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[171742_x_at] cyclin A-associated protein

Description C31412_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C52D10.9 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C31412 /WB_GENE_ID=C52D10.9 /WP=CE17593 /CHR=4 /FEA=Genomic Cluster /GEN=skr-8 /DEF=cyclin A-associated protein; C.elegans cDNA clone yk282d6 : 3prime end, single read.
Cluster 6grp_total > 68      4grp_total > 18      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.
4 279
1 2 3 4 range
A 165.8
(-2.7)
A 		153.1
(-3)
A 		180.5
(-2.3)
A 		378.8
(3)
A 		226
B 134
(-1.9)
A 		141.8
(-1.4)
A 		116
(-3)
A 		214.6
(3)
P 		99
C 100.2
(-3)
A 		205.8
(1.6)
A 		139.1
(-1.3)
A 		237.2
(3)
P 		137
avr 133.3
(-3) 		166.9
(-1.6) 		145.2
(-2.5) 		276.9
(3) 		144

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1448
1 2 3 4 5 6 range
A 177.1
(-2.8)
A 		176.7
(-2.8)
A 		155.7
(-2.9)
A 		138
(-3)
A 		396.3
(-1.9)
P 		1520.9
(3)
P 		1383
B 234.9
(-2.5)
A 		186.1
(-2.7)
A 		126.4
(-3)
A 		141.2
(-2.9)
A 		355.2
(-2)
P 		1452.2
(3)
P 		1326
C 266
(-2.5)
P 		256.7
(-2.6)
P 		172.1
(-2.9)
A 		151.4
(-3)
A 		317.2
(-2.3)
M 		1574.7
(3)
P 		1423
avr 226
(-2.6) 		206.5
(-2.7) 		151.4
(-3) 		143.5
(-3) 		356.2
(-2.1) 		1515.9
(3) 		1372
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 34
1 2 3 4 range
A 60.4
(3)
A 		33.2
(-3)
A 		47.2
(0.1)
A 		55.5
(1.9)
A 		27
B 42.7
(2)
A 		35
(-0.4)
A 		26.9
(-3)
A 		45.7
(3)
P 		19
C 33.2
(-3)
A 		59.2
(3)
A 		48.5
(0.5)
A 		40
(-1.4)
P 		26
avr 45.4
(1.4) 		42.5
(-1.5) 		40.9
(-3) 		47.1
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 511
1 2 3 4 5 6 range
A 32.6
(-3)
A 		62.8
(-2.5)
A 		33.9
(-3)
A 		35
(-3)
A 		119.6
(-1.5)
P 		370.3
(3)
P 		338
B 81.7
(-2.4)
A 		61.9
(-2.6)
A 		30.7
(-3)
A 		37.4
(-2.9)
A 		144.3
(-1.7)
P 		541.5
(3)
P 		511
C 98.6
(-2.2)
P 		78.3
(-2.4)
P 		43.8
(-2.8)
A 		30.4
(-3)
A 		102.7
(-2.1)
M 		527.1
(3)
P 		497
avr 71
(-2.5) 		67.7
(-2.5) 		36.1
(-3) 		34.3
(-3) 		122.2
(-1.8) 		479.6
(3) 		445
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171742_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24791
Sequence Type Exemplar sequence
Representative Public ID C31412 NCBI
Target Description C31412_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C52D10.9 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C31412 /WB_GENE_ID=C52D10.9 /WP=CE17593 /CHR=4 /FEA=Genomic Cluster /GEN=skr-8 /DEF=cyclin A-associated protein; C.elegans cDNA clone yk282d6 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_070643(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070643 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-8) (skr-8) mRNA, complete cds. 11/11 A 
SNAP00000030639 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17165206:17165790:-1 10/11 None
GENEFINDER00000030658 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17165206:17165790:-1 10/11 None
C52D10.9 ENSEMBL cdna:known chromosome:CEL140:IV:17165206:17165790:-1 gene:C52D10.9 10/11 A 
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_070642 7/11 Cross Hyb Matching Probes A 
SNAP00000018397 1/11 Cross Hyb Matching Probes None
GENEFINDER00000018421 1/11 Cross Hyb Matching Probes None
SNAP00000030638 7/11 Cross Hyb Matching Probes None
GENEFINDER00000030655 7/11 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 
C52D10.7 7/11 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:17163533-17164125(+) 89.62 89.62
chrIV:17165161-17165797(-) 100.0 100.0
Public Domain and Genome References
Gene Title cyclin A-associated protein
Gene Symbol skr-8
Ensembl C52D10.9
Entrez Gene 178495 Entrez gene
SwissProt Q966N8 EMBL-EBI
WormBase CE17593 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
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] 5.0E-78
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] 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 1.4E-37
Pfam IPR001232 EMBL-EBI SKP1 component 3.7E-25
Sequence
Target Sequence 
>C. ELEGANS:171742_X_AT
tgaagccgccgcggtcgaagttcaagccaacgaggctccagttgttgctccaatcatgta
caaggtcgaatcgaatgatggaaaagtgttcgaaatcagtgatgaagcagttaaacaatc
aaatatcctctccaatctgatctctacttgtgctccagaggatgttgcttcaatggatcc
aattccaatcacaaatgtcactggaaatatcctgaagatggtcattgagtggtgtgagaa
gcacaaaggagaagcgcttccagttgaagatgacagtgttccaaagaatataaatgttcc
cgaatgggataccaacttcttgaaaatcgacaacgaagtgctcttcgacttgatcgttgc
ctgcaactaccttgatgtgcctggattaatgaattatggatgcaagatggttgccaacat
ggctatcggaaaatctcctgatgagttgagaatcatctttgcaattccaactgatgaaga
agatgaagctgcggagagagctgcaaaggagaaggctgaagctgagaagaaggcaattgc
tgacaaggacgcagctgaaccatcaacttccaaataactttcatgctct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAAGCCGCCGCGGTCGAAGTTCAA 664 573 22 Antisense
GCCAACGAGGCTCCAGTTGTTGCTC 174 279 47 Antisense
GTTGCTCCAATCATGTACAAGGTCG 277 439 65 Antisense
CAAATATCCTCTCCAATCTGATCTC 74 195 141 Antisense
ATCTGATCTCTACTTGTGCTCCAGA 22 35 156 Antisense
TGCTCCAGAGGATGTTGCTTCAATG 421 581 172 Antisense
CGAAGTGCTCTTCGACTTGATCGTT 670 253 355 Antisense
GATCGTTGCCTGCAACTACCTTGAT 503 417 373 Antisense
ACTACCTTGATGTGCCTGGATTAAT 633 99 387 Antisense
AAGGACGCAGCTGAACCATCAACTT 502 159 566 Antisense
AACTTCCAAATAACTTTCATGCTCT 248 139 586 Antisense
Sequence Source Affymetrix Proprietary Database