General information for g4516.t3
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.t3 | isoform | g4516.t3 | 2966570 | 2970577 |
| chr_2 | g4516 | g4516.t3 | exon | g4516.t3.exon1 | 2966570 | 2966680 |
| chr_2 | g4516 | g4516.t3 | exon | g4516.t3.exon2 | 2968761 | 2969081 |
| chr_2 | g4516 | g4516.t3 | cds | g4516.t3.CDS1 | 2969079 | 2969081 |
| chr_2 | g4516 | g4516.t3 | exon | g4516.t3.exon3 | 2969516 | 2969894 |
| chr_2 | g4516 | g4516.t3 | cds | g4516.t3.CDS2 | 2969516 | 2969894 |
| chr_2 | g4516 | g4516.t3 | exon | g4516.t3.exon4 | 2969958 | 2970577 |
| chr_2 | g4516 | g4516.t3 | cds | g4516.t3.CDS3 | 2969958 | 2970577 |
| chr_2 | g4516 | g4516.t3 | TTS | g4516.t3 | 2970937 | 2970937 |
| chr_2 | g4516 | g4516.t3 | TSS | g4516.t3 | NA | NA |
Sequences
>g4516.t3 Gene=g4516 Length=1431
TCTGCTTCGTGGCAAACGTTGTTTTTATGTACGAATGAGATTTTAAAGTGGAGAGTGAGA
GAGGCAGGTAGTTATAATGTTGCAAGTACAGTTGAGAATGAAAAAGAATAATTCCAACAA
GAGAGATTTGATATTGGAATGATTTTCAACTATAACACACAATTTAGCAGTCACTTAATT
TTTCAAACTGTCATTGATAAAACCCAAAGATAGGACGATGATTACTGGCGTTTATTTTTA
ACGGAAAATCCAGCCAAAACAGTTTTTTCAATGAAAACATTCCCCTCTATAAAAAAATTT
TTTTCTCCACAGTTGAGGTACTTAAAAGATAAGTCGTTGGTCGAAAGGCAGTCATCGTAG
TTGTCTAAAATTATCGCACGCAATAGTTTGATTTTTGTTAATCAAATAAGTAATTAACAA
TTCATTATAATGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCT
TACTCATTGCTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATT
CTCACACTTTTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTA
TCAGACTGTGCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCA
TTTAAGGATGTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAG
CGCAAAGATCTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTGAAT
ACATATGCAAAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTAATGCA
TTAATTTGCTCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACAAGA
CTCGATCAAAATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTACAAAA
GTCAAGAATCTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTTCAAAT
GGTACGGTTGATGGTAAGCCTGTTACAGACCTTGTCGACGCATCTTATTTGGAGAATGAA
TTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAAAATGAGTTCA
GCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGATAGGCACACAA
TCAGGCAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATATAATGTTCCA
GAGGGCATCGTTTTCTCATTCCCAGTTGAGATCAAGAATAAACAGTGGAGCATTGTTCCT
GGATTCAAAATCAATGACTTTGCTCGCAGTAAATTGGATATTACAACAAAAGAATTGTTG
GAGGAAAAAGAAGAAGCAATGGCAGTCTGCAATGCAGATGCAAAAATCTAA
>g4516.t3 Gene=g4516 Length=333
MSEPIKVVVTGAAGQIAYSLLYMIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDC
AFTLLTEVIPTTDVAVAFKDVSVVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTYA
KKDVKVLVVGNPANTNALICSHYAPSIPKENFTAMTRLDQNRACAQIAQKVGSDITKVKN
LFIWGNHSATQFPDCSNGTVDGKPVTDLVDASYLENEFVTTVQKRGAAVIAARKMSSAMS
AAKAAADHVRDWWIGTQSGNYVSMGVVTPKDNPYNVPEGIVFSFPVEIKNKQWSIVPGFK
INDFARSKLDITTKELLEEKEEAMAVCNADAKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4516.t3 | CDD | cd01336 | MDH_cytoplasmic_cytosolic | 3 | 311 | 0.0 |
| 8 | g4516.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 154 | 9.5E-63 |
| 7 | g4516.t3 | Gene3D | G3DSA:3.90.110.10 | - | 155 | 331 | 3.6E-65 |
| 4 | g4516.t3 | Hamap | MF_01517 | Malate dehydrogenase [mdh]. | 1 | 327 | 48.18359 |
| 3 | g4516.t3 | PANTHER | PTHR23382 | MALATE DEHYDROGENASE | 1 | 327 | 5.1E-152 |
| 9 | g4516.t3 | PIRSF | PIRSF000102 | Lac_mal_DH | 1 | 327 | 1.1E-72 |
| 2 | g4516.t3 | Pfam | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 5 | 152 | 1.1E-37 |
| 1 | g4516.t3 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 156 | 325 | 2.6E-33 |
| 11 | g4516.t3 | ProSitePatterns | PS00068 | Malate dehydrogenase active site signature. | 155 | 167 | - |
| 6 | g4516.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 155 | 3.95E-46 |
| 5 | g4516.t3 | SUPERFAMILY | SSF56327 | LDH C-terminal domain-like | 156 | 327 | 1.34E-56 |
| 12 | g4516.t3 | TIGRFAM | TIGR01759 | MalateDH-SF1: malate dehydrogenase | 3 | 323 | 1.3E-152 |
| 13 | g4516.t3 | TIGRFAM | TIGR01758 | MDH_euk_cyt: malate dehydrogenase, NAD-dependent | 6 | 325 | 1.5E-155 |
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:0006108 | malate metabolic process | BP |
| GO:0019752 | carboxylic acid metabolic process | BP |
| GO:0016615 | malate dehydrogenase activity | MF |
| 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 K00025 (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.
