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[173823_at] cytochrome C1, heme protein

Description C48490 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C54G4.8 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48490 /WB_GENE_ID=C54G4.8 /WP=CE05514 /CHR=1 /FEA=Genomic Cluster /DEF=cytochrome C1, heme protein; C.elegans cDNA clone yk457c1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 02      6grp_high1_10_10 > 11      4grp_highest_8_8 > 40      4grp_high_8_8 > 50      6grp_highest_nonorm > 13      6grp_total > 23      4grp_total > 53      6grp_cgc > 20      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2741
1 2 3 4 range
A 4333.2
(3)
P 		3954.8
(2.1)
P 		3383.6
(0.8)
P 		1759.9
(-3)
P 		2573
B 4500.8
(3)
P 		3387.8
(-0.3)
P 		3518
(0.1)
P 		2499.6
(-3)
P 		2001
C 4082.3
(3)
P 		3676.9
(1.8)
P 		3523.5
(1.4)
P 		1969.5
(-3)
P 		2113
avr 4305.4
(3) 		3673.2
(1.3) 		3475
(0.8) 		2076.3
(-3) 		2229

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2103
1 2 3 4 5 6 range
A 3326.9
(3)
P 		3019.9
(2)
P 		2321.7
(-0.2)
P 		2466.4
(0.3)
P 		1896.8
(-1.5)
P 		1419.7
(-3)
P 		1907
B 3305.2
(2.4)
P 		2868.3
(1.1)
P 		3522.8
(3)
P 		2514.5
(0)
P 		1646.4
(-2.5)
P 		1472.8
(-3)
P 		2050
C 3456.4
(3)
P 		2492.6
(-0.1)
P 		3126.9
(1.9)
P 		2802.9
(0.9)
P 		2051.5
(-1.5)
P 		1573.9
(-3)
P 		1883
avr 3362.8
(3) 		2793.6
(1.2) 		2990.5
(1.8) 		2594.6
(0.5) 		1864.9
(-1.8) 		1488.8
(-3) 		1874
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1320
1 2 3 4 range
A 1577.7
(3)
P 		858.5
(-0.3)
P 		884.5
(-0.2)
P 		257.6
(-3)
P 		1320
B 1435.3
(3)
P 		836.7
(-1)
P 		815.2
(-1.1)
P 		532.7
(-3)
P 		903
C 1351.4
(3)
P 		1057.1
(1.3)
P 		1228.1
(2.3)
P 		332.1
(-3)
P 		1019
avr 1454.8
(3) 		917.4
(0) 		975.9
(0.3) 		374.1
(-3) 		1081

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 936
1 2 3 4 5 6 range
A 613.3
(-0.8)
P 		1074
(3)
P 		505.6
(-1.7)
P 		625.5
(-0.7)
P 		572.4
(-1.1)
P 		345.6
(-3)
P 		728
B 1150.1
(3)
P 		954.7
(1)
P 		855.4
(0.1)
P 		666
(-1.8)
P 		668.9
(-1.8)
P 		549.2
(-3)
P 		601
C 1281.1
(3)
P 		760.6
(-1.1)
P 		795.8
(-0.9)
P 		563.7
(-2.7)
P 		663.8
(-1.9)
P 		526.9
(-3)
P 		754
avr 1014.8
(3) 		929.8
(2.1) 		718.9
(-0.3) 		618.4
(-1.4) 		635
(-1.2) 		473.9
(-3) 		541
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173823_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22575
Sequence Type Exemplar sequence
Representative Public ID C48490 NCBI
Target Description C48490 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C54G4.8 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48490 /WB_GENE_ID=C54G4.8 /WP=CE05514 /CHR=1 /FEA=Genomic Cluster /DEF=cytochrome C1, heme protein; C.elegans cDNA clone yk457c1 : 5prime 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_059806(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059806 NCBI Caenorhabditis elegans C54G4.8 (cyc-1) mRNA, complete cds. 11/11 None
C54G4.8.1 ENSEMBL cdna:known chromosome:CEL140:I:8030811:8032548:-1 gene:C54G4.8 11/11 None
C54G4.8.2 ENSEMBL cdna:known chromosome:CEL140:I:8030816:8032550:-1 gene:C54G4.8 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:8030804-8032461(-) 100.0 100.0
Public Domain and Genome References
Gene Title cytochrome C1, heme protein
Gene Symbol cyc-1
Ensembl C54G4.8
Entrez Gene 172582 Entrez gene
SwissProt Q18853 EMBL-EBI
WormBase CE05514 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249324_AT cytochrome c1, putative at
CANINE:1588432_AT similar to cytochrome c-1 cfa
CANINE_2:CFAAFFX.3191.1.S1_S_AT similar to cytochrome c-1 cfa
DROSGENOME1:153348_AT dm
DROSOPHILA_2:1625412_AT dm
HG-U95AV2:1160_AT cytochrome c-1 hs
HC-G110:1160_AT cytochrome c-1 hs
HG-U133A_2:201066_AT cytochrome c-1 hs
HG-U133A:201066_AT cytochrome c-1 hs
HG-U133_PLUS_2:201066_AT cytochrome c-1 hs
HG-FOCUS:201066_AT cytochrome c-1 hs
HUGENEFL:J04444_AT cytochrome c-1 hs
U133_X3P:G4503184_3P_S_AT cytochrome c-1 hs
HG-U95AV2:35819_AT cytochrome c-1 hs
MU11KSUBA:AA466050_S_AT cytochrome c-1 mm
MG-U74AV2:95072_AT cytochrome c-1 mm
MG-U74AV2:162469_R_AT cytochrome c-1 mm
MOE430A:1416604_AT cytochrome c-1 mm
MOUSE430A_2:1416604_AT cytochrome c-1 mm
MOUSE430_2:1416604_AT cytochrome c-1 mm
MU19KSUBA:TC15264_AT Cytochrome c-1, mRNA (cDNA clone MGC:11682 IMAGE:3711323) mm
MU19KSUBB:TC26605_F_AT Cytochrome c-1, mRNA (cDNA clone MGC:11682 IMAGE:3711323) mm
MU19KSUBC:TC37945_F_AT Cytochrome c-1, mRNA (cDNA clone MGC:11682 IMAGE:3711323) mm
RT-U34:RC_AA799474_AT cytochrome c-1 (predicted) rn
RG-U34A:RC_AA799474_AT cytochrome c-1 (predicted) rn
RAE230A:1371342_AT cytochrome c-1 (predicted) rn
RAT230_2:1371342_AT cytochrome c-1 (predicted) rn
YEAST_2:1776968_AT Cytochrome c1, component of the mitochondrial respiratory chain; expression is regulated by the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex Sc
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
5746 mitochondrial electron transport chain inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
20037 heme binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA99820 Hypothetical protein C54G4.8 [Caenorhabditis elegans] ref|NP_492207.1| C54G4.8 [Caenorhabditis elegans] 1.0E-143
blast CAE63697 Hypothetical protein CBG08212 [Caenorhabditis briggsae] 1.0E-141
blast EAA04119 ENSANGP00000021712 [Anopheles gambiae str. PEST] ref|XP_308821.2| ENSANGP00000021712 [Anopheles gambiae str. PEST] 2.0E-65
Protein Domains
Database ID Description E-Value
scop a.3.1.Cytochrome bc1 domain All alpha proteins; Cytochrome c; Cytochrome c; Cytochrome bc1 domain 0.0
Pfam IPR002326 EMBL-EBI Cytochrome c1 1.8E-106
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492207.1 1 12-31
C54G4.8.1 1 12-31
C54G4.8.2 1 12-31
Sequence
Target Sequence 
>C. ELEGANS:173823_AT
aaggctcagtaatcaccagctttccgctattttttcattatcctcttcattcgtccgcaa
tttccatcagcgatcatttgctcgcaatttcataaaatattgtgagattaatcgtttgta
aatttaatgaaattgcgagtatttgtaaccctcctctcctagttcattttttcacagcct
ccatcccctcaaaaaaaaagaacgcgctctccctcgatccgaccgtcgtagtcaccaaaa
ttttcaaattggggacgacgtcgggagccgtttagaaaaatttagttgtcgccgttgttt
gttaattgtgaaaataaaatggagagtttagtatgagtatttttccattttctgagagtt
tttgctgtattcgaaatagtcagactcctttttaaactaaaaagctcacgaactttttcg
atgcatcattactttctcgaatattttttttatataggaaatctcttatccgttttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGGCTCAGTAATCACCAGCTTTCC 564 159 860 Antisense
ACCAGCTTTCCGCTATTTTTTCATT 238 85 874 Antisense
TATTTTTTCATTATCCTCTTCATTC 309 663 887 Antisense
ATTCGTCCGCAATTTCCATCAGCGA 598 9 908 Antisense
CCATCAGCGATCATTTGCTCGCAAT 94 271 923 Antisense
TTGCGAGTATTTGTAACCCTCCTCT 702 699 992 Antisense
TCCTAGTTCATTTTTTCACAGCCTC 633 591 1016 Antisense
TCCGACCGTCGTAGTCACCAAAATT 37 595 1077 Antisense
AGTTGTCGCCGTTGTTTGTTAATTG 148 65 1143 Antisense
AGCTCACGAACTTTTTCGATGCATC 538 79 1262 Antisense
TATAGGAAATCTCTTATCCGTTTTT 456 657 1312 Antisense
Sequence Source Affymetrix Proprietary Database