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[177136_at]

Description Y38C1AA.I /REP_DB=WormBase Gene ID /WP=CE25250 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59470.1
Cluster 6grp_highest_10_10 > 58      6grp_high1_10_10 > 84      4grp_highest_8_8 > 33      4grp_high_8_8 > 59      6grp_highest_nonorm > 64      6grp_total > 84      4grp_total > 60      6grp_cgc > 66      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 302
1 2 3 4 range
A 651.2
(2.1)
P 		567.6
(0.4)
P 		695.4
(3)
P 		399.3
(-3)
P 		296
B 654.9
(2.2)
P 		606.1
(0.6)
P 		680.1
(3)
P 		497.6
(-3)
P 		183
C 701.1
(3)
P 		661.4
(1.9)
P 		651.3
(1.7)
P 		479.1
(-3)
P 		222
avr 669.1
(2.8) 		611.7
(1.2) 		675.6
(3) 		458.7
(-3) 		217

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 441
1 2 3 4 5 6 range
A 602.8
(-3)
P 		761.8
(0.4)
P 		881.9
(3)
P 		829.2
(1.9)
P 		882.1
(3)
P 		864.7
(2.6)
P 		279
B 635.3
(-3)
P 		788.9
(-0.6)
P 		1022.2
(3)
P 		866.7
(0.6)
P 		1017.7
(2.9)
P 		911.7
(1.3)
P 		387
C 583.7
(-3)
P 		677.5
(-1.7)
P 		770.7
(-0.5)
P 		905
(1.4)
P 		848
(0.6)
P 		1024.8
(3)
P 		441
avr 607.3
(-3) 		742.7
(-0.5) 		891.6
(2.2) 		867
(1.8) 		915.9
(2.7) 		933.7
(3) 		326
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 179
1 2 3 4 range
A 237.1
(3)
P 		123.2
(-0.8)
P 		181.8
(1.1)
P 		58.5
(-3)
P 		179
B 208.8
(3)
P 		149.7
(-0.4)
P 		157.6
(0)
P 		106
(-3)
P 		103
C 232.1
(3)
P 		190.1
(1.3)
P 		227
(2.8)
P 		80.8
(-3)
P 		151
avr 226
(3) 		154.3
(0) 		188.8
(1.5) 		81.8
(-3) 		144

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 302
1 2 3 4 5 6 range
A 111.1
(-3)
P 		270.9
(3)
P 		192.1
(0)
P 		210.3
(0.7)
P 		266.2
(2.8)
P 		210.5
(0.7)
P 		160
B 221
(-3)
P 		262.6
(-1.7)
P 		248.2
(-2.2)
P 		229.6
(-2.7)
P 		413.5
(3)
P 		340
(0.7)
P 		193
C 216.3
(-1.7)
P 		206.7
(-2.1)
P 		196.2
(-2.5)
P 		182
(-3)
P 		274.4
(0.4)
P 		343.1
(3)
P 		161
avr 182.8
(-3) 		246.7
(-0.2) 		212.2
(-1.7) 		207.3
(-1.9) 		318
(3) 		297.9
(2.1) 		135
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177136_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19218
Sequence Type Exemplar sequence
Representative Public ID Y38C1AA.I NCBI
Target Description Y38C1AA.I /REP_DB=WormBase Gene ID /WP=CE25250 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAF59470.1
Cluster Evidence This cluster is supported by a Sanger Annotation.
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_067477(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067477 NCBI Caenorhabditis elegans COP-9 SigNalosome subunit family member (csn-3) (csn-3) mRNA, complete cds. 11/11 None
SNAP00000038648 ENSEMBL cdna:SNAP chromosome:CEL140:IV:194778:202441:1 11/11 None
GENEFINDER00000038654 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:192482:202441:1 11/11 None
Y38C1AA.2 ENSEMBL cdna:known chromosome:CEL140:IV:194745:202549:1 gene:Y38C1AA.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
chrIV:192481-202441(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol csn-3
Ensembl Y38C1AA.2
Entrez Gene 176834 Entrez gene
WormBase CE33861 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6511 ubiquitin-dependent protein catabolism inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
8180 signalosome complex inferred from physical interaction QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5515 protein binding inferred from physical interaction QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAP13759 Cop-9 signalosome subunit protein 3 [Caenorhabditis elegans] ref|NP_499878.3| COP-9 SigNalosome subunit family member (csn-3) [Caenorhabditis elegans] sp|Q9N425|CSN3_CAEEL COP9 signalosome complex subunit 3 (Signalosome subunit 3) 0.0
blast CAE58511 Hypothetical protein CBG01662 [Caenorhabditis briggsae] 1.0E-164
blast CAE58511 Hypothetical protein CBG01662 [Caenorhabditis briggsae] 1.0E-162
blast AAP13757 Hypothetical protein Y38C1AA.12 [Caenorhabditis elegans] ref|NP_001023447.1| Y38C1AA.12 [Caenorhabditis elegans] 2.0E-97
blast AAL49197 RE63441p [Drosophila melanogaster] 2.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR000717 EMBL-EBI Proteasome component region PCI 3.2E-15
Pfam IPR000717 EMBL-EBI Proteasome component region PCI 3.2E-15
Pfam IPR000717 EMBL-EBI Proteasome component region PCI 3.2E-15
Sequence
Target Sequence 
>C. ELEGANS:177136_AT
tatgtgctcatttcgctaattctgaaaggaaaagtggacgtgacggaaaacggtgacaaa
tcagcgattcgtcacttcaaaaccaaaagtcctgaatacaaacaattctcagagattcgg
ttctcccgaagttcgaatacccattcagcagtggagagtcttgtgaaatcggcaaaagat
cgtttgagaaaagacggaaatacagaaattgccaaatatttggtcgttgaaatgaagaaa
aagacaattatgtcgctgacaagaatgttcacatcaattcggatttctgaaattgaggag
ttggcatttttgaagtcacgggatcaagttacagagcttattggtcaattggttgaggag
cagaggattactgtacgaattgatggagatatggtcttttggactgaattgagccctgtt
ccatctaaaaatgatgttgagaataagattagaatcgtcgatcacctgaacactcttctt
cacgagaaaaacactactatgaaagccggttcaggacgtatgagaccat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATGTGCTCATTTCGCTAATTCTGA 344 655 1621 Antisense
ATCAGCGATTCGTCACTTCAAAACC 353 29 1680 Antisense
GAGATTCGGTTCTCCCGAAGTTCGA 703 387 1732 Antisense
AGTTCGAATACCCATTCAGCAGTGG 79 65 1750 Antisense
TGTTCACATCAATTCGGATTTCTGA 471 561 1886 Antisense
GGAGTTGGCATTTTTGAAGTCACGG 557 515 1917 Antisense
AGTCACGGGATCAAGTTACAGAGCT 147 61 1934 Antisense
GGTCTTTTGGACTGAATTGAGCCCT 419 503 2013 Antisense
ATTGAGCCCTGTTCCATCTAAAAAT 647 3 2028 Antisense
TAGAATCGTCGATCACCTGAACACT 527 651 2070 Antisense
GCCGGTTCAGGACGTATGAGACCAT 71 283 2125 Antisense
Sequence Source Affymetrix Proprietary Database