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.t12 TTS g9301.t12 1646010 1646010
chr_1 g9301 g9301.t12 isoform g9301.t12 1646256 1647630
chr_1 g9301 g9301.t12 exon g9301.t12.exon1 1646256 1646995
chr_1 g9301 g9301.t12 cds g9301.t12.CDS1 1646256 1646948
chr_1 g9301 g9301.t12 exon g9301.t12.exon2 1647136 1647297
chr_1 g9301 g9301.t12 exon g9301.t12.exon3 1647565 1647630
chr_1 g9301 g9301.t12 TSS g9301.t12 1647730 1647730

Sequences

>g9301.t12 Gene=g9301 Length=968
ATGTTCTCAAGAGTCTTAAGAACCGCAGCACATCAAGGAGCCAAGAGCTTCTCAACTTCA
CAACAAAACAATGTTAAAGTTGCAGTATGTGGTGCATCGGGTGGCATTGGTCAACCATTA
TCATTGCTATTGAAACAAAGTCCACTCATCACTGAGCTTTCTCTTTACGATATTGTTCAC
ACACCTGGAGTTGCTGCTGATTTGTCACACATTGATACAGCTAGCAAAATGCTGATGTTG
TTATTATTCCTGCTGGAGTTCCTCGCAAGCCAGGAATGACTCGTGACGATCTTTTCAACA
CAAATGCTTCAATTGTTCGTGACTTGGCTATCGCATGTGGAAAGGCTTGCCCTAAAGCTC
TCGTGGGTATTATTTCAAATCCAGTTAACTCAACTGTCCCAATTGCCAGCGAAGCATTGG
CTAAACTTGGAGTTTTAGATCCAAAGCGAATTTTTGGTGTCTCAACACTTGATGTTGTAA
GAGCAAATGCTTTTATCGGTGAAGCAGCAGGTGTCGATCCAGCAAAAGTTAATTTGCCAG
TTATTGGCGGTCACTCAGGTGTCACAATCATGCCATTGCTCTCACAATGCAAACCTGCCG
TCAACTTCCCAGCTGATAAGGTCAAGGCTCTCACTGAACGCATCCAGGAAGCTGGTACTG
AAGTTGTCAAGGCAAAGGCTGGCGCTGGATCTGCTACTCTTTCAATGGCATATGCCGGTG
CTCGTTTCGCTATTTCACTTATTCGTGCTATCAAAGGTGAACAAAATGTTGTCGAATGTG
CTTATGTTCGTTCAGATGTTACAGAAGCCAAATATTTCTCAACACCTCTCTTGTTGGGCA
AGAATGGCATTGAAAAGAACTTGGGAATTGGATCATTGAATGCTTTCGAGCAGGAACTTC
TTGCAAAGGCTATCCCAGAATTGAAAAAGAACATTCAAACTGGCGAGGACTTTATCAATA
AGAACTAA

>g9301.t12 Gene=g9301 Length=230
MTRDDLFNTNASIVRDLAIACGKACPKALVGIISNPVNSTVPIASEALAKLGVLDPKRIF
GVSTLDVVRANAFIGEAAGVDPAKVNLPVIGGHSGVTIMPLLSQCKPAVNFPADKVKALT
ERIQEAGTEVVKAKAGAGSATLSMAYAGARFAISLIRAIKGEQNVVECAYVRSDVTEAKY
FSTPLLLGKNGIEKNLGIGSLNAFEQELLAKAIPELKKNIQTGEDFINKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g9301.t12 CDD cd01337 MDH_glyoxysomal_mitochondrial 1 227 0
8 g9301.t12 Gene3D G3DSA:3.40.50.720 - 1 62 0
7 g9301.t12 Gene3D G3DSA:3.90.110.10 - 63 229 0
3 g9301.t12 PANTHER PTHR11540:SF16 MALATE DEHYDROGENASE, MITOCHONDRIAL 1 229 0
4 g9301.t12 PANTHER PTHR11540 MALATE AND LACTATE DEHYDROGENASE 1 229 0
2 g9301.t12 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 1 61 0
1 g9301.t12 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 64 226 0
6 g9301.t12 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 61 0
5 g9301.t12 SUPERFAMILY SSF56327 LDH C-terminal domain-like 63 229 0
9 g9301.t12 TIGRFAM TIGR01772 MDH_euk_gproteo: malate dehydrogenase, NAD-dependent 1 228 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:0006099 tricarboxylic acid cycle BP
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0005975 carbohydrate metabolic process BP
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0030060 L-malate dehydrogenase activity MF
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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