General information for g9301.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Malate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g9301 is located on chr_1: 1646256..1647630 (- strand)
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.t2 | isoform | g9301.t2 | 1639763 | 1647630 |
| chr_1 | g9301 | g9301.t2 | exon | g9301.t2.exon1 | 1639763 | 1639769 |
| chr_1 | g9301 | g9301.t2 | exon | g9301.t2.exon2 | 1646013 | 1646995 |
| chr_1 | g9301 | g9301.t2 | cds | g9301.t2.CDS1 | 1646256 | 1646995 |
| chr_1 | g9301 | g9301.t2 | exon | g9301.t2.exon3 | 1647090 | 1647297 |
| chr_1 | g9301 | g9301.t2 | cds | g9301.t2.CDS2 | 1647090 | 1647297 |
| chr_1 | g9301 | g9301.t2 | exon | g9301.t2.exon4 | 1647565 | 1647630 |
| chr_1 | g9301 | g9301.t2 | cds | g9301.t2.CDS3 | 1647565 | 1647630 |
| chr_1 | g9301 | g9301.t2 | TSS | g9301.t2 | 1647730 | 1647730 |
| chr_1 | g9301 | g9301.t2 | TTS | g9301.t2 | NA | NA |
Sequences
>g9301.t2 Gene=g9301 Length=1264
ATGTTCTCAAGAGTCTTAAGAACCGCAGCACATCAAGGAGCCAAGAGCTTCTCAACTTCA
CAACAAAACAATGTTAAAGTTGCAGTATGTGGTGCATCGGGTGGCATTGGTCAACCATTA
TCATTGCTATTGAAACAAAGTCCACTCATCACTGAGCTTTCTCTTTACGATATTGTTCAC
ACACCTGGAGTTGCTGCTGATTTGTCACACATTGATACAGCTAGCAAAGTTGTTGGCTAC
AATGGACCAGAAAACTTGGAAAAGGCCTTGAAAGATGCTGATGTTGTTATTATTCCTGCT
GGAGTTCCTCGCAAGCCAGGAATGACTCGTGACGATCTTTTCAACACAAATGCTTCAATT
GTTCGTGACTTGGCTATCGCATGTGGAAAGGCTTGCCCTAAAGCTCTCGTGGGTATTATT
TCAAATCCAGTTAACTCAACTGTCCCAATTGCCAGCGAAGCATTGGCTAAACTTGGAGTT
TTAGATCCAAAGCGAATTTTTGGTGTCTCAACACTTGATGTTGTAAGAGCAAATGCTTTT
ATCGGTGAAGCAGCAGGTGTCGATCCAGCAAAAGTTAATTTGCCAGTTATTGGCGGTCAC
TCAGGTGTCACAATCATGCCATTGCTCTCACAATGCAAACCTGCCGTCAACTTCCCAGCT
GATAAGGTCAAGGCTCTCACTGAACGCATCCAGGAAGCTGGTACTGAAGTTGTCAAGGCA
AAGGCTGGCGCTGGATCTGCTACTCTTTCAATGGCATATGCCGGTGCTCGTTTCGCTATT
TCACTTATTCGTGCTATCAAAGGTGAACAAAATGTTGTCGAATGTGCTTATGTTCGTTCA
GATGTTACAGAAGCCAAATATTTCTCAACACCTCTCTTGTTGGGCAAGAATGGCATTGAA
AAGAACTTGGGAATTGGATCATTGAATGCTTTCGAGCAGGAACTTCTTGCAAAGGCTATC
CCAGAATTGAAAAAGAACATTCAAACTGGCGAGGACTTTATCAATAAGAACTAAATTATG
AACTCTTCATTATCATCTTTTGAATGATTCCTTATTTATGTTTTATTCTCCCCTTAATAA
GATTTCCTTTGCACTGACCCGCCTTTAAAAATTTACTTACAATTTTATAATTTAAATTTT
ACTTGATGATTATTAGGGCTAGCGTTAATATTTAGGAAATCTTTGATTGGCAATTTACGT
CTAAGAAAATTTTCCGAAACGGAAATAAAAAGTGAAACACAACCGAAATGTTACAAAAAT
TTAA
>g9301.t2 Gene=g9301 Length=337
MFSRVLRTAAHQGAKSFSTSQQNNVKVAVCGASGGIGQPLSLLLKQSPLITELSLYDIVH
TPGVAADLSHIDTASKVVGYNGPENLEKALKDADVVIIPAGVPRKPGMTRDDLFNTNASI
VRDLAIACGKACPKALVGIISNPVNSTVPIASEALAKLGVLDPKRIFGVSTLDVVRANAF
IGEAAGVDPAKVNLPVIGGHSGVTIMPLLSQCKPAVNFPADKVKALTERIQEAGTEVVKA
KAGAGSATLSMAYAGARFAISLIRAIKGEQNVVECAYVRSDVTEAKYFSTPLLLGKNGIE
KNLGIGSLNAFEQELLAKAIPELKKNIQTGEDFINKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g9301.t2 | CDD | cd01337 | MDH_glyoxysomal_mitochondrial | 25 | 334 | 0 |
| 8 | g9301.t2 | Gene3D | G3DSA:3.40.50.720 | - | 18 | 169 | 0 |
| 7 | g9301.t2 | Gene3D | G3DSA:3.90.110.10 | - | 170 | 336 | 0 |
| 3 | g9301.t2 | PANTHER | PTHR11540:SF16 | MALATE DEHYDROGENASE, MITOCHONDRIAL | 16 | 336 | 0 |
| 4 | g9301.t2 | PANTHER | PTHR11540 | MALATE AND LACTATE DEHYDROGENASE | 16 | 336 | 0 |
| 10 | g9301.t2 | PIRSF | PIRSF000102 | Lac_mal_DH | 21 | 337 | 0 |
| 2 | g9301.t2 | Pfam | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 25 | 168 | 0 |
| 1 | g9301.t2 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 171 | 333 | 0 |
| 6 | g9301.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 4 | 169 | 0 |
| 5 | g9301.t2 | SUPERFAMILY | SSF56327 | LDH C-terminal domain-like | 170 | 336 | 0 |
| 9 | g9301.t2 | TIGRFAM | TIGR01772 | MDH_euk_gproteo: malate dehydrogenase, NAD-dependent | 26 | 335 | 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
- This transcript has been annotated with K00026 (malate dehydrogenase)
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.
