General information for g1576.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative NADP-dependent malic enzyme.
Parent gene
- The parent gene g1576 is located on chr_3: 11969200..11969918 (+ 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_3 | g1576 | g1576.t17 | isoform | g1576.t17 | 11964183 | 11968248 |
| chr_3 | g1576 | g1576.t17 | exon | g1576.t17.exon1 | 11964183 | 11964464 |
| chr_3 | g1576 | g1576.t17 | cds | g1576.t17.CDS1 | 11964219 | 11964464 |
| chr_3 | g1576 | g1576.t17 | exon | g1576.t17.exon2 | 11967614 | 11967996 |
| chr_3 | g1576 | g1576.t17 | cds | g1576.t17.CDS2 | 11967614 | 11967996 |
| chr_3 | g1576 | g1576.t17 | exon | g1576.t17.exon3 | 11968063 | 11968248 |
| chr_3 | g1576 | g1576.t17 | cds | g1576.t17.CDS3 | 11968063 | 11968099 |
| chr_3 | g1576 | g1576.t17 | TSS | g1576.t17 | NA | NA |
| chr_3 | g1576 | g1576.t17 | TTS | g1576.t17 | NA | NA |
Sequences
>g1576.t17 Gene=g1576 Length=851
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGAC
GGTAAGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGT
TGGAAAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAAT
CACACTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATT
GCGTCAAAAAC
>g1576.t17 Gene=g1576 Length=221
MSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKITILSPFGLNTKSNIMSESRDRLGQWP
VESEAELTGQGLQRLKNNHYNKGLAFTHEERQILGIHGLLAPGIKSIDEQIKHAHILLER
CATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLY
ISIYDKGHIYDVIKNWPEFDVRAIVVTDGKRKNFRFGRSWS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1576.t17 | Gene3D | G3DSA:3.40.50.10380 | - | 69 | 212 | 7.2E-51 |
| 8 | g1576.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 2 | g1576.t17 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 38 | 211 | 1.0E-66 |
| 3 | g1576.t17 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 38 | 211 | 1.0E-66 |
| 5 | g1576.t17 | PRINTS | PR00072 | Malic enzyme signature | 141 | 165 | 2.1E-9 |
| 4 | g1576.t17 | PRINTS | PR00072 | Malic enzyme signature | 201 | 221 | 2.1E-9 |
| 1 | g1576.t17 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 135 | 211 | 6.2E-24 |
| 7 | g1576.t17 | SMART | SM01274 | malic_2 | 135 | 221 | 1.0E-6 |
| 6 | g1576.t17 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 65 | 211 | 4.32E-46 |
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:0004471 | malate dehydrogenase (decarboxylating) (NAD+) activity | MF |
| GO:0004470 | malic enzyme 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. There were no conditions that were differentially expressed