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[188165_at]

Description C42D4.6 /REP_DB=WormBase Gene ID /WP=CE04194 /GEN=skr-16 /TR=Q18567 /GB=AAA83342.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 23      6grp_high1_10_10 > 02      4grp_highest_8_8 > 37      4grp_high_8_8 > 03      6grp_highest_nonorm > 71      6grp_total > 34      4grp_total > 06      6grp_highest_sub > 01_02_03      6grp_cgc > 34      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 185
1 2 3 4 range
A 321.1
(-2.5)
P 		317.6
(-3)
P 		331.4
(-1.1)
P 		360.5
(3)
P 		43
B 365.5
(0.2)
P 		266.6
(-3)
P 		313.3
(-1.5)
P 		451.1
(3)
P 		185
C 408
(2.4)
P 		324.3
(-3)
P 		334.9
(-2.3)
P 		417.6
(3)
P 		93
avr 364.9
(0.5) 		302.8
(-3) 		326.5
(-1.7) 		409.7
(3) 		107

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 257
1 2 3 4 5 6 range
A 348.5
(0.7)
P 		296.3
(-0.5)
P 		447.1
(3)
P 		278.5
(-0.9)
P 		190.1
(-3)
P 		201.4
(-2.7)
P 		257
B 346.6
(0.7)
P 		404.4
(2.8)
P 		410.3
(3)
P 		245.1
(-3)
P 		285.5
(-1.5)
P 		362.1
(1.2)
P 		165
C 352.7
(2.3)
P 		365.5
(3)
P 		262.3
(-2.3)
P 		301
(-0.3)
P 		249.4
(-3)
P 		316.8
(0.5)
P 		116
avr 349.3
(1.9) 		355.4
(2.2) 		373.2
(3) 		274.9
(-1.5) 		241.7
(-3) 		293.4
(-0.6) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 82
1 2 3 4 range
A 116.9
(3)
P 		68.9
(-1.5)
P 		86.6
(0.2)
P 		52.8
(-3)
P 		64
B 116.5
(3)
P 		65.8
(-3)
P 		72.6
(-2.2)
P 		96.1
(0.6)
P 		51
C 135
(3)
P 		93.2
(-0.9)
P 		116.7
(1.3)
P 		70.4
(-3)
P 		65
avr 122.8
(3) 		76
(-2.6) 		92
(-0.7) 		73.1
(-3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 86
1 2 3 4 5 6 range
A 64.2
(-1.4)
P 		105.4
(3)
P 		97.4
(2.1)
P 		70.6
(-0.7)
P 		57.4
(-2.1)
P 		49
(-3)
P 		56
B 120.6
(1.8)
P 		134.6
(3)
P 		99.6
(-0)
P 		64.9
(-3)
P 		116
(1.4)
P 		135
(3)
P 		70
C 130.7
(3)
P 		111.5
(1.4)
P 		66.8
(-2.5)
P 		60.5
(-3)
P 		80.7
(-1.3)
P 		106
(0.9)
P 		70
avr 105.2
(1.6) 		117.2
(3) 		87.9
(-0.4) 		65.3
(-3) 		84.7
(-0.8) 		96.7
(0.6) 		52
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188165_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9052
Sequence Type Exemplar sequence
Representative Public ID C42D4.6 NCBI
Target Description C42D4.6 /REP_DB=WormBase Gene ID /WP=CE04194 /GEN=skr-16 /TR=Q18567 /GB=AAA83342.1 /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_068727(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068727 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-16) (skr-16) mRNA, complete cds. 11/11 None
SNAP00000029579 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7168693:7169238:1 11/11 None
GENEFINDER00000029591 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7168693:7169238:1 11/11 None
C42D4.6 ENSEMBL cdna:known chromosome:CEL140:IV:7168693:7169276:1 gene:C42D4.6 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:7166946-7169244(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol skr-16
Ensembl C42D4.6
Entrez Gene 191765 Entrez gene
SwissProt Q18567 EMBL-EBI
WormBase CE37712 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_501128 SKp1 Related (ubiquitin ligase complex component) family member (skr-16) [Caenorhabditis elegans] gb|AAA83342.2| Skp1 related (ubiquitin ligase complex component) protein 16 [Caenorhabditis elegans] 1.0E-89
blast CAE61821 Hypothetical protein CBG05791 [Caenorhabditis briggsae] 4.0E-62
blast NP_503045 SKp1 Related (ubiquitin ligase complex component) family member (skr-12) [Caenorhabditis elegans] gb|AAK77208.1| Skp1 related (ubiquitin ligase complex component) protein 12 [Caenorhabditis elegans] gb|AAL34101.1| SKR-12 [Caenorhabditis elegans] gb|AAB17536.1| homolog to Skp1p, an evolutionarily conserved kinetochore protein in budding yeast [Caenorhabditis elegans] 3.0E-21
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 2.7E-25
Pfam IPR001232 EMBL-EBI SKP1 component 3.5E-7
Sequence
Target Sequence 
>C. ELEGANS:188165_AT
aaaaggctgcagcgagagcggcaaaagcccgtgaaactgctgaaaccaatgcattcctgg
atagtatattcattttaatatcgtcagatggtgaaaaatttcaaacggatggtcattgca
taaggcattcaaaagttctcatgcaagcgtcaaaatcattagaaacaccggatacaccaa
ttcaagttgaaaaagtgcaaggagacacactgaatcgagttctggaatggtgtaataatc
atcgagacgatggaaaatatgtgtcacaatgtggacctagtctacgtcttccacaatggg
attttcgatggcttaaagatttggataatcaggagctagttgatttaatcaatgcgtcga
atgatctacaaatgcaacaattgatggattatgcatgcaagacagtggcaaatatggcaa
aaggaaagaatcccgcacaattgagagaactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAAGGCTGCAGCGAGAGCGGCAAA 148 133 512 Antisense
GAGCGGCAAAAGCCCGTGAAACTGC 132 385 527 Antisense
ACTGCTGAAACCAATGCATTCCTGG 212 99 547 Antisense
AACGGATGGTCATTGCATAAGGCAT 291 133 615 Antisense
TCAAAAGTTCTCATGCAAGCGTCAA 560 629 640 Antisense
TCATTAGAAACACCGGATACACCAA 510 605 667 Antisense
GGAGACACACTGAATCGAGTTCTGG 340 519 712 Antisense
AATGTGGACCTAGTCTACGTCTTCC 510 163 779 Antisense
TACGTCTTCCACAATGGGATTTTCG 670 647 794 Antisense
AATGCGTCGAATGATCTACAAATGC 180 167 862 Antisense
GAATCCCGCACAATTGAGAGAACTT 598 329 939 Antisense
Sequence Source Affymetrix Proprietary Database