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[192658_s_at] malate dehydrogenase

Description F20H11.3 /REP_DB=WormBase Gene ID /WP=CE09512 /GEN=mdh-1 /TR=SW:O02640 /GB=AAB53985.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=malate dehydrogenase
Cluster 6grp_highest_10_10 > 03      6grp_high1_10_10 > 12      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 06      6grp_total > 33      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 70      6grp_high1_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10069
1 2 3 4 range
A 11543.9
(3)
P 		11563.9
(3)
P 		11531.9
(3)
P 		1783.8
(-3)
P 		9780
B 10883.3
(3)
P 		10695.8
(2.9)
P 		9703.8
(2.2)
P 		1678.6
(-3)
P 		9205
C 10482.7
(2.9)
P 		10521.5
(3)
P 		10572.1
(3)
P 		1495
(-3)
P 		9077
avr 10970
(3) 		10927.1
(3) 		10602.6
(2.8) 		1652.5
(-3) 		9318

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8817
1 2 3 4 5 6 range
A 13557.5
(3)
P 		10601
(0.8)
P 		11959.8
(1.8)
P 		8350.5
(-0.8)
P 		8125.3
(-1)
P 		5395.9
(-3)
P 		8162
B 11334.4
(2.4)
P 		10909.7
(2)
P 		12040.8
(3)
P 		9558.7
(0.7)
P 		8278.8
(-0.4)
P 		5451.2
(-3)
P 		6590
C 11100.2
(3)
P 		10339
(2.3)
P 		10766.5
(2.7)
P 		6981.1
(-0.9)
P 		8267.5
(0.3)
P 		4741
(-3)
P 		6359
avr 11997.4
(3) 		10616.6
(1.8) 		11589
(2.6) 		8296.8
(-0.3) 		8223.9
(-0.3) 		5196
(-3) 		6801
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3951
1 2 3 4 range
A 4203.2
(3)
P 		2510.2
(0.4)
P 		3014.7
(1.2)
P 		261.1
(-3)
P 		3942
B 3470.6
(3)
P 		2641.6
(1.4)
P 		2248.6
(0.6)
P 		357.7
(-3)
P 		3113
C 3470.1
(2.6)
P 		3025
(1.8)
P 		3684.7
(3)
P 		252.1
(-3)
P 		3433
avr 3714.6
(3) 		2725.6
(1.3) 		2982.7
(1.7) 		290.3
(-3) 		3424

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2801
1 2 3 4 5 6 range
A 2499.2
(-0.1)
P 		3770.2
(3)
P 		2604.6
(0.2)
P 		2117.9
(-1)
P 		2451.9
(-0.2)
P 		1313.7
(-3)
P 		2457
B 3943.8
(3)
P 		3631.4
(2)
P 		2923.9
(-0.2)
P 		2531.8
(-1.4)
P 		3363.6
(1.2)
P 		2032.7
(-3)
P 		1911
C 4114.3
(3)
P 		3154.8
(0.9)
P 		2740.3
(-0)
P 		1403.9
(-3)
P 		2675.2
(-0.2)
P 		1587.1
(-2.6)
P 		2710
avr 3519.1
(3) 		3518.8
(3) 		2756.3
(0.6) 		2017.9
(-1.8) 		2830.2
(0.8) 		1644.5
(-3) 		1875
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192658_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7413
Sequence Type Exemplar sequence
Representative Public ID F20H11.3 NCBI
Target Description F20H11.3 /REP_DB=WormBase Gene ID /WP=CE09512 /GEN=mdh-1 /TR=SW:O02640 /GB=AAB53985.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=malate dehydrogenase
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_066056(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066056 NCBI Caenorhabditis elegans Malate DeHydrogenase family member (mdh-1) (mdh-1) mRNA, complete cds. 11/11 None
SNAP00000039389 ENSEMBL cdna:SNAP chromosome:CEL140:III:6606761:6608038:-1 11/11 None
GENEFINDER00000039393 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6606761:6608038:-1 11/11 None
F20H11.3.4 ENSEMBL cdna:known chromosome:CEL140:III:6606050:6608048:-1 gene:F20H11.3 11/11 None
F20H11.3.1 ENSEMBL cdna:known chromosome:CEL140:III:6606185:6608041:-1 gene:F20H11.3 11/11 A 
F20H11.3.3 ENSEMBL cdna:known chromosome:CEL140:III:6606185:6608109:-1 gene:F20H11.3 11/11 A 
F20H11.3.2 ENSEMBL cdna:known chromosome:CEL140:III:6606185:6608048:-1 gene:F20H11.3 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:6606759-6608037(-) 100.0 100.0
Public Domain and Genome References
Gene Title malate dehydrogenase
Gene Symbol mdh-1
Ensembl F20H11.3
Entrez Gene 175936 Entrez gene
SwissProt O02640 EMBL-EBI
WormBase CE09512 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257213_AT malate dehydrogenase (NAD), mitochondrial, putative at
CANINE:1605673_AT similar to malate dehydrogenase, mitochondrial cfa
CANINE_2:CFAAFFX.10234.1.S1_S_AT similar to malate dehydrogenase, mitochondrial cfa
CANINE_2:CFAAFFX.20906.1.S1_AT similar to malate dehydrogenase, mitochondrial cfa
DROSOPHILA_2:1640928_AT dm
DROSGENOME1:150121_AT dm
CHICKEN:GGA.4839.1.S1_A_AT malate dehydrogenase 2, NAD (mitochondrial) gga
HG-U95AV2:39001_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133_PLUS_2:213333_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133A_2:213333_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133A:213333_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133A:209036_S_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133A_2:209036_S_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133_PLUS_2:209036_S_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-FOCUS:209036_S_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HU35KSUBA:RC_AA242776_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HU35KSUBA:AA263028_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HU35KSUBD:RC_N71096_AT malate dehydrogenase 2, NAD (mitochondrial) hs
U133_X3P:G12804928_3P_A_AT malate dehydrogenase 2, NAD (mitochondrial) hs
U133_X3P:HS.111076.1.S1_3P_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U95E:88089_AT malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133_PLUS_2:234084_X_AT Malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133B:234084_X_AT Malate dehydrogenase 2, NAD (mitochondrial) hs
U133_X3P:HS.296692.0.S1_3P_AT Malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133_PLUS_2:233777_AT Malate dehydrogenase 2, NAD (mitochondrial) hs
HG-U133B:233777_AT Malate dehydrogenase 2, NAD (mitochondrial) hs
MOE430A:1433984_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MOUSE430A_2:1433984_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MOUSE430_2:1433984_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MU11KSUBA:M16229_F_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MG-U74AV2:93991_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MOE430A:1416478_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MOUSE430A_2:1416478_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MOUSE430_2:1416478_A_AT malate dehydrogenase 2, NAD (mitochondrial) mm
MU19KSUBC:TC37545_AT Malate dehydrogenase 2, NAD (mitochondrial), mRNA (cDNA clone MGC:31009 IMAGE:5251192) mm
MU19KSUBC:TC37546_AT Malate dehydrogenase 2, NAD (mitochondrial), mRNA (cDNA clone MGC:31009 IMAGE:5251192) mm
MU19KSUBC:TC39823_AT Malate dehydrogenase 2, NAD (mitochondrial), mRNA (cDNA clone MGC:31009 IMAGE:5251192) mm
RG-U34A:RC_AI010480_AT malate dehydrogenase, mitochondrial rn
RG-U34A:RC_AI010480_G_AT malate dehydrogenase, mitochondrial rn
RAE230A:1369927_AT malate dehydrogenase, mitochondrial rn
RAT230_2:1369927_AT malate dehydrogenase, mitochondrial rn
YEAST_2:1769857_AT Mitochondrial malate dehydrogenase, catalyzes interconversion of malate and oxaloacetate; involved in the tricarboxylic acid (TCA) cycle 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
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
16615 malate dehydrogenase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB53985 Malate dehydrogenase protein 1 [Caenorhabditis elegans] ref|NP_498457.1| Malate DeHydrogenase family member (mdh-1) [Caenorhabditis elegans] sp|O02640|MDHM_CAEEL Probable malate dehydrogenase, mitochondrial precursor 0.0
blast CAE69180 Hypothetical protein CBG15213 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001236 EMBL-EBI Lactate/malate dehydrogenase 8.2E-63
Pfam IPR001236 EMBL-EBI Lactate/malate dehydrogenase 1.4E-54
Sequence
Target Sequence 
>C. ELEGANS:192658_S_AT
ttcaccaaaggctctcatcgcaattatcaccaacccagtcaattctactgtcccaatcgc
ttccgaagttctcaagaaggctggtgtctatgacccaaaacgtgtcttcggagtgacaac
cctcgacgtcgtcagatctcaagcattcgtttccgagcttaagggacatgacgcctccaa
gaccgttgttccagttgtcggaggacatgctggaatcaccatcattccacttctctccca
agtcaaaccatccaccaaattctcggaggaagaaatctccaagttgaccccaagaatcca
ggacgccggaactgaagtcgtcaacgccaaggctggagccggatccgctactctttcaat
ggctcttgctggagcccgtttcgccaatgctcttgttcgtggaattaagggagaaaagaa
cgtccaatgcgcatatgttgcttccgatgccgtcaagggagtcgaatacttctctacccc
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCACCAAAGGCTCTCATCGCAATT 58 687 417 Antisense
TTATCACCAACCCAGTCAATTCTAC 668 679 440 Antisense
GTCAGATCTCAAGCATTCGTTTCCG 56 467 547 Antisense
AAACCATCCACCAAATTCTCGGAGG 409 125 661 Antisense
AGTTGACCCCAAGAATCCAGGACGC 41 1 698 Antisense
CGCCGGAACTGAAGTCGTCAACGCC 585 257 720 Antisense
TACTCTTTCAATGGCTCTTGCTGGA 697 645 765 Antisense
TTTCGCCAATGCTCTTGTTCGTGGA 226 669 795 Antisense
GTCCAATGCGCATATGTTGCTTCCG 580 477 838 Antisense
TGCTTCCGATGCCGTCAAGGGAGTC 137 579 855 Antisense
GGGAGTCGAATACTTCTCTACCCCA 261 495 873 Antisense
Sequence Source Affymetrix Proprietary Database