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[188228_at]

Description Y60A3A.18 /REP_DB=WormBase Gene ID /WP=CE24523 /GEN=skr-4 /TR=Q9U1Y9 /GB=CAB60402.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 73      4grp_highest_8_8 > 20      4grp_high_8_8 > 31      6grp_highest_nonorm > 54      6grp_total > 74      4grp_total > 32      6grp_cgc > 66      6grp_high1_sub > 03_04      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 356
1 2 3 4 range
A 254.8
(-3)
P 		283.8
(-2.5)
P 		586
(3)
P 		425.3
(0.1)
P 		331
B 293.8
(-3)
P 		412.5
(-0.8)
P 		610.5
(3)
P 		557.3
(2)
P 		317
C 302.1
(-3)
P 		386.2
(-0.7)
P 		512.9
(2.7)
P 		522.5
(3)
P 		220
avr 283.6
(-3) 		360.8
(-1.4) 		569.8
(3) 		501.7
(1.6) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1876
1 2 3 4 5 6 range
A 209.9
(-3)
P 		721.3
(-1)
P 		1369.1
(1.6)
P 		1712.1
(3)
P 		1389.2
(1.7)
P 		1098
(0.5)
P 		1502
B 182.5
(-3)
P 		612.2
(-1)
P 		1464.5
(3)
P 		1272.2
(2.1)
P 		1367
(2.5)
P 		1257.4
(2)
P 		1282
C 305.5
(-3)
P 		779.4
(-1.4)
P 		2058.4
(3)
P 		938.3
(-0.8)
P 		1222.3
(0.1)
P 		1588.2
(1.4)
P 		1753
avr 232.6
(-3) 		704.3
(-1) 		1630.7
(3) 		1307.5
(1.6) 		1326.2
(1.7) 		1314.5
(1.6) 		1398
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 117
1 2 3 4 range
A 92.8
(-1)
P 		61.6
(-3)
P 		153.2
(3)
P 		62.3
(-3)
P 		92
B 93.7
(-3)
P 		101.9
(-2)
P 		141.5
(3)
P 		118.8
(0.2)
P 		48
C 100
(-2.2)
P 		111
(-1.5)
P 		178.8
(3)
P 		88.1
(-3)
P 		91
avr 95.5
(-2.5) 		91.5
(-2.8) 		157.8
(3) 		89.7
(-3) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 517
1 2 3 4 5 6 range
A 38.7
(-3)
P 		256.5
(0.3)
P 		298.2
(0.9)
P 		434.2
(3)
P 		419.2
(2.8)
P 		267.3
(0.5)
P 		396
B 63.5
(-3)
P 		203.8
(-1.3)
P 		355.6
(0.6)
P 		337
(0.3)
P 		555.4
(3)
P 		468.9
(1.9)
P 		492
C 113.3
(-3)
P 		237.8
(-1.2)
P 		523.9
(2.9)
P 		188.7
(-1.9)
P 		395.5
(1)
P 		531.7
(3)
P 		418
avr 71.8
(-3) 		232.7
(-0.5) 		392.6
(2) 		320
(0.9) 		456.7
(3) 		422.6
(2.5) 		385
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188228_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13502
Sequence Type Exemplar sequence
Representative Public ID Y60A3A.18 NCBI
Target Description Y60A3A.18 /REP_DB=WormBase Gene ID /WP=CE24523 /GEN=skr-4 /TR=Q9U1Y9 /GB=CAB60402.1 /SUBMIT=HINXTON /CHR=5 /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_075456(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075456 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-4) (skr-4) mRNA, complete cds. 11/11 A 
GENEFINDER00000032831 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:19922250:19922858:1 11/11 None
Y60A3A.18 ENSEMBL cdna:known chromosome:CEL140:V:19922219:19923027:1 gene:Y60A3A.18 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:19922249-19922858(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol skr-4
Ensembl Y60A3A.18
Entrez Gene 191762 Entrez gene
SwissProt Q9U1Y9 EMBL-EBI
WormBase CE24523 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251440_AT E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At13), putative at
Protein Similarities
Method ID Description E-Value
blast CAB60402 Hypothetical protein Y60A3A.18 [Caenorhabditis elegans] ref|NP_507857.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-4) [Caenorhabditis elegans] 2.0E-77
blast CAB05516 Hypothetical protein F44G3.6 [Caenorhabditis elegans] ref|NP_507059.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-3) [Caenorhabditis elegans] gb|AAL34095.1| SKR-3 [Caenorhabditis elegans] 7.0E-66
blast CAB03110 Hypothetical protein F46A9.5 [Caenorhabditis elegans] emb|CAB03027.1| Hypothetical protein F46A9.5 [Caenorhabditis elegans] ref|NP_492513.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-1) [Caenorhabditis elegans] 8.0E-38
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 1.1E-41
Pfam IPR001232 EMBL-EBI SKP1 component 8.6E-10
Pfam IPR001232 EMBL-EBI SKP1 component 7.6E-12
Sequence
Target Sequence 
>C. ELEGANS:188228_AT
aacaaatcaagctcatctcgtctgatgataaaactttcacggtctcacgaaaagtgatca
gccaatccaagaccatatctggattcacttctgaagacacgattccacttccaaaagtga
cttctgcgatccttgagaagattatcacctggtgcgagcatcacgccgacgatgagccaa
agaaagtcgaaaagatagaaaaaggaaataaaaagacggtagaaattagtgaatgggacg
ccgagttcatgaaagtcgaccaggggactttgttcgaaatcatcttggcagccaactacc
tcgacatccgtgggcttttggaagtgaccacccagaatgtggctaacatgatgaagggta
aaactccaagccaagtccgaaccctgttcaaaattgacaacttctccgaggaggaactgg
aggcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACAAATCAAGCTCATCTCGTCTGA 49 135 35 Antisense
GATCAGCCAATCCAAGACCATATCT 467 421 90 Antisense
AGACCATATCTGGATTCACTTCTGA 302 71 104 Antisense
CCAAAAGTGACTTCTGCGATCCTTG 166 275 145 Antisense
AAGTGACTTCTGCGATCCTTGAGAA 516 157 149 Antisense
GAGTTCATGAAAGTCGACCAGGGGA 656 397 277 Antisense
GACCAGGGGACTTTGTTCGAAATCA 68 383 292 Antisense
TTGTTCGAAATCATCTTGGCAGCCA 31 707 304 Antisense
GCCAAGTCCGAACCCTGTTCAAAAT 337 277 404 Antisense
AAATTGACAACTTCTCCGAGGAGGA 490 115 425 Antisense
CTTCTCCGAGGAGGAACTGGAGGCC 67 19 435 Antisense
Sequence Source Affymetrix Proprietary Database