Gene loci information

Transcript annotation

  • This transcript has been annotated as Malate dehydrogenase, mitochondrial.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g9301 g9301.t7 TTS g9301.t7 1646010 1646010
chr_1 g9301 g9301.t7 isoform g9301.t7 1646013 1647630
chr_1 g9301 g9301.t7 exon g9301.t7.exon1 1646013 1647001
chr_1 g9301 g9301.t7 cds g9301.t7.CDS1 1646256 1647001
chr_1 g9301 g9301.t7 exon g9301.t7.exon2 1647090 1647297
chr_1 g9301 g9301.t7 cds g9301.t7.CDS2 1647090 1647297
chr_1 g9301 g9301.t7 exon g9301.t7.exon3 1647565 1647630
chr_1 g9301 g9301.t7 cds g9301.t7.CDS3 1647565 1647630
chr_1 g9301 g9301.t7 TSS g9301.t7 1647730 1647730

Sequences

>g9301.t7 Gene=g9301 Length=1263
ATGTTCTCAAGAGTCTTAAGAACCGCAGCACATCAAGGAGCCAAGAGCTTCTCAACTTCA
CAACAAAACAATGTTAAAGTTGCAGTATGTGGTGCATCGGGTGGCATTGGTCAACCATTA
TCATTGCTATTGAAACAAAGTCCACTCATCACTGAGCTTTCTCTTTACGATATTGTTCAC
ACACCTGGAGTTGCTGCTGATTTGTCACACATTGATACAGCTAGCAAAGTTGTTGGCTAC
AATGGACCAGAAAACTTGGAAAAGGCCTTGAAAGTTTTAGATGCTGATGTTGTTATTATT
CCTGCTGGAGTTCCTCGCAAGCCAGGAATGACTCGTGACGATCTTTTCAACACAAATGCT
TCAATTGTTCGTGACTTGGCTATCGCATGTGGAAAGGCTTGCCCTAAAGCTCTCGTGGGT
ATTATTTCAAATCCAGTTAACTCAACTGTCCCAATTGCCAGCGAAGCATTGGCTAAACTT
GGAGTTTTAGATCCAAAGCGAATTTTTGGTGTCTCAACACTTGATGTTGTAAGAGCAAAT
GCTTTTATCGGTGAAGCAGCAGGTGTCGATCCAGCAAAAGTTAATTTGCCAGTTATTGGC
GGTCACTCAGGTGTCACAATCATGCCATTGCTCTCACAATGCAAACCTGCCGTCAACTTC
CCAGCTGATAAGGTCAAGGCTCTCACTGAACGCATCCAGGAAGCTGGTACTGAAGTTGTC
AAGGCAAAGGCTGGCGCTGGATCTGCTACTCTTTCAATGGCATATGCCGGTGCTCGTTTC
GCTATTTCACTTATTCGTGCTATCAAAGGTGAACAAAATGTTGTCGAATGTGCTTATGTT
CGTTCAGATGTTACAGAAGCCAAATATTTCTCAACACCTCTCTTGTTGGGCAAGAATGGC
ATTGAAAAGAACTTGGGAATTGGATCATTGAATGCTTTCGAGCAGGAACTTCTTGCAAAG
GCTATCCCAGAATTGAAAAAGAACATTCAAACTGGCGAGGACTTTATCAATAAGAACTAA
ATTATGAACTCTTCATTATCATCTTTTGAATGATTCCTTATTTATGTTTTATTCTCCCCT
TAATAAGATTTCCTTTGCACTGACCCGCCTTTAAAAATTTACTTACAATTTTATAATTTA
AATTTTACTTGATGATTATTAGGGCTAGCGTTAATATTTAGGAAATCTTTGATTGGCAAT
TTACGTCTAAGAAAATTTTCCGAAACGGAAATAAAAAGTGAAACACAACCGAAATGTTAC
AAA

>g9301.t7 Gene=g9301 Length=339
MFSRVLRTAAHQGAKSFSTSQQNNVKVAVCGASGGIGQPLSLLLKQSPLITELSLYDIVH
TPGVAADLSHIDTASKVVGYNGPENLEKALKVLDADVVIIPAGVPRKPGMTRDDLFNTNA
SIVRDLAIACGKACPKALVGIISNPVNSTVPIASEALAKLGVLDPKRIFGVSTLDVVRAN
AFIGEAAGVDPAKVNLPVIGGHSGVTIMPLLSQCKPAVNFPADKVKALTERIQEAGTEVV
KAKAGAGSATLSMAYAGARFAISLIRAIKGEQNVVECAYVRSDVTEAKYFSTPLLLGKNG
IEKNLGIGSLNAFEQELLAKAIPELKKNIQTGEDFINKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9301.t7 CDD cd01337 MDH_glyoxysomal_mitochondrial 25 336 0
8 g9301.t7 Gene3D G3DSA:3.40.50.720 - 18 171 0
7 g9301.t7 Gene3D G3DSA:3.90.110.10 - 172 338 0
3 g9301.t7 PANTHER PTHR11540:SF16 MALATE DEHYDROGENASE, MITOCHONDRIAL 16 338 0
4 g9301.t7 PANTHER PTHR11540 MALATE AND LACTATE DEHYDROGENASE 16 338 0
10 g9301.t7 PIRSF PIRSF000102 Lac_mal_DH 21 339 0
2 g9301.t7 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 25 170 0
1 g9301.t7 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 173 335 0
6 g9301.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 4 171 0
5 g9301.t7 SUPERFAMILY SSF56327 LDH C-terminal domain-like 172 338 0
9 g9301.t7 TIGRFAM TIGR01772 MDH_euk_gproteo: malate dehydrogenase, NAD-dependent 26 337 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0006099 tricarboxylic acid cycle BP
GO:0019752 carboxylic acid metabolic process BP
GO:0005975 carbohydrate metabolic process BP
GO:0030060 L-malate dehydrogenase activity MF
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values