General information for g4516.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Malate dehydrogenase, cytoplasmic.
Parent gene
- The parent gene g4516 is located on chr_2: 2969953..2979916 (+ 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_2 | g4516 | g4516.t12 | TSS | g4516.t12 | 2968976 | 2968976 |
| chr_2 | g4516 | g4516.t12 | isoform | g4516.t12 | 2969079 | 2979916 |
| chr_2 | g4516 | g4516.t12 | exon | g4516.t12.exon1 | 2969079 | 2969081 |
| chr_2 | g4516 | g4516.t12 | cds | g4516.t12.CDS1 | 2969079 | 2969081 |
| chr_2 | g4516 | g4516.t12 | exon | g4516.t12.exon2 | 2969516 | 2969894 |
| chr_2 | g4516 | g4516.t12 | cds | g4516.t12.CDS2 | 2969516 | 2969894 |
| chr_2 | g4516 | g4516.t12 | exon | g4516.t12.exon3 | 2969958 | 2970059 |
| chr_2 | g4516 | g4516.t12 | cds | g4516.t12.CDS3 | 2969958 | 2970059 |
| chr_2 | g4516 | g4516.t12 | exon | g4516.t12.exon4 | 2970221 | 2970944 |
| chr_2 | g4516 | g4516.t12 | cds | g4516.t12.CDS4 | 2970221 | 2970225 |
| chr_2 | g4516 | g4516.t12 | exon | g4516.t12.exon5 | 2979911 | 2979916 |
| chr_2 | g4516 | g4516.t12 | TTS | g4516.t12 | NA | NA |
Sequences
>g4516.t12 Gene=g4516 Length=1214
ATGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTCATTG
CTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATTCTCACACTT
TTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTATCAGACTGT
GCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCATTTAAGGAT
GTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAGCGCAAAGAT
CTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTGAATACATATGCA
AAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTAATGCATTAATTTGC
TCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACAAGACTCGATCAA
AATCAATGAATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAA
AATGAGTTCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGAT
AGGCACACAATCAGGCAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATA
TAATGTTCCAGAGGGCATCGTTTTCTCATTCCCAGTTGAGATCAAGAATAAACAGTGGAG
CATTGTTCCTGGATTCAAAATCAATGACTTTGCTCGCAGTAAATTGGATATTACAACAAA
AGAATTGTTGGAGGAAAAAGAAGAAGCAATGGCAGTCTGCAATGCAGATGCAAAAATCTA
AATACCTGAAAAGAATATTACACTATTGTTGTTGAAATTCTCCATTTATGCTACAATTTA
TAAGCTGGGATGTTTAACTTACACGCATTTTTATTTGAATTCCTTAAAATATATTTTTTT
TCGTTTATAATATACATAGCATTCCTTCAAAATGTTTGTTTCTAATTCATCATGTACTTC
CAAATTGAGATTATATTTTGTTTTATCGTTTTTATGTTAGCTTTTTTCAAAGTCTTATTT
TTTATTTTCGGAATTATCAGGAATTAAAAGATTTTATTTTTTTATTTTGTTTTAATTAGG
GATGCAAACATCCTACATAAAACATGTTTTTGGAGAATTAATGAAATAAAGTTAATTAAT
TAAAAAAAAAATTA
>g4516.t12 Gene=g4516 Length=162
MSEPIKVVVTGAAGQIAYSLLYMIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDC
AFTLLTEVIPTTDVAVAFKDVSVVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTYA
KKDVKVLVVGNPANTNALICSHYAPSIPKENFTAMTRLDQNQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4516.t12 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 154 | 0 |
| 2 | g4516.t12 | PANTHER | PTHR23382 | MALATE DEHYDROGENASE | 1 | 162 | 0 |
| 1 | g4516.t12 | Pfam | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 5 | 152 | 0 |
| 3 | g4516.t12 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 155 | 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:0016615 | malate dehydrogenase activity | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
| GO:0006108 | malate metabolic process | BP |
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.
