General information for g4516.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Malate dehydrogenase.
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.t16 | TSS | g4516.t16 | 2968976 | 2968976 |
| chr_2 | g4516 | g4516.t16 | isoform | g4516.t16 | 2969953 | 2970941 |
| chr_2 | g4516 | g4516.t16 | exon | g4516.t16.exon1 | 2969953 | 2970941 |
| chr_2 | g4516 | g4516.t16 | cds | g4516.t16.CDS1 | 2970038 | 2970577 |
| chr_2 | g4516 | g4516.t16 | TTS | g4516.t16 | 2970937 | 2970937 |
Sequences
>g4516.t16 Gene=g4516 Length=989
TTTAGTTGTTGGAAATCCTGCAAATACTAATGCATTAATTTGCTCGCATTATGCACCTTC
AATTCCAAAGGAAAATTTTACAGCCATGACAAGACTCGATCAAAATCGTGCATGTGCTCA
AATTGCACAAAAAGTTGGAAGTGATATTACAAAAGTCAAGAATCTTTTCATTTGGGGTAA
TCATTCGGCAACACAATTCCCAGATTGTTCAAATGGTACGGTTGATGGTAAGCCTGTTAC
AGACCTTGTCGACGCATCTTATTTGGAGAATGAATTTGTCACAACTGTCCAAAAGAGAGG
TGCAGCTGTTATTGCAGCAAGAAAAATGAGTTCAGCAATGAGTGCTGCTAAAGCTGCTGC
TGATCATGTTCGTGATTGGTGGATAGGCACACAATCAGGCAACTATGTTTCAATGGGAGT
TGTTACACCGAAAGATAATCCATATAATGTTCCAGAGGGCATCGTTTTCTCATTCCCAGT
TGAGATCAAGAATAAACAGTGGAGCATTGTTCCTGGATTCAAAATCAATGACTTTGCTCG
CAGTAAATTGGATATTACAACAAAAGAATTGTTGGAGGAAAAAGAAGAAGCAATGGCAGT
CTGCAATGCAGATGCAAAAATCTAAATACCTGAAAAGAATATTACACTATTGTTGTTGAA
ATTCTCCATTTATGCTACAATTTATAAGCTGGGATGTTTAACTTACACGCATTTTTATTT
GAATTCCTTAAAATATATTTTTTTTCGTTTATAATATACATAGCATTCCTTCAAAATGTT
TGTTTCTAATTCATCATGTACTTCCAAATTGAGATTATATTTTGTTTTATCGTTTTTATG
TTAGCTTTTTTCAAAGTCTTATTTTTTATTTTCGGAATTATCAGGAATTAAAAGATTTTA
TTTTTTTATTTTGTTTTAATTAGGGATGCAAACATCCTACATAAAACATGTTTTTGGAGA
ATTAATGAAATAAAGTTAATTAATTAAAA
>g4516.t16 Gene=g4516 Length=179
MTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDGKPVTDLVDASYL
ENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYVSMGVVTPKDNPY
NVPEGIVFSFPVEIKNKQWSIVPGFKINDFARSKLDITTKELLEEKEEAMAVCNADAKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4516.t16 | Coils | Coil | Coil | 163 | 179 | - |
| 5 | g4516.t16 | Gene3D | G3DSA:3.90.110.10 | - | 1 | 178 | 4.5E-66 |
| 2 | g4516.t16 | PANTHER | PTHR23382 | MALATE DEHYDROGENASE | 1 | 173 | 9.1E-66 |
| 1 | g4516.t16 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 2 | 171 | 3.7E-34 |
| 4 | g4516.t16 | ProSitePatterns | PS00068 | Malate dehydrogenase active site signature. | 1 | 13 | - |
| 3 | g4516.t16 | SUPERFAMILY | SSF56327 | LDH C-terminal domain-like | 2 | 173 | 1.85E-57 |
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:0016615 | malate dehydrogenase activity | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0055114 | NA | NA |
| 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.
