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[189842_s_at] Citrate synthase

Description T20G5.2 /REP_DB=WormBase Gene ID /WP=CE00513 /TR=SW:P34575 /GB=CAA83004.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Citrate synthase
Cluster 6grp_highest_10_10 > 23      6grp_high1_10_10 > 20      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 18      6grp_total > 32      4grp_total > 62      6grp_highest_sub > 01_02_03      6grp_cgc > 71      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6690
1 2 3 4 range
A 17964.2
(3)
P 		15035.1
(0.4)
P 		16342.4
(1.5)
P 		11274.4
(-3)
P 		6690
B 17900.8
(3)
P 		15047.8
(0.3)
P 		15217.1
(0.4)
P 		11665
(-3)
P 		6236
C 16159.5
(3)
P 		14188.2
(-0.1)
P 		13833.1
(-0.7)
P 		12399.3
(-3)
P 		3760
avr 17341.5
(3) 		14757
(0.2) 		15130.9
(0.6) 		11779.6
(-3) 		5562

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8109
1 2 3 4 5 6 range
A 19632.7
(3)
P 		16625
(0.3)
P 		16732.7
(0.4)
P 		15155.2
(-1.1)
P 		13057.9
(-3)
P 		14072.2
(-2.1)
P 		6575
B 15930.2
(2)
P 		16364.7
(2.5)
P 		16766.7
(3)
P 		16306.1
(2.5)
P 		11940.5
(-2.5)
P 		11523.5
(-3)
P 		5243
C 12899.4
(-2.3)
P 		17436.8
(2)
P 		18494.1
(3)
P 		14094.3
(-1.1)
P 		12132.9
(-3)
P 		13490.1
(-1.7)
P 		6361
avr 16154.1
(1.6) 		16808.8
(2.4) 		17331.2
(3) 		15185.2
(0.4) 		12377.1
(-3) 		13028.6
(-2.2) 		4954
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4890
1 2 3 4 range
A 6540.8
(3)
P 		3263.7
(-1)
P 		4272.2
(0.2)
P 		1650.4
(-3)
P 		4890
B 5708.4
(3)
P 		3716.5
(-0.7)
P 		3526.1
(-1.1)
P 		2485.8
(-3)
P 		3223
C 5349.3
(3)
P 		4079.2
(0.7)
P 		4821.3
(2)
P 		2090.7
(-3)
P 		3259
avr 5866.2
(3) 		3686.5
(-0.5) 		4206.5
(0.4) 		2075.6
(-3) 		3791

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3078
1 2 3 4 5 6 range
A 3619.1
(-2.5)
P 		5912.7
(3)
P 		3644
(-2.5)
P 		3843.7
(-2)
P 		3940.3
(-1.8)
P 		3426.1
(-3)
P 		2487
B 5542.9
(3)
P 		5447.1
(2.6)
P 		4071.5
(-3)
P 		4318.9
(-2)
P 		4851.3
(0.2)
P 		4297.1
(-2.1)
P 		1471
C 4781.2
(1.7)
P 		5320.5
(3)
P 		4707.1
(1.5)
P 		2834.4
(-3)
P 		3926
(-0.4)
P 		4515.9
(1.1)
P 		2486
avr 4647.7
(0.1) 		5560.1
(3) 		4140.9
(-1.5) 		3665.7
(-3) 		4239.2
(-1.2) 		4079.7
(-1.7) 		1894
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189842_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6631
Sequence Type Exemplar sequence
Representative Public ID T20G5.2 NCBI
Target Description T20G5.2 /REP_DB=WormBase Gene ID /WP=CE00513 /TR=SW:P34575 /GB=CAA83004.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Citrate synthase
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_066863(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066863 NCBI Caenorhabditis elegans CiTrate Synthase family member (cts-1) (cts-1) mRNA, complete cds. 11/11 None
SNAP00000033307 ENSEMBL cdna:SNAP chromosome:CEL140:III:10214945:10216506:-1 11/11 None
GENEFINDER00000033349 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10214945:10216506:-1 11/11 None
T20G5.2.3 ENSEMBL cdna:known chromosome:CEL140:III:10214703:10216526:-1 gene:T20G5.2 11/11 None
T20G5.2.2 ENSEMBL cdna:known chromosome:CEL140:III:10214703:10216533:-1 gene:T20G5.2 11/11 None
T20G5.2.1 ENSEMBL cdna:known chromosome:CEL140:III:10214703:10216524:-1 gene:T20G5.2 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
chrIII:10214940-10216502(-) 100.0 100.0
Public Domain and Genome References
Gene Title Citrate synthase
Gene Symbol cts-1
Ensembl T20G5.2
Entrez Gene 176437 Entrez gene
SwissProt P34575 EMBL-EBI
WormBase CE00513 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18698_S_AT citrate synthase, mitochondrial, putative at
ATH1-121501:267368_AT citrate synthase, mitochondrial, putative at
CANINE_2:CFA.17251.1.S1_AT similar to citrate synthase cfa
CANINE_2:CFA.17251.1.S1_S_AT similar to citrate synthase cfa
DROSOPHILA_2:1623252_A_AT dm
DROSGENOME1:144596_AT dm
HG-U133_PLUS_2:208660_AT citrate synthase hs
HG-U133A_2:208660_AT citrate synthase hs
HG-U133A:208660_AT citrate synthase hs
HU35KSUBA:AA112941_AT citrate synthase hs
HU35KSUBD:RC_N26086_AT citrate synthase hs
U133_X3P:G12652712_3P_AT citrate synthase hs
HG-U95AV2:41314_AT citrate synthase hs
HG-U95C:56913_R_AT Citrate synthase hs
HG-U95C:60743_AT Citrate synthase hs
HG-U95D:85002_AT Citrate synthase hs
HG-U95D:86056_R_AT Citrate synthase hs
HU35KSUBC:RC_AA283714_AT Citrate synthase hs
MOE430A:1422577_AT citrate synthase mm
MOUSE430_2:1422577_AT citrate synthase mm
MOUSE430A_2:1422577_AT citrate synthase mm
MOE430A:1450667_A_AT citrate synthase mm
MOUSE430_2:1450667_A_AT citrate synthase mm
MOUSE430A_2:1450667_A_AT citrate synthase mm
MOUSE430_2:1422578_AT citrate synthase mm
MOE430A:1422578_AT citrate synthase mm
MOUSE430A_2:1422578_AT citrate synthase mm
MU11KSUBA:AA389346_S_AT citrate synthase mm
MG-U74AV2:99666_AT citrate synthase mm
MG-U74BV2:164575_F_AT citrate synthase mm
MU19KSUBC:TC40740_AT Citrate synthase, mRNA (cDNA clone MGC:6896 IMAGE:2655044) mm
MU19KSUBC:TC40740_G_AT Citrate synthase, mRNA (cDNA clone MGC:6896 IMAGE:2655044) mm
RG-U34C:RC_AI176862_AT citrate synthase rn
RAE230A:1369967_AT citrate synthase rn
RAT230_2:1369967_AT citrate synthase rn
RAE230A:1375295_AT Citrate synthase rn
RAT230_2:1375295_AT Citrate synthase rn
RG-U34B:RC_AA964751_AT Citrate synthase rn
YEAST_2:1773515_AT Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate, peroxisomal isozyme involved in glyoxylate cycle; expression is controlled by Rtg1p and Rtg2p transcription factors Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6099 tricarboxylic acid cycle inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4108 citrate (Si)-synthase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA83004 Hypothetical protein T20G5.2 [Caenorhabditis elegans] ref|NP_499264.1| CiTrate Synthase family member (cts-1) [Caenorhabditis elegans] sp|P34575|CISY_CAEEL Probable citrate synthase, mitochondrial precursor 0.0
blast CAE64976 Hypothetical protein CBG09810 [Caenorhabditis briggsae] 0.0
blast NP_999441 citrate synthase [Sus scrofa] sp|P00889|CISY_PIG Citrate synthase, mitochondrial precursor gb|AAA31017.1| citrate synthase precursor (EC 4.1.3.7) 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002020 EMBL-EBI Citrate synthase 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:189842_S_AT
ctcacacttcccatcttgtaggatctgctctttctgatccatacctttccttctccgccg
ccatggctggacttgctggaccactccacggattggctaaccaagaggttctcgttttct
tgaacaagattgttggagaaatcggttttaactacaccgaggaacaacttaaggaatggg
tatggaagcacttgaagagcggccaagttgtaccaggatatggacatgccgtacttagaa
aaaccgatccaagatacgagtgccaacgtgaattcgcccttaaacatttgccaaacgatg
atcttttcaagctggtctcgactctttacaagatcactccaggaattcttctcgaacaag
gaaaagccaagaacccatggccaaacgtggactcccactccggtgtccttcttcaatact
ttggaatgaccgagatgtccttctacactgttcttttcggagtttctagagctctcggat
gtctctcgcaattgatctgggccagaggtatgggacttccactcgaacgtcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCACACTTCCCATCTTGTAGGATC 150 229 833 Antisense
GGATCTGCTCTTTCTGATCCATACC 257 513 853 Antisense
ACCACTCCACGGATTGGCTAACCAA 629 83 912 Antisense
ACGAGTGCCAACGTGAATTCGCCCT 307 93 1088 Antisense
GAATTCGCCCTTAAACATTTGCCAA 239 323 1102 Antisense
TTCAAGCTGGTCTCGACTCTTTACA 333 683 1138 Antisense
AGATCACTCCAGGAATTCTTCTCGA 160 67 1163 Antisense
GAATGACCGAGATGTCCTTCTACAC 640 331 1256 Antisense
CCTTCTACACTGTTCTTTTCGGAGT 214 269 1271 Antisense
GTCTCTCGCAATTGATCTGGGCCAG 180 471 1313 Antisense
TATGGGACTTCCACTCGAACGTCCA 399 651 1341 Antisense
Sequence Source Affymetrix Proprietary Database