General information for g1576.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t28 | isoform | g1576.t28 | 11966571 | 11968480 |
| chr_3 | g1576 | g1576.t28 | exon | g1576.t28.exon1 | 11966571 | 11967192 |
| chr_3 | g1576 | g1576.t28 | exon | g1576.t28.exon2 | 11967614 | 11967992 |
| chr_3 | g1576 | g1576.t28 | cds | g1576.t28.CDS1 | 11967761 | 11967992 |
| chr_3 | g1576 | g1576.t28 | exon | g1576.t28.exon3 | 11968063 | 11968480 |
| chr_3 | g1576 | g1576.t28 | cds | g1576.t28.CDS2 | 11968063 | 11968478 |
| chr_3 | g1576 | g1576.t28 | TSS | g1576.t28 | NA | NA |
| chr_3 | g1576 | g1576.t28 | TTS | g1576.t28 | NA | NA |
Sequences
>g1576.t28 Gene=g1576 Length=1419
TGTTAATAGACAATATATTTATTATACCTTCATTTAATCAATTGAACCATCCTATTTACC
ATTTCAATAAGGGGAAGAGAAAATATCTATCTATCAACGCATGTTACTGTTTGTGATAGT
TAAAGTTAAATAATCTGATAAATTAGAAATGGAAGAGAGGAATTGTTTGTTACATACATA
GATGATAATATTAAACCTGAAAAAAAACTCATGACAGAAAAAAAGTAGAAACAGCTGTTA
TGACGTTTAATTGATTCAAGTGTGATATTGTTTTCCACAAGTGGGCATATCACGCTCGTG
TGAATTTTTTCGACTGCTGATAATTGATAAAAAAAATTTGATTGAAATTCAATAATCAGC
TGTTGATTATTGCAATGAAATGACACACTGAAATGCAATTGAATAAAACATTATTTTTAA
GGGAAATTAAAATTTCCTGGCAATAAAATTTAATTTTTATTACAATTTCATGTTTGTAAA
CATTAATGACATTATGTAAAGAAATTAAAACTAACTAAATATTACAAAATTTTATTATAT
ACATATGCAACACTTTCGTTTTCTACGCTCCACATTATTATGTTACTGACACATATACCT
ACTTAGTTGGAAAAATATAAAAGGCCTTGCTTTCACTCATGAAGAACGACAAATTTTGGG
AATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGATGAACAAATTAAGCATGCCCA
TATTTTATTGGAACGATGTGCGACTGATTTAGACAAATATATTTATTTGATGGGACTTCA
AGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCCGATATTGCAAACATGATGCC
TTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAGTATTCGATGATTTACACTAA
TCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCATATTTACGATGTCATCAAAAA
TTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGACGGAGAAAGAATTTTAGGTTT
GGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGAAAATTGGCACTCTACACTGC
ACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACACTCGATGTTGGCACAAATAC
TCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGACA
AGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAAAG
TTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAATA
TCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTTGC
TGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTT
>g1576.t28 Gene=g1576 Length=216
MGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLYISIYDKGHIYD
VIKNWPEFDVRAIVVTDGERILGLGDLGANGMGIPVGKLALYTALAGIKPHQCLPITLDV
GTNTQSILDDPLYIGLRQKRVTGQEYDDFIEEFMQAAVRRFGQSCLIQFEDFGNSNAFRL
IEKYREDYCTFNDDIQGTAAVAVAGLLASLRVTKTR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1576.t28 | Gene3D | G3DSA:3.40.50.10380 | - | 1 | 192 | 2.0E-99 |
| 11 | g1576.t28 | Gene3D | G3DSA:3.40.50.720 | - | 193 | 216 | 8.2E-6 |
| 2 | g1576.t28 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 1 | 216 | 4.0E-125 |
| 3 | g1576.t28 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 1 | 216 | 4.0E-125 |
| 12 | g1576.t28 | PIRSF | PIRSF000106 | ME | 1 | 216 | 1.2E-102 |
| 6 | g1576.t28 | PRINTS | PR00072 | Malic enzyme signature | 10 | 34 | 4.7E-59 |
| 8 | g1576.t28 | PRINTS | PR00072 | Malic enzyme signature | 70 | 99 | 4.7E-59 |
| 7 | g1576.t28 | PRINTS | PR00072 | Malic enzyme signature | 106 | 128 | 4.7E-59 |
| 5 | g1576.t28 | PRINTS | PR00072 | Malic enzyme signature | 166 | 184 | 4.7E-59 |
| 4 | g1576.t28 | PRINTS | PR00072 | Malic enzyme signature | 191 | 207 | 4.7E-59 |
| 1 | g1576.t28 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 4 | 185 | 2.4E-79 |
| 13 | g1576.t28 | ProSitePatterns | PS00331 | Malic enzymes signature. | 191 | 207 | - |
| 15 | g1576.t28 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 35 | 5.0 |
| 14 | g1576.t28 | SMART | SM01274 | malic_2 | 4 | 185 | 4.5E-104 |
| 9 | g1576.t28 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 2 | 194 | 1.08E-86 |
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.
