General information for g9301.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t18 | TTS | g9301.t18 | 1646010 | 1646010 |
| chr_1 | g9301 | g9301.t18 | isoform | g9301.t18 | 1646256 | 1647630 |
| chr_1 | g9301 | g9301.t18 | exon | g9301.t18.exon1 | 1646256 | 1646931 |
| chr_1 | g9301 | g9301.t18 | cds | g9301.t18.CDS1 | 1646256 | 1646654 |
| chr_1 | g9301 | g9301.t18 | exon | g9301.t18.exon2 | 1647175 | 1647297 |
| chr_1 | g9301 | g9301.t18 | exon | g9301.t18.exon3 | 1647565 | 1647630 |
| chr_1 | g9301 | g9301.t18 | TSS | g9301.t18 | 1647730 | 1647730 |
Sequences
>g9301.t18 Gene=g9301 Length=865
ATGTTCTCAAGAGTCTTAAGAACCGCAGCACATCAAGGAGCCAAGAGCTTCTCAACTTCA
CAACAAAACAATGTTAAAGTTGCAGTATGTGGTGCATCGGGTGGCATTGGTCAACCATTA
TCATTGCTATTGAAACAAAGTCCACTCATCACTGAGCTTTCTCTTTACGATATTGTTCAC
ACACCTGGATTTCAACACAAATGCTTCAATTGTTCGTGACTTGGCTATCGCATGTGGAAA
GGCTTGCCCTAAAGCTCTCGTGGGTATTATTTCAAATCCAGTTAACTCAACTGTCCCAAT
TGCCAGCGAAGCATTGGCTAAACTTGGAGTTTTAGATCCAAAGCGAATTTTTGGTGTCTC
AACACTTGATGTTGTAAGAGCAAATGCTTTTATCGGTGAAGCAGCAGGTGTCGATCCAGC
AAAAGTTAATTTGCCAGTTATTGGCGGTCACTCAGGTGTCACAATCATGCCATTGCTCTC
ACAATGCAAACCTGCCGTCAACTTCCCAGCTGATAAGGTCAAGGCTCTCACTGAACGCAT
CCAGGAAGCTGGTACTGAAGTTGTCAAGGCAAAGGCTGGCGCTGGATCTGCTACTCTTTC
AATGGCATATGCCGGTGCTCGTTTCGCTATTTCACTTATTCGTGCTATCAAAGGTGAACA
AAATGTTGTCGAATGTGCTTATGTTCGTTCAGATGTTACAGAAGCCAAATATTTCTCAAC
ACCTCTCTTGTTGGGCAAGAATGGCATTGAAAAGAACTTGGGAATTGGATCATTGAATGC
TTTCGAGCAGGAACTTCTTGCAAAGGCTATCCCAGAATTGAAAAAGAACATTCAAACTGG
CGAGGACTTTATCAATAAGAACTAA
>g9301.t18 Gene=g9301 Length=132
MPLLSQCKPAVNFPADKVKALTERIQEAGTEVVKAKAGAGSATLSMAYAGARFAISLIRA
IKGEQNVVECAYVRSDVTEAKYFSTPLLLGKNGIEKNLGIGSLNAFEQELLAKAIPELKK
NIQTGEDFINKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9301.t18 | Gene3D | G3DSA:3.90.110.10 | - | 1 | 131 | 0 |
| 2 | g9301.t18 | PANTHER | PTHR11540:SF16 | MALATE DEHYDROGENASE, MITOCHONDRIAL | 1 | 131 | 0 |
| 3 | g9301.t18 | PANTHER | PTHR11540 | MALATE AND LACTATE DEHYDROGENASE | 1 | 131 | 0 |
| 1 | g9301.t18 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 2 | 128 | 0 |
| 4 | g9301.t18 | SUPERFAMILY | SSF56327 | LDH C-terminal domain-like | 1 | 131 | 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:0005975 | carbohydrate metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0055114 | NA | NA |
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.
