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[188229_s_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 > 26      6grp_high1_10_10 > 62      4grp_highest_8_8 > 26      4grp_high_8_8 > 59      6grp_highest_nonorm > 34      6grp_total > 62      4grp_total > 60      6grp_highest_sub > 03      6grp_cgc > 92      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 774
1 2 3 4 range
A 1844.8
(1.7)
P 		1904.2
(3)
P 		1786
(0.5)
P 		1621.4
(-3)
P 		283
B 1877.2
(0.9)
P 		1805.7
(0.4)
P 		2146.1
(3)
P 		1372.1
(-3)
P 		774
C 1857.6
(1.1)
P 		1693.7
(-0.9)
P 		2006.6
(3)
P 		1528.6
(-3)
P 		478
avr 1859.9
(1.5) 		1801.2
(0.7) 		1979.6
(3) 		1507.4
(-3) 		472

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3026
1 2 3 4 5 6 range
A 1987.4
(-2.5)
P 		2663.1
(-0.7)
P 		3983
(3)
P 		3423.9
(1.4)
P 		2251.7
(-1.8)
P 		1819.5
(-3)
P 		2164
B 2047.1
(-2.6)
P 		2362.6
(-2)
P 		4845
(3)
P 		2844.5
(-1)
P 		2368.6
(-2)
P 		1863.4
(-3)
P 		2982
C 2071.8
(-3)
P 		2537.8
(-1.2)
P 		3658.1
(3)
P 		3470.7
(2.3)
P 		2185.6
(-2.6)
P 		2394.2
(-1.8)
P 		1586
avr 2035.4
(-3) 		2521.2
(-1.6) 		4162
(3) 		3246.4
(0.4) 		2268.6
(-2.3) 		2025.7
(-3) 		2136
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 462
1 2 3 4 range
A 671.7
(3)
P 		413.3
(-0.6)
P 		466.9
(0.2)
P 		237.3
(-3)
P 		434
B 598.6
(3)
P 		446
(0)
P 		497.3
(1)
P 		292.4
(-3)
P 		306
C 614.9
(1.9)
P 		486.9
(0.1)
P 		699.4
(3)
P 		257.7
(-3)
P 		442
avr 628.4
(3) 		448.7
(0.1) 		554.5
(1.8) 		262.5
(-3) 		366

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 810
1 2 3 4 5 6 range
A 366.4
(-3)
P 		947.1
(3)
P 		867.4
(2.2)
P 		868.4
(2.2)
P 		679.5
(0.2)
P 		443
(-2.2)
P 		581
B 712.3
(-2.8)
P 		786.4
(-1.9)
P 		1176.5
(3)
P 		753.4
(-2.3)
P 		962.4
(0.3)
P 		694.8
(-3)
P 		482
C 767.9
(-1.2)
P 		774.4
(-1)
P 		931
(3)
P 		698
(-3)
P 		707.2
(-2.8)
P 		801.5
(-0.3)
P 		233
avr 615.5
(-3) 		836
(0.5) 		991.6
(3) 		773.3
(-0.5) 		783
(-0.3) 		646.4
(-2.5) 		376
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188229_s_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), NM_074658(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 
NM_074658 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-3) (skr-3) mRNA, complete cds. 11/11 A 
SNAP00000003417 ENSEMBL cdna:SNAP chromosome:CEL140:V:16124436:16125056:1 11/11 None
GENEFINDER00000003430 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16124436:16125056:1 11/11 None
GENEFINDER00000032831 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:19922250:19922858:1 11/11 None
F44G3.6.2 ENSEMBL cdna:known chromosome:CEL140:V:16124405:16125224:1 gene:F44G3.6 11/11 None
F44G3.6.1 ENSEMBL cdna:known chromosome:CEL140:V:16124407:16125231:1 gene:F44G3.6 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-3
skr-4
Ensembl F44G3.6
Y60A3A.18
Entrez Gene 180081 Entrez gene
191762 Entrez gene
SwissProt O45517 EMBL-EBI
Q9U1Y9 EMBL-EBI
WormBase CE16037 Wormbase
CE24523 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:265899_S_AT E3 ubiquitin ligase SCF complex subunit, putative at
ATH1-121501:251440_AT E3 ubiquitin ligase SCF complex subunit SKP1/ASK1 (At13), putative at
Protein Similarities
Method ID Description E-Value
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] 2.0E-90
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 CAB60402 Hypothetical protein Y60A3A.18 [Caenorhabditis elegans] ref|NP_507857.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-4) [Caenorhabditis elegans] 1.0E-70
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 1.1E-50
Pfam IPR001232 EMBL-EBI SKP1 component 1.4E-33
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:188229_S_AT
atgtcagacgccgacagccagaaacaaatcaagctcatctcgtctgatgataaaactttc
acggtctcacgaaaagtgatcagccaatccaagaccatatctggattcacttctgaagac
acgattccacttccaaaagtgacttctgcgatccttgagaagattatcacctggtgcgag
catcacgccgacgatgagccaaagaaagtcgaaaagatagaaaaaggaaataaaaagacg
gtagaaattagtgaatgggacgccgagttcatgaaagtcgaccaggggactttgttcgaa
atcatcttggcagccaactacctcgacatccgtgggcttttggaagtgaccacccagaat
gtggctaacatgatgaagggtaaaactccaagccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTCAGACGCCGACAGCCAGAAAC 67 49 13 Antisense
GACGCCGACAGCCAGAAACAAATCA 583 379 19 Antisense
GATAAAACTTTCACGGTCTCACGAA 273 423 61 Antisense
TTTCACGGTCTCACGAAAAGTGATC 171 671 69 Antisense
CACTTCTGAAGACACGATTCCACTT 214 195 120 Antisense
TGAGAAGATTATCACCTGGTGCGAG 406 563 168 Antisense
TTATCACCTGGTGCGAGCATCACGC 60 681 176 Antisense
AGCATCACGCCGACGATGAGCCAAA 243 79 191 Antisense
ACGCCGACGATGAGCCAAAGAAAGT 329 89 197 Antisense
GTGACCACCCAGAATGTGGCTAACA 290 483 358 Antisense
GATGAAGGGTAAAACTCCAAGCCAA 484 391 384 Antisense
Sequence Source Affymetrix Proprietary Database