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[187513_at]

Description Y55F3AM.15 /REP_DB=WormBase Gene ID /WP=CE25482 /TR=Q9N359 /GB=AAF60803.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 45      4grp_total > 60      6grp_cgc > 45      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 102
1 2 3 4 range
A 200.8
(1.1)
P 		188.6
(0.3)
A 		229.1
(3)
P 		139.1
(-3)
A 		90
B 230
(3)
P 		198.1
(-3)
A 		223.1
(1.7)
M 		198
(-3)
A 		32
C 201.9
(-0.7)
A 		177.9
(-3)
A 		241.2
(3)
A 		201.1
(-0.8)
A 		63
avr 210.9
(0.7) 		188.2
(-2) 		231.1
(3) 		179.4
(-3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 122
1 2 3 4 5 6 range
A 144.8
(0.4)
A 		175.1
(3)
P 		175.3
(3)
A 		131.9
(-0.7)
A 		104.8
(-3)
A 		164.1
(2)
M 		71
B 203.3
(3)
P 		171.2
(1)
P 		153.4
(-0)
A 		105
(-3)
A 		121.9
(-2)
A 		175.3
(1.3)
P 		98
C 182.4
(0.7)
P 		171.6
(0.1)
P 		187.2
(1)
A 		111.7
(-3)
M 		111.1
(-3)
A 		226.4
(3)
P 		115
avr 176.8
(2.1) 		172.6
(1.7) 		172
(1.7) 		116.2
(-2.7) 		112.6
(-3) 		188.6
(3) 		76
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 73.1
(3)
P 		41
(-0.7)
A 		59.9
(1.5)
P 		20.4
(-3)
A 		53
B 73.3
(3)
P 		48.9
(-1.7)
A 		51.7
(-1.2)
M 		42.2
(-3)
A 		31
C 66.8
(0.9)
A 		51.2
(-0.9)
A 		84.1
(3)
A 		33.9
(-3)
A 		50
avr 71.1
(3) 		47
(-0.7) 		65.2
(2.1) 		32.2
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 53
1 2 3 4 5 6 range
A 26.7
(-3)
A 		62.3
(3)
P 		38.2
(-1.1)
A 		33.4
(-1.9)
A 		31.6
(-2.2)
A 		39.9
(-0.8)
M 		36
B 70.7
(3)
P 		57
(1.1)
P 		37.2
(-1.7)
A 		27.8
(-3)
A 		49.5
(0)
A 		65.4
(2.3)
P 		43
C 67.6
(2.1)
P 		52.4
(0.4)
P 		47.6
(-0.2)
A 		22.5
(-3)
M 		35.9
(-1.5)
A 		75.8
(3)
P 		53
avr 55
(2) 		57.2
(2.4) 		41
(-0.6) 		27.9
(-3) 		39
(-1) 		60.4
(3) 		33
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187513_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10913
Sequence Type Exemplar sequence
Representative Public ID Y55F3AM.15 NCBI
Target Description Y55F3AM.15 /REP_DB=WormBase Gene ID /WP=CE25482 /TR=Q9N359 /GB=AAF60803.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=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_067633(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067633 NCBI Caenorhabditis elegans COP-9 SigNalosome subunit family member (csn-4) (csn-4) mRNA, complete cds. 11/11 None
Y55F3AM.15 ENSEMBL cdna:known chromosome:CEL140:IV:1077471:1087013:-1 gene:Y55F3AM.15 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:1077920-1087013(-) 99.92 100.0
Public Domain and Genome References
Gene Title
Gene Symbol csn-4
Ensembl Y55F3AM.15
Entrez Gene 176927 Entrez gene
SwissProt Q9N359 EMBL-EBI
WormBase CE25482 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAF60803 Cop-9 signalosome subunit protein 4 [Caenorhabditis elegans] ref|NP_500034.1| COP-9 SigNalosome subunit family member (csn-4) [Caenorhabditis elegans] sp|Q9N359|CSN4_CAEEL COP9 signalosome complex subunit 4 (Signalosome subunit 4) 0.0
blast CAE63864 Hypothetical protein CBG08426 [Caenorhabditis briggsae] 0.0
blast XP_623684 PREDICTED: similar to ENSANGP00000015673 [Apis mellifera] 1.0E-62
Protein Domains
Database ID Description E-Value
Pfam IPR000717 EMBL-EBI Proteasome component region PCI 9.1E-25
Sequence
Target Sequence 
>C. ELEGANS:187513_AT
gagtttcagatgccaagcgtcgattcgttgaagctgctcaaagatactacgagctcagtg
caacagagcaacttcccaactctgacaagctcaccgcactgggaaaagccatcgtctgcg
tacttttggccaaaccgggaccccagcgatcacggcttctaactctgattttcaaggacg
aacgggctccaaaatgtgcatcttttgagcttatcgcaaagatgtacttgacaaaagtca
tccataaagatgagcttgaagagtttgagcatcaacttcaagaccatcaaaaagctgatg
aacatggagaatctattctgaaaggagttattcaagagcataatattactgcgattagtc
agttgtacattaatatctcgtttaaaactcttggacagttgctcggagttgatacggaag
cggcagaatcaatggctggagagatgatttcatcggaacgtcttcacggatacattgatc
aaaccaacggaattcttcattttgaagattcaaatccgatgagagtatgggattcacaga
ttctttcgacattggaacaaattaacaaagtcagcgatatgattgttgcccgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTTTCAGATGCCAAGCGTCGATT 343 399 629 Antisense
AGCGTCGATTCGTTGAAGCTGCTCA 63 81 644 Antisense
GATACTACGAGCTCAGTGCAACAGA 583 423 671 Antisense
GTGCAACAGAGCAACTTCCCAACTC 383 481 686 Antisense
CAAGCTCACCGCACTGGGAAAAGCC 443 185 714 Antisense
GCCATCGTCTGCGTACTTTTGGCCA 704 277 736 Antisense
CACGGCTTCTAACTCTGATTTTCAA 377 199 779 Antisense
TCTTGGACAGTTGCTCGGAGTTGAT 409 619 1017 Antisense
GATTTCATCGGAACGTCTTCACGGA 190 427 1074 Antisense
GGGATTCACAGATTCTTTCGACATT 607 495 1157 Antisense
AGTCAGCGATATGATTGTTGCCCGG 584 61 1197 Antisense
Sequence Source Affymetrix Proprietary Database