General information for g4516.t11
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.t11 | TSS | g4516.t11 | 2968976 | 2968976 |
| chr_2 | g4516 | g4516.t11 | isoform | g4516.t11 | 2969079 | 2970955 |
| chr_2 | g4516 | g4516.t11 | exon | g4516.t11.exon1 | 2969079 | 2969085 |
| chr_2 | g4516 | g4516.t11 | exon | g4516.t11.exon2 | 2969516 | 2969894 |
| chr_2 | g4516 | g4516.t11 | cds | g4516.t11.CDS1 | 2969579 | 2969894 |
| chr_2 | g4516 | g4516.t11 | exon | g4516.t11.exon3 | 2969958 | 2970955 |
| chr_2 | g4516 | g4516.t11 | cds | g4516.t11.CDS2 | 2969958 | 2970577 |
| chr_2 | g4516 | g4516.t11 | TTS | g4516.t11 | NA | NA |
Sequences
>g4516.t11 Gene=g4516 Length=1384
ATGGTAAAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTC
ATTGCTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATTCTCAC
ACTTTTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTATCAGA
CTGTGCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCATTTAA
GGATGTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAGCGCAA
AGATCTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTGAATACATA
TGCAAAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTAATGCATTAAT
TTGCTCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACAAGACTCGA
TCAAAATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTACAAAAGTCAA
GAATCTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTTCAAATGGTAC
GGTTGATGGTAAGCCTGTTACAGACCTTGTCGACGCATCTTATTTGGAGAATGAATTTGT
CACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAAAATGAGTTCAGCAAT
GAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGATAGGCACACAATCAGG
CAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATATAATGTTCCAGAGGG
CATCGTTTTCTCATTCCCAGTTGAGATCAAGAATAAACAGTGGAGCATTGTTCCTGGATT
CAAAATCAATGACTTTGCTCGCAGTAAATTGGATATTACAACAAAAGAATTGTTGGAGGA
AAAAGAAGAAGCAATGGCAGTCTGCAATGCAGATGCAAAAATCTAAATACCTGAAAAGAA
TATTACACTATTGTTGTTGAAATTCTCCATTTATGCTACAATTTATAAGCTGGGATGTTT
AACTTACACGCATTTTTATTTGAATTCCTTAAAATATATTTTTTTTCGTTTATAATATAC
ATAGCATTCCTTCAAAATGTTTGTTTCTAATTCATCATGTACTTCCAAATTGAGATTATA
TTTTGTTTTATCGTTTTTATGTTAGCTTTTTTCAAAGTCTTATTTTTTATTTTCGGAATT
ATCAGGAATTAAAAGATTTTATTTTTTTATTTTGTTTTAATTAGGGATGCAAACATCCTA
CATAAAACATGTTTTTGGAGAATTAATGAAATAAAGTTAATTAATTAAAAAAAATATATG
ATAG
>g4516.t11 Gene=g4516 Length=311
MIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDCAFTLLTEVIPTTDVAVAFKDVS
VVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTYAKKDVKVLVVGNPANTNALICSH
YAPSIPKENFTAMTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDG
KPVTDLVDASYLENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYV
SMGVVTPKDNPYNVPEGIVFSFPVEIKNKQWSIVPGFKINDFARSKLDITTKELLEEKEE
AMAVCNADAKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4516.t11 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 132 | 3.9E-51 |
| 7 | g4516.t11 | Gene3D | G3DSA:3.90.110.10 | - | 133 | 309 | 3.0E-65 |
| 3 | g4516.t11 | PANTHER | PTHR23382 | MALATE DEHYDROGENASE | 1 | 305 | 1.2E-139 |
| 11 | g4516.t11 | PIRSF | PIRSF000102 | Lac_mal_DH | 1 | 305 | 3.7E-63 |
| 2 | g4516.t11 | Pfam | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 4 | 130 | 2.5E-29 |
| 1 | g4516.t11 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 134 | 303 | 2.2E-33 |
| 6 | g4516.t11 | ProSitePatterns | PS00068 | Malate dehydrogenase active site signature. | 133 | 145 | - |
| 5 | g4516.t11 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 133 | 5.59E-35 |
| 4 | g4516.t11 | SUPERFAMILY | SSF56327 | LDH C-terminal domain-like | 134 | 305 | 1.11E-56 |
| 9 | g4516.t11 | TIGRFAM | TIGR01759 | MalateDH-SF1: malate dehydrogenase | 1 | 301 | 4.4E-140 |
| 10 | g4516.t11 | TIGRFAM | TIGR01758 | MDH_euk_cyt: malate dehydrogenase, NAD-dependent | 1 | 303 | 1.5E-144 |
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 K00024 (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.
