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[172782_x_at] cyclin A-associated protein

Description C52D10.7 /REP_DB=WormBase Gene ID /WP=CE17591 /GEN=skr-9 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cyclin A-associated protein
Cluster 6grp_total > 68      4grp_total > 19      6grp_cgc > 48      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 175
1 2 3 4 range
A 84.2
(-3)
A 		129.9
(2.6)
A 		125.6
(2)
A 		133.6
(3)
A 		49
B 80.2
(-1.2)
A 		73.8
(-1.5)
A 		33
(-3)
A 		193.1
(3)
A 		160
C 45.1
(-1.8)
A 		116.4
(1.5)
A 		18.6
(-3)
A 		147.9
(3)
A 		129
avr 69.8
(-2.4) 		106.7
(-0.1) 		59.1
(-3) 		158.2
(3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1298
1 2 3 4 5 6 range
A 183.8
(-2.3)
A 		54.9
(-3)
A 		106.2
(-2.7)
A 		73.8
(-2.9)
A 		250.5
(-2)
P 		1223.8
(3)
P 		1169
B 177.4
(-2.5)
A 		155.7
(-2.6)
A 		93.5
(-2.9)
A 		81.6
(-3)
A 		199.4
(-2.3)
M 		1139
(3)
P 		1057
C 140.5
(-2.7)
A 		84.1
(-3)
A 		131.4
(-2.8)
A 		80.2
(-3)
A 		199.5
(-2.4)
P 		1352.6
(3)
P 		1272
avr 167.2
(-2.5) 		98.2
(-2.9) 		110.4
(-2.8) 		78.5
(-3) 		216.5
(-2.3) 		1238.5
(3) 		1160
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 35
1 2 3 4 range
A 30.7
(2)
A 		28.2
(0.9)
A 		32.8
(3)
A 		19.6
(-3)
A 		13
B 25.6
(0.2)
A 		18.2
(-1.1)
A 		7.6
(-3)
A 		41.1
(3)
A 		34
C 14.9
(-1.1)
A 		33.5
(3)
A 		6.5
(-3)
A 		24.9
(1.1)
A 		27
avr 23.7
(0.8) 		26.6
(2.1) 		15.6
(-3) 		28.5
(3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 437
1 2 3 4 5 6 range
A 33.9
(-2.7)
A 		19.5
(-3)
A 		23.1
(-2.9)
A 		18.7
(-3)
A 		75.6
(-1.8)
P 		297.9
(3)
P 		279
B 61.7
(-2.4)
A 		51.8
(-2.6)
A 		22.7
(-3)
A 		21.6
(-3)
A 		81
(-2.1)
M 		424.7
(3)
P 		403
C 52.1
(-2.5)
A 		25.7
(-2.9)
A 		33.4
(-2.8)
A 		16.1
(-3)
A 		64.6
(-2.3)
P 		452.8
(3)
P 		437
avr 49.2
(-2.5) 		32.3
(-2.8) 		26.4
(-2.9) 		18.8
(-3) 		73.7
(-2.1) 		391.8
(3) 		373
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172782_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9594
Sequence Type Exemplar sequence
Representative Public ID C52D10.7 NCBI
Target Description C52D10.7 /REP_DB=WormBase Gene ID /WP=CE17591 /GEN=skr-9 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cyclin A-associated protein
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_070642(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070642 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-9) (skr-9) mRNA, complete cds. 11/11 None
SNAP00000030638 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17163529:17164113:1 11/11 None
GENEFINDER00000030655 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17163529:17164113:1 11/11 None
C52D10.7 ENSEMBL cdna:known chromosome:CEL140:IV:17163529:17164113:1 gene:C52D10.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_071820 1/11 Cross Hyb Matching Probes A 
NM_070501 1/11 Cross Hyb Matching Probes A 
NM_070643 6/11 Cross Hyb Matching Probes A 
SNAP00000018397 1/11 Cross Hyb Matching Probes None
GENEFINDER00000018421 1/11 Cross Hyb Matching Probes None
SNAP00000030639 6/11 Cross Hyb Matching Probes None
GENEFINDER00000030658 6/11 Cross Hyb Matching Probes None
SNAP00000043263 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043273 1/11 Cross Hyb Matching Probes None
Y105C5B.13 1/11 Cross Hyb Matching Probes A 
C52D10.9 6/11 Cross Hyb Matching Probes A 
Y47D7A.1.2 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17163534-17164119(+) 100.0 100.0
chrIV:17165211-17165796(-) 96.24 96.24
Public Domain and Genome References
Gene Title cyclin A-associated protein
Gene Symbol skr-9
Ensembl C52D10.7
Entrez Gene 178494 Entrez gene
SwissProt Q966N9 EMBL-EBI
WormBase CE17591 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_503043 SKp1 Related (ubiquitin ligase complex component) family member (skr-9) [Caenorhabditis elegans] gb|AAK77209.1| Skp1 related (ubiquitin ligase complex component) protein 9 [Caenorhabditis elegans] gb|AAL34099.1| SKR-9 [Caenorhabditis elegans] 5.0E-78
blast NP_503044 SKp1 Related (ubiquitin ligase complex component) family member (skr-8) [Caenorhabditis elegans] gb|AAK77211.1| Skp1 related (ubiquitin ligase complex component) protein 8 [Caenorhabditis elegans] gb|AAL34098.1| SKR-8 [Caenorhabditis elegans] 6.0E-75
blast CAB54358 Hypothetical protein Y105C5B.13 [Caenorhabditis elegans] ref|NP_502902.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-10) [Caenorhabditis elegans] gb|AAL34100.1| SKR-10 [Caenorhabditis elegans] 3.0E-74
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 4.1E-35
Pfam IPR001232 EMBL-EBI SKP1 component 1.7E-23
Sequence
Target Sequence 
>C. ELEGANS:172782_X_AT
tgaagccgccgcggtcgaagttcaagccaacgaggctccagttgttgctccaatcatgta
caaggtcgaatcgaatgatggaaaagtgttcgaaatcagtgatgaagcagttaaacaatc
aaatatcctctccaatctgatctctacttgtgctccagaggatgttgcttcaatggatcc
aattccaatcacaaatgtcattggaaatatcctgaagatggtcattgagtggtgtgagaa
acacaaaggagaagcgcttccagttgaagatgacagtgttccaaagcatgtcaatgttcc
cgaatgggataccaacttcttgaaaatcgacaacgacgtgctcttcgacttgatcgttgc
ctgtaactaccttgatgtgcctggattaatgaattacggatgtaagattgttgccatgat
ggccattggaaagtctccagat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAAGCCGCCGCGGTCGAAGTTCAA 662 573 21 Antisense
GCCAACGAGGCTCCAGTTGTTGCTC 172 279 46 Antisense
CAAATATCCTCTCCAATCTGATCTC 72 195 140 Antisense
ATCTGATCTCTACTTGTGCTCCAGA 20 35 155 Antisense
TGCTCCAGAGGATGTTGCTTCAATG 419 581 171 Antisense
AAAGCATGTCAATGTTCCCGAATGG 422 123 303 Antisense
ATCGACAACGACGTGCTCTTCGACT 259 35 346 Antisense
GACTTGATCGTTGCCTGTAACTACC 595 369 367 Antisense
AACTACCTTGATGTGCCTGGATTAA 2 141 385 Antisense
ATGTAAGATTGTTGCCATGATGGCC 44 49 420 Antisense
GATGGCCATTGGAAAGTCTCCAGAT 172 407 438 Antisense
Sequence Source Affymetrix Proprietary Database