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[189990_at] cytochrome C oxidase

Description F26E4.9 /REP_DB=WormBase Gene ID /WP=CE09693 /TR=P90849 /GB=CAB03002.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=cytochrome C oxidase
Cluster 6grp_highest_10_10 > 26      6grp_high1_10_10 > 51      4grp_highest_8_8 > 05      4grp_high_8_8 > 30      6grp_highest_nonorm > 08      6grp_total > 62      4grp_total > 25      6grp_highest_sub > 03      6grp_cgc > 83      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3837
1 2 3 4 range
A 14275.5
(-3)
P 		16687.5
(0.8)
P 		16554
(0.6)
P 		18112.7
(3)
P 		3837
B 16640.6
(-0)
P 		16126.7
(-3)
P 		17158.3
(3)
P 		16618.4
(-0.1)
P 		1032
C 14575
(-3)
P 		16688.1
(0.9)
P 		15303.4
(-1.7)
P 		17854.6
(3)
P 		3280
avr 15163.7
(-3) 		16500.8
(0.4) 		16338.6
(-0) 		17528.6
(3) 		2365

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15139
1 2 3 4 5 6 range
A 17358.2
(-2.1)
P 		19459.8
(-1.2)
P 		28760
(3)
P 		26139.7
(1.8)
P 		17134.4
(-2.2)
P 		15471.1
(-3)
P 		13289
B 15886.2
(-0.9)
P 		18089.9
(1.1)
P 		20086
(3)
P 		19887
(2.8)
P 		16531.4
(-0.3)
P 		13621.5
(-3)
P 		6465
C 16485.4
(-1.6)
P 		17754.6
(-0.8)
P 		24156.3
(3)
P 		20451.7
(0.8)
P 		19132.6
(0)
P 		14064.4
(-3)
P 		10092
avr 16576.6
(-1.7) 		18434.8
(-0.6) 		24334.1
(3) 		22159.5
(1.7) 		17599.5
(-1.1) 		14385.7
(-3) 		9948
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2682
1 2 3 4 range
A 5197.7
(3)
P 		3622.4
(-0.7)
P 		4327.5
(0.9)
P 		2651.3
(-3)
P 		2546
B 5306.6
(3)
P 		3982.9
(-1.5)
P 		3976
(-1.5)
P 		3541.4
(-3)
P 		1765
C 4824.7
(1.7)
P 		4797.9
(1.6)
P 		5333.7
(3)
P 		3010.6
(-3)
P 		2323
avr 5109.7
(3) 		4134.4
(0.1) 		4545.7
(1.3) 		3067.8
(-3) 		2042

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3721
1 2 3 4 5 6 range
A 3199.9
(-3)
P 		6920.9
(3)
P 		6263.3
(1.9)
P 		6629.6
(2.5)
P 		5170.4
(0.2)
P 		3766.7
(-2.1)
P 		3721
B 5527.6
(-0.9)
P 		6021.4
(0.7)
P 		4877.5
(-3)
P 		5267.4
(-1.7)
P 		6716.5
(3)
P 		5079.4
(-2.3)
P 		1839
C 6110.4
(2.8)
P 		5417.5
(0.8)
P 		6148.2
(2.9)
P 		4112.9
(-3)
P 		6191
(3)
P 		4708.2
(-1.3)
P 		2078
avr 4946
(-1.4) 		6119.9
(3) 		5763
(1.7) 		5336.6
(0.1) 		6026
(2.6) 		4518.1
(-3) 		1602
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189990_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.600
Sequence Type Exemplar sequence
Representative Public ID F26E4.9 NCBI
Target Description F26E4.9 /REP_DB=WormBase Gene ID /WP=CE09693 /TR=P90849 /GB=CAB03002.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=cytochrome C oxidase
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_060200(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060200 NCBI Caenorhabditis elegans Cytochrome C Oxidase family member (cco-1) (cco-1) mRNA, complete cds. 11/11 None
SNAP00000026231 ENSEMBL cdna:SNAP chromosome:CEL140:I:9797130:9797884:1 11/11 None
GENEFINDER00000026233 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9797130:9797884:1 11/11 None
F26E4.9.4 ENSEMBL cdna:known chromosome:CEL140:I:9796870:9798079:1 gene:F26E4.9 11/11 None
F26E4.9.2 ENSEMBL cdna:known chromosome:CEL140:I:9796901:9798043:1 gene:F26E4.9 11/11 None
F26E4.9.3 ENSEMBL cdna:known chromosome:CEL140:I:9797128:9798031:1 gene:F26E4.9 11/11 None
F26E4.9.1 ENSEMBL cdna:known chromosome:CEL140:I:9797130:9798043:1 gene:F26E4.9 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
chrI:9797060-9797815(+) 100.0 100.0
Public Domain and Genome References
Gene Title cytochrome C oxidase
Gene Symbol cco-1
Ensembl F26E4.9
Entrez Gene 172832 Entrez gene
SwissProt P90849 EMBL-EBI
WormBase CE09693 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1640672_AT dm
DROSGENOME1:145908_AT dm
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 CAB03002 Hypothetical protein F26E4.9 [Caenorhabditis elegans] ref|NP_492601.1| Cytochrome C Oxidase family member (cco-1) [Caenorhabditis elegans] 1.0E-73
blast CAE60225 Hypothetical protein CBG03796 [Caenorhabditis briggsae] 2.0E-72
Protein Domains
Database ID Description E-Value
Pfam IPR002124 EMBL-EBI Cytochrome c oxidase, subunit Vb 2.0E-13
Sequence
Target Sequence 
>C. ELEGANS:189990_AT
atggctcaacttgctaagacggctgttgccgccctttcgaagaagctcgtcgctccagct
gccgtggcccgtcgtactttggccactgaagcctcgccagaagactacggatactaccca
gatccacttgagcacgctaccggacgtgaaaagaagatgcttctcgctcgtcttgctgga
gatgatcgttacgagccaaaagtctactatcgcgctgaggcttccaccaagcagaagcca
aatttggtcccatctcactacgacttcagaatcattggatgcatgtgtgagcaagattcc
ggacatgtcaatttcatgacaattcgcaaaggagatccaaagagatgcgagtgcggacac
tggttcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGCTCAACTTGCTAAGACGGCTG 530 51 13 Antisense
TGAAGCCTCGCCAGAAGACTACGGA 671 573 99 Antisense
GGATACTACCCAGATCCACTTGAGC 652 509 121 Antisense
CACTTGAGCACGCTACCGGACGTGA 119 197 137 Antisense
AAAGAAGATGCTTCTCGCTCGTCTT 427 123 162 Antisense
CGCTCGTCTTGCTGGAGATGATCGT 157 255 177 Antisense
CAAAAGTCTACTATCGCGCTGAGGC 562 189 209 Antisense
GAAGCCAAATTTGGTCCCATCTCAC 427 345 246 Antisense
TCCCATCTCACTACGACTTCAGAAT 222 599 260 Antisense
GTGTGAGCAAGATTCCGGACATGTC 321 487 297 Antisense
GATGCGAGTGCGGACACTGGTTCAA 58 415 356 Antisense
Sequence Source Affymetrix Proprietary Database