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[171927_x_at] Cytochrome C oxidase

Description CEK100E6R_rc /REP_DB=TREMBL Accession /GB=D66444 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk100e6 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 36      6grp_high1_10_10 > 63      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 28      6grp_total > 53      4grp_total > 09      6grp_highest_sub > 03      6grp_cgc > 91      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10652
1 2 3 4 range
A 11257
(-3)
P 		14090.9
(-1.3)
P 		13164.8
(-1.8)
P 		21101.8
(3)
P 		9845
B 12453
(-2.2)
P 		11859.7
(-3)
P 		13796.7
(-0.3)
P 		16226.9
(3)
P 		4367
C 10449.4
(-3)
P 		12603.1
(-1.7)
P 		11776.6
(-2.2)
P 		20149.2
(3)
P 		9700
avr 11386.5
(-3) 		12851.2
(-1.9) 		12912.7
(-1.8) 		19159.3
(3) 		7773

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4131
1 2 3 4 5 6 range
A 11616.3
(-0.5)
P 		10773.3
(-1.7)
P 		14012.4
(3)
P 		11883.6
(-0.1)
P 		9908.8
(-3)
P 		10176.9
(-2.6)
P 		4104
B 9937.1
(-3)
P 		10417.5
(-1.9)
P 		12596.2
(3)
P 		10596.9
(-1.5)
P 		11315.5
(0.1)
P 		10734.8
(-1.2)
P 		2659
C 9881.5
(-3)
P 		10754.8
(-0.4)
P 		11865.7
(3)
P 		10864.1
(-0)
P 		11415.1
(1.6)
P 		10912.4
(0.1)
P 		1984
avr 10478.3
(-3) 		10648.5
(-2.6) 		12824.8
(3) 		11114.9
(-1.4) 		10879.8
(-2) 		10608
(-2.7) 		2347
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1175
1 2 3 4 range
A 4098.7
(3)
P 		3058.7
(-3)
P 		3441.5
(-0.8)
P 		3088.9
(-2.8)
P 		1040
B 3971.2
(3)
P 		2929.1
(-3)
P 		3197
(-1.5)
P 		3458
(0)
P 		1042
C 3459
(-2.5)
P 		3623.5
(-1.1)
P 		4104.5
(3)
P 		3397.5
(-3)
P 		707
avr 3843
(3) 		3203.8
(-3) 		3581
(0.5) 		3314.8
(-2) 		639

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2456
1 2 3 4 5 6 range
A 2141.4
(-3)
P 		3831.5
(3)
P 		3051.6
(0.2)
P 		3014
(0.1)
P 		2990
(0)
P 		2477.8
(-1.8)
P 		1690
B 3457.6
(-0.8)
P 		3467.6
(-0.8)
P 		3058.7
(-2.2)
P 		2806.8
(-3)
P 		4597.3
(3)
P 		4002.9
(1)
P 		1791
C 3662.6
(2.9)
P 		3281.6
(1.4)
P 		3020
(0.3)
P 		2184.8
(-3)
P 		3693.8
(3)
P 		3653
(2.8)
P 		1509
avr 3087.2
(-0.7) 		3526.9
(1.7) 		3043.4
(-0.9) 		2668.5
(-3) 		3760.4
(3) 		3377.9
(0.9) 		1092
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171927_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27983
Sequence Type Exemplar sequence
Representative Public ID CEK100E6R NCBI
Target Description CEK100E6R_rc /REP_DB=TREMBL Accession /GB=D66444 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk100e6 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_065681(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065681 NCBI Caenorhabditis elegans F54D8.2 (F54D8.2) mRNA, complete cds. 9/11 A 
F54D8.2.2 ENSEMBL cdna:known chromosome:CEL140:III:5081683:5082955:1 gene:F54D8.2 9/11 A 
F54D8.2.4 ENSEMBL cdna:known chromosome:CEL140:III:5081683:5082955:1 gene:F54D8.2 9/11 None
F54D8.2.3 ENSEMBL cdna:known chromosome:CEL140:III:5081685:5082969:1 gene:F54D8.2 9/11 A 
F54D8.2.1 ENSEMBL cdna:known chromosome:CEL140:III:5081685:5083350:1 gene:F54D8.2 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000022621 5/11 Cross Hyb Matching Probes None
GENEFINDER00000022632 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:5082714-5082931(+) 75.7 75.7
Public Domain and Genome References
Gene Title Cytochrome C oxidase
Ensembl F54D8.2
Entrez Gene 175693 Entrez gene
SwissProt Q20779 EMBL-EBI
WormBase CE01308 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5740 mitochondrial membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4129 cytochrome-c oxidase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA20614 Hypothetical protein F54D8.2 [Caenorhabditis elegans] ref|NP_498082.1| F54D8.2 [Caenorhabditis elegans] sp|Q20779|COX6A_CAEEL Probable cytochrome c oxidase polypeptide VIa, mitochondrial precursor 5.0E-72
blast CAE75086 Hypothetical protein CBG23006 [Caenorhabditis briggsae] 3.0E-63
Protein Domains
Database ID Description E-Value
Pfam IPR001349 EMBL-EBI Cytochrome c oxidase, subunit VIa 9.4E-68
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498082.1 1 54-71
F54D8.2.2 1 54-71
F54D8.2.4 1 54-71
F54D8.2.3 1 54-71
F54D8.2.1 1 54-71
Sequence
Target Sequence 
>C. ELEGANS:171927_X_AT
cgccttcttgtacgttcgcaacaagccattcccatggtccgatggaaatcactcattgtt
ccacaacaaggcggagcaatttgttccaggagttggattcgaggctgaccgtgagaagca
ctaaacaatgctggacgatacaattaatcatcatatttaacgtcatccatttgtgtgtgt
gcttcgagttgtttagtttaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGCCTTCTTGTACGTTCGCAACAAG 685 257 56 Antisense
TTGTACGTTCGCAACAAGCCATTCC 444 705 63 Antisense
AGCCATTCCCATGGTCCGATGGAAA 483 83 79 Antisense
GTCCGATGGAAATCACTCATTGTTC 189 477 92 Antisense
CACTCATTGTTCCACAACAAGGCGG 86 193 105 Antisense
GGCGGAGCAATTTGTTCCAGGAGTT 290 539 125 Antisense
GGAGTTGGATTCGAGGCTGACCGTG 412 517 144 Antisense
GAGGCTGACCGTGAGAAGCACTAAA 93 405 156 Antisense
ATCATCATATTTAACGTCATCCATT 630 29 202 Antisense
GTCATCCATTTGTGTGTGTGCTTCG 354 467 217 Antisense
GTGTGCTTCGAGTTGTTTAGTTTAA 174 483 232 Antisense
Sequence Source Affymetrix Proprietary Database