_AT coatomer protein dm
DROSGENOME1:142358_AT coatomer protein dm
HG-U133A:201176_S_AT archain 1 hs
HG-U133_PLUS_2:201176_S_AT archain 1 hs
HG-U133A_2:201176_S_AT archain 1 hs
HG-FOCUS:201176_S_AT archain 1 hs
HUGENEFL:X81198_AT archain 1 hs
U133_X3P:G11863153_3P_A_AT archain 1 hs
HG-U95AV2:34370_AT archain 1 hs
MOE430A:1423743_AT archain 1 mm
MOUSE430A_2:1423743_AT archain 1 mm
MOUSE430_2:1423743_AT archain 1 mm
MOE430A:1451089_A_AT archain 1 mm
MOUSE430A_2:1451089_A_AT archain 1 mm
MOUSE430_2:1451089_A_AT archain 1 mm
MOE430B:1436062_AT archain 1 mm
MOUSE430_2:1436062_AT archain 1 mm
MU11KSUBA:AA544759_S_AT archain 1 mm
MG-U74AV2:94512_F_AT archain 1 mm
MG-U74AV2:94513_R_AT archain 1 mm
MG-U74AV2:94514_S_AT archain 1 mm
MG-U74BV2:111446_AT archain 1 mm
MG-U74BV2:115361_AT Archain 1, mRNA (cDNA clone MGC:36506 IMAGE:5368060) mm
MU19KSUBB:TC30464_AT Archain 1, mRNA (cDNA clone MGC:36506 IMAGE:5368060) mm
MU19KSUBB:TC30566_AT Archain 1, mRNA (cDNA clone MGC:36506 IMAGE:5368060) mm
RG-U34B:RC_AA946440_AT archain rn
RAE230A:1398896_AT archain rn
RAT230_2:1398896_AT archain rn
RAE230B:1391658_AT archain rn
RAT230_2:1391658_AT archain rn
YEAST_2:1773173_AT Delta subunit of the coatomer complex (COPI), which coats Golgi-derived transport vesicles; involved in retrograde transport between Golgi and ER 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
30125 clathrin vesicle coat inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAN73882 Hypothetical protein C13B9.3 [Caenorhabditis elegans] ref|NP_498463.1| C13B9.3 [Caenorhabditis elegans] sp|Q09236|COPD_CAEEL Probable coatomer delta subunit (Delta-coat protein) (Delta-COP) 0.0
blast CAE69165 Hypothetical protein CBG15197 [Caenorhabditis briggsae] 0.0
blast AAH33387 Archain 1 [Mus musculus] gb|AAH17124.1| Archain 1 [Mus musculus] gb|AAH34754.1| Archain 1 [Mus musculus] dbj|BAC26007.1| unnamed protein product [Mus musculus] gb|AAH23728.1| Archain 1 [Mus musculus] 1.0E-117
Sequence
Target Sequence 
>C. ELEGANS:173566_AT
aaattgtgtaatttattcctattcgagagatcttcaagattgatatttttattgcttcca
ataccaccaccaagccactaatttttctagagattcatgattccttttttgcaaatcatg
ttatccctttgattgctgtgatgcataagccactctcctccgacccaattcatactgtat
tt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATTGTGTAATTTATTCCTATTCG 46 115 1551 Antisense
TTATTCCTATTCGAGAGATCTTCAA 225 679 1563 Antisense
TGATATTTTTATTGCTTCCAATACC 283 565 1591 Antisense
CACCACCAAGCCACTAATTTTTCTA 57 199 1615 Antisense
TTTTTCTAGAGATTCATGATTCCTT 302 675 1632 Antisense
GAGATTCATGATTCCTTTTTTGCAA 576 397 1640 Antisense
TTTTTTGCAAATCATGTTATCCCTT 480 675 1655 Antisense
TCATGTTATCCCTTTGATTGCTGTG 358 623 1666 Antisense
TGTTATCCCTTTGATTGCTGTGATG 593 561 1669 Antisense
TGCTGTGATGCATAAGCCACTCTCC 258 583 1684 Antisense
CTCCGACCCAATTCATACTGTATTT 118 235 1708 Antisense
Sequence Source Affymetrix Proprietary Database