General information for g1576.t11
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.t11 | TSS | g1576.t11 | 11963117 | 11963117 |
| chr_3 | g1576 | g1576.t11 | isoform | g1576.t11 | 11963299 | 11967974 |
| chr_3 | g1576 | g1576.t11 | exon | g1576.t11.exon1 | 11963299 | 11963336 |
| chr_3 | g1576 | g1576.t11 | cds | g1576.t11.CDS1 | 11963299 | 11963336 |
| chr_3 | g1576 | g1576.t11 | exon | g1576.t11.exon2 | 11964182 | 11964464 |
| chr_3 | g1576 | g1576.t11 | cds | g1576.t11.CDS2 | 11964182 | 11964464 |
| chr_3 | g1576 | g1576.t11 | exon | g1576.t11.exon3 | 11967614 | 11967974 |
| chr_3 | g1576 | g1576.t11 | cds | g1576.t11.CDS3 | 11967614 | 11967973 |
| chr_3 | g1576 | g1576.t11 | TTS | g1576.t11 | NA | NA |
Sequences
>g1576.t11 Gene=g1576 Length=682
ATGTCTTTAATCAATGGAAAATTGCAGAATGGTCATGCAGTCGCAACGGAAAATGGAAAT
GAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAATATAAAACGCAAACGAATGAA
AATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACATCGTTCGTAGAAAAAATTACA
ATTCTTTCACCATTTGGATTGAATACTAAATCAAACATTATGAGTGAAAGCCGAGATAGA
CTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACAGGACAAGGATTGCAACGTTTG
AAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCATGAAGAACGACAAATTTTGGGA
ATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGATGAACAAATTAAGCATGCCCAT
ATTTTATTGGAACGATGTGCGACTGATTTAGACAAATATATTTATTTGATGGGACTTCAA
GACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCCGATATTGCAAACATGATGCCT
TTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAGTATTCGATGATTTACACTAAT
CCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCATATTTACGATGTCATCAAAAAT
TGGCCAGAATTTGATGTAAGAG
>g1576.t11 Gene=g1576 Length=227
MSLINGKLQNGHAVATENGNENHDVMSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKIT
ILSPFGLNTKSNIMSESRDRLGQWPVESEAELTGQGLQRLKNNHYNKGLAFTHEERQILG
IHGLLAPGIKSIDEQIKHAHILLERCATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMP
LVYTPTVGLACQKYSMIYTNPKGLYISIYDKGHIYDVIKNWPEFDVR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1576.t11 | Gene3D | G3DSA:3.40.50.10380 | - | 94 | 227 | 9.3E-45 |
| 6 | g1576.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 7 | g1576.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 2 | g1576.t11 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 58 | 227 | 5.1E-61 |
| 3 | g1576.t11 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 58 | 227 | 5.1E-61 |
| 1 | g1576.t11 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 160 | 226 | 1.8E-18 |
| 5 | g1576.t11 | SMART | SM01274 | malic_2 | 160 | 227 | 0.0016 |
| 4 | g1576.t11 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 90 | 225 | 1.37E-40 |
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: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