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[172848_x_at] Cytochrome C oxidase

Description F54D8.2 /REP_DB=WormBase Gene ID /WP=CE01308 /TR=SW:Q20779 /GB=AAA20614.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Cytochrome C oxidase
Cluster 6grp_highest_10_10 > 37      6grp_high1_10_10 > 63      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 18      6grp_total > 61      4grp_total > 09      6grp_highest_sub > 03_04      6grp_cgc > 93      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12094
1 2 3 4 range
A 15006
(-3)
P 		16970
(-2)
P 		16657.5
(-2.2)
P 		26903
(3)
P 		11897
B 16050.9
(-2.4)
P 		15752.1
(-3)
P 		18535.3
(2.5)
P 		18795.9
(3)
P 		3044
C 14809.4
(-3)
P 		17056.1
(-1.6)
P 		14996.7
(-2.9)
P 		24534
(3)
P 		9725
avr 15288.8
(-3) 		16592.7
(-2) 		16729.8
(-1.9) 		23411
(3) 		8122

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7852
1 2 3 4 5 6 range
A 16336.2
(-0.8)
P 		13892.9
(-3)
P 		20554.6
(3)
P 		17990.7
(0.7)
P 		14493.6
(-2.5)
P 		15943
(-1.2)
P 		6662
B 15039.1
(-0.9)
P 		12702.2
(-3)
P 		19379.1
(3)
P 		17100.5
(1)
P 		13450.3
(-2.3)
P 		13091.7
(-2.6)
P 		6677
C 13816.4
(-2.5)
P 		13410.8
(-3)
P 		15702.5
(-0.4)
P 		18624
(3)
P 		14817.8
(-1.4)
P 		15270.5
(-0.9)
P 		5213
avr 15063.9
(-1) 		13335.3
(-3) 		18545.4
(3) 		17905.1
(2.3) 		14253.9
(-1.9) 		14768.4
(-1.3) 		5210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1780
1 2 3 4 range
A 5463.7
(3)
P 		3683.7
(-3)
P 		4354.6
(-0.7)
P 		3938.1
(-2.1)
P 		1780
B 5118.5
(3)
P 		3890.4
(-3)
P 		4295
(-1)
P 		4005.4
(-2.4)
P 		1228
C 4902.3
(1.2)
P 		4903.7
(1.2)
P 		5226.8
(3)
P 		4136.8
(-3)
P 		1090
avr 5161.5
(3) 		4159.3
(-2.3) 		4625.5
(0.2) 		4026.8
(-3) 		1135

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2453
1 2 3 4 5 6 range
A 3011.4
(-3)
P 		4941
(3)
P 		4476.3
(1.6)
P 		4562.9
(1.8)
P 		4373.5
(1.2)
P 		3881.6
(-0.3)
P 		1930
B 5232.9
(1.9)
P 		4228
(-3)
P 		4705.8
(-0.7)
P 		4529.3
(-1.5)
P 		5464.7
(3)
P 		4881.8
(0.2)
P 		1237
C 5121.1
(3)
P 		4092
(-1.5)
P 		3996.5
(-1.9)
P 		3745.3
(-3)
P 		4794.8
(1.6)
P 		5111.9
(3)
P 		1376
avr 4455.1
(-1.2) 		4420.3
(-1.6) 		4392.9
(-1.9) 		4279.2
(-3) 		4877.7
(3) 		4625.1
(0.5) 		599
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172848_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7762
Sequence Type Exemplar sequence
Representative Public ID F54D8.2 NCBI
Target Description F54D8.2 /REP_DB=WormBase Gene ID /WP=CE01308 /TR=SW:Q20779 /GB=AAA20614.1 /SUBMIT=ST.LOUIS /CHR=3 /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_065681(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065681 NCBI Caenorhabditis elegans F54D8.2 (F54D8.2) mRNA, complete cds. 11/11 A 
SNAP00000022621 ENSEMBL cdna:SNAP chromosome:CEL140:III:5081694:5082816:1 11/11 None
GENEFINDER00000022632 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5081694:5082816:1 11/11 None
F54D8.2.2 ENSEMBL cdna:known chromosome:CEL140:III:5081683:5082955:1 gene:F54D8.2 11/11 A 
F54D8.2.4 ENSEMBL cdna:known chromosome:CEL140:III:5081683:5082955:1 gene:F54D8.2 11/11 None
F54D8.2.3 ENSEMBL cdna:known chromosome:CEL140:III:5081685:5082969:1 gene:F54D8.2 11/11 A 
F54D8.2.1 ENSEMBL cdna:known chromosome:CEL140:III:5081685:5083350:1 gene:F54D8.2 11/11 A 
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
chrIII:5081692-5082815(+) 100.0 100.0
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
SNAP00000022621 1 54-71
GENEFINDER00000022632 1 54-71
Sequence
Target Sequence 
>C. ELEGANS:172848_X_AT
tcgtcaagaccttccaacgcaaatcctcaggatcattttacggatccaacaatgtcgaag
gattcaaagagtcatatgtcactccactcaagcaagctcacaatgctagcgagacctgga
agaaaatcttcttcattgcttcgattccatgcttggctcttaccatgtatgccgccttca
aggatcacaaaaaacacatgagccacgaacgcccagagcacgtcgagtacgccttcttga
acgttcgcaacaagccattcccatggtccgatggaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCGTCAAGACCTTCCAACGCAAATC 377 601 47 Antisense
CTTCCAACGCAAATCCTCAGGATCA 454 217 57 Antisense
AGAGTCATATGTCACTCCACTCAAG 62 69 114 Antisense
GCAAGCTCACAATGCTAGCGAGACC 292 321 138 Antisense
AATCTTCTTCATTGCTTCGATTCCA 602 169 171 Antisense
TTCCATGCTTGGCTCTTACCATGTA 621 697 191 Antisense
TTACCATGTATGCCGCCTTCAAGGA 298 679 206 Antisense
AAAAACACATGAGCCACGAACGCCC 620 129 236 Antisense
CGAGTACGCCTTCTTGAACGTTCGC 292 155 270 Antisense
TTGAACGTTCGCAACAAGCCATTCC 442 705 283 Antisense
AGCCATTCCCATGGTCCGATGGAAA 481 83 299 Antisense
Sequence Source Affymetrix Proprietary Database