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[188417_at]

Description ZC395.2 /REP_DB=WormBase Gene ID /WP=CE01438 /GEN=clk-1 /TR=SW:P48376 /GB=AAG00035.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 37      6grp_high1_10_10 > 63      4grp_highest_8_8 > 07      4grp_high_8_8 > 20      6grp_highest_nonorm > 75      6grp_total > 63      4grp_total > 19      6grp_highest_sub > 03_04      6grp_cgc > 93      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 343
1 2 3 4 range
A 632.8
(-2)
P 		723.4
(0.3)
P 		591.3
(-3)
P 		833.7
(3)
P 		242
B 721.4
(-0.3)
P 		720.9
(-0.3)
P 		577.9
(-3)
P 		892.9
(3)
P 		315
C 628.6
(-3)
P 		728.1
(-1)
P 		654.6
(-2.5)
P 		920.6
(3)
P 		292
avr 660.9
(-1.8) 		724.1
(-0.5) 		607.9
(-3) 		882.4
(3) 		275

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 531
1 2 3 4 5 6 range
A 960.4
(-0.8)
P 		928.7
(-1.4)
P 		1115.6
(2.5)
P 		1138.8
(3)
P 		855
(-3)
P 		992.1
(-0.1)
P 		284
B 762.5
(-3)
P 		810.5
(-2.1)
P 		1081.1
(3)
P 		993
(1.3)
P 		908.3
(-0.3)
P 		924.5
(0.1)
P 		319
C 804.8
(-3)
P 		884.7
(-2)
P 		1293.3
(3)
P 		1189.5
(1.7)
P 		804.7
(-3)
P 		955.4
(-1.1)
P 		489
avr 842.6
(-3) 		874.6
(-2.4) 		1163.3
(3) 		1107.1
(1.9) 		856
(-2.7) 		957.3
(-0.9) 		321
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 108
1 2 3 4 range
A 230.4
(3)
P 		157
(-1.1)
P 		154.6
(-1.2)
P 		122
(-3)
P 		108
B 230
(3)
P 		178
(-0.2)
P 		133.9
(-3)
P 		190.3
(0.5)
P 		96
C 208.1
(1.3)
P 		209.3
(1.4)
P 		228.2
(3)
P 		155.2
(-3)
P 		73
avr 222.8
(3) 		181.4
(-0.7) 		172.2
(-1.5) 		155.8
(-3) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 192
1 2 3 4 5 6 range
A 177
(-3)
P 		330.3
(3)
P 		243
(-0.4)
P 		288.8
(1.4)
P 		258
(0.2)
P 		241.6
(-0.5)
P 		153
B 265.3
(-2.8)
P 		269.8
(-2.6)
P 		262.5
(-3)
P 		263
(-3)
P 		369
(3)
P 		344.8
(1.6)
P 		107
C 298.3
(0.9)
P 		270
(-0.9)
P 		329.2
(3)
P 		239.2
(-3)
P 		260.4
(-1.6)
P 		319.8
(2.4)
P 		90
avr 246.9
(-3) 		290
(1.7) 		278.2
(0.4) 		263.7
(-1.2) 		295.8
(2.3) 		302.1
(3) 		55
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188417_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7728
Sequence Type Exemplar sequence
Representative Public ID ZC395.2 NCBI
Target Description ZC395.2 /REP_DB=WormBase Gene ID /WP=CE01438 /GEN=clk-1 /TR=SW:P48376 /GB=AAG00035.1 /SUBMIT=ST.LOUIS /CHR=3 /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_065727(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065727 NCBI Caenorhabditis elegans CLocK (biological timing) abnormality family member (clk-1) (clk-1) mRNA, complete cds. 11/11 None
SNAP00000016753 ENSEMBL cdna:SNAP chromosome:CEL140:III:5277851:5279125:1 11/11 None
ZC395.2 ENSEMBL cdna:known chromosome:CEL140:III:5277851:5279290:1 gene:ZC395.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000016759 3/11 Cross Hyb Matching Probes None
GENEFINDER00000016757 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:5277849-5279124(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol clk-1
Ensembl ZC395.2
Entrez Gene 175729 Entrez gene
SwissProt P48376 EMBL-EBI
WormBase CE01438 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1598607_AT similar to Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing protein clk-1 homolog) cfa
CANINE:1592120_AT similar to Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing protein clk-1 homolog) cfa
CANINE_2:CFA.8940.1.A1_S_AT similar to Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing protein clk-1 homolog) cfa
CANINE_2:CFA.8940.2.A1_AT similar to Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing protein clk-1 homolog) cfa
DROSOPHILA_2:1635151_AT dm
DROSGENOME1:144615_AT dm
CHICKEN:GGA.8387.1.S1_A_AT coenzyme Q7 homolog, ubiquinone (yeast) gga
CHICKEN:GGA.8387.1.S1_X_AT coenzyme Q7 homolog, ubiquinone (yeast) gga
HG-U133_PLUS_2:209746_S_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A_2:209746_S_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A:209746_S_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-FOCUS:209746_S_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133_PLUS_2:210820_X_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A:210820_X_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A_2:210820_X_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HU35KSUBA:RC_AA150274_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HU35KSUBA:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HU35KSUBB:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HU35KSUBC:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HU35KSUBD:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HUGENEFL:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HC-G110:HUM_ALU_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
U133_X3P:G3811294_3P_A_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
U133_X3P:HS.157113.0.S2_3P_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A_2:209745_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133_PLUS_2:209745_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U133A:209745_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U95AV2:35385_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U95B:43996_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
HG-U95E:75727_AT coenzyme Q7 homolog, ubiquinone (yeast) hs
MG-U74AV2:93582_AT demethyl-Q 7 mm
MOE430A:1416665_AT demethyl-Q 7 mm
MOUSE430A_2:1416665_AT demethyl-Q 7 mm
MOUSE430_2:1416665_AT demethyl-Q 7 mm
MU19KSUBB:TC34677_AT Demethyl-Q 7, mRNA (cDNA clone MGC:48033 IMAGE:1380996) mm
RAE230A:1370506_AT demethyl-Q 7 rn
RAT230_2:1370506_AT demethyl-Q 7 rn
RG-U34A:RC_AA943150_AT demethyl-Q 7 rn
YEAST_2:1770584_AT Mitochondrial inner membrane protein directly involved in ubiquinone biosynthesis, essential for several other metabolic pathways including respiration and gluconeogenic gene activation Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6744 ubiquinone biosynthesis inferred from electronic annotation QuickGO AmiGO
6744 ubiquinone biosynthesis inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5739 mitochondrion inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAG00035 Clock (biological timing) abnormality protein 1 [Caenorhabditis elegans] ref|NP_498128.1| CLocK (biological timing) abnormality family member (clk-1) [Caenorhabditis elegans] sp|P48376|COQ7_CAEEL Ubiquinone biosynthesis protein COQ7 homolog (Clock abnormal protein 1) (Protein clk-1) 1.0E-102
blast CAE73680 Hypothetical protein CBG21190 [Caenorhabditis briggsae] 3.0E-96
blast NP_034070 demethyl-Q 7 [Mus musculus] gb|AAH38681.1| Demethyl-Q 7 [Mus musculus] sp|P97478|COQ7_MOUSE Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing protein clk-1 homolog) gb|AAD43649.1| COQ7 protein [Mus musculus] gb|AAC31572.1| CLK-1 [Mus musculus] 4.0E-53
Protein Domains
Database ID Description E-Value
scop a.1.1.Truncated hemoglobin All alpha proteins; Globin-like; Globin-like; Truncated hemoglobin 8.0
Pfam IPR004916 EMBL-EBI Ubiquinone biosyntheis protein COQ7 1.1E-53
Pfam IPR004916 EMBL-EBI Ubiquinone biosyntheis protein COQ7 5.5E-44
Sequence
Target Sequence 
>C. ELEGANS:188417_AT
taacccgtggagcacatactgctgcttctcgtcaagcacttatagagaagatcattcgag
ttgatcatgctggagagcttggagccgatcggatttacgctggacagttggctgttttgc
aaggttcatctgttggttcagtaatcaaaaagatgtgggatgaggagaaagaacatttag
atacaatggaaagattagctgctaaacacaatgtacctcatactgttttctctccagttt
tcagtgtggctgcttatgctctcggtgtcggttcagcacttctaggaaaagaaggtgcaa
tggcttgtacaattgcagttgaagaactcattggacaacattataatgatcaattgaaag
aactccttgccgacgatcctgaaacacacaaagaattgctgaaaattctcacaagattac
gtgatgaggagcttcatcatcatgatactggagtagaacacgatggaatgaaggctccag
cctactcggctctcaaatggatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAACCCGTGGAGCACATACTGCTGC 684 637 26 Antisense
TGCTGCTTCTCGTCAAGCACTTATA 141 581 45 Antisense
GGAGCCGATCGGATTTACGCTGGAC 169 523 106 Antisense
GGCTGTTTTGCAAGGTTCATCTGTT 359 539 135 Antisense
AATGTACCTCATACTGTTTTCTCTC 152 165 235 Antisense
GTTTTCTCTCCAGTTTTCAGTGTGG 329 449 250 Antisense
TTCAGTGTGGCTGCTTATGCTCTCG 607 687 265 Antisense
GTGTCGGTTCAGCACTTCTAGGAAA 59 441 290 Antisense
TTGAAAGAACTCCTTGCCGACGATC 362 705 379 Antisense
TGCCGACGATCCTGAAACACACAAA 657 585 393 Antisense
AGCCTACTCGGCTCTCAAATGGATT 89 83 504 Antisense
Sequence Source Affymetrix Proprietary Database