General information for g1576.t19
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.t19 | isoform | g1576.t19 | 11964183 | 11968948 |
| chr_3 | g1576 | g1576.t19 | exon | g1576.t19.exon1 | 11964183 | 11964464 |
| chr_3 | g1576 | g1576.t19 | exon | g1576.t19.exon2 | 11967614 | 11967967 |
| chr_3 | g1576 | g1576.t19 | exon | g1576.t19.exon3 | 11968063 | 11968948 |
| chr_3 | g1576 | g1576.t19 | cds | g1576.t19.CDS1 | 11968104 | 11968946 |
| chr_3 | g1576 | g1576.t19 | TTS | g1576.t19 | 11969767 | 11969767 |
| chr_3 | g1576 | g1576.t19 | TSS | g1576.t19 | NA | NA |
Sequences
>g1576.t19 Gene=g1576 Length=1522
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGAGAAAGAATTTTAGGTTTGGGCG
ATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGAAAATTGGCACTCTACACTGCACTTG
CTGGAATCAAACCTCATCAATGTTTACCAATCACACTCGATGTTGGCACAAATACTCAAT
CAATTCTTGATGATCCTCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGACAAGAAT
ATGATGACTTTATTGAGGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAAAGTTGTC
TCATTCAATTTGAGGACTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAATATCGCG
AAGATTATTGCACTTTTAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTTGCTGGCT
TGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTATCAGATAATAAAATTTTGTTCCAAG
GTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTATGTGTCATGGCAATGATTAAAGAAG
GTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGGCTTGTAGATAGTAAAGGATTGATTG
TCAAAGATCGTCCAAAAGGTGGACTCAACCATCATAAGAGTAAATTTGCTCACGCTCATC
ACCCAGTTGATACATTAGCAGAAGCTGTAGATATTTTGAAACCAACAGTCTTGATTGGTG
CTGCTGCAATTGGTGGAGCTTTTACACCCGAAATTATCAAAGCAATGGCTAGTTTTAATG
AACGCCCAATTATTTTTGCTTTGTCAAATCCAACAAGCAAGGCTGAATGTACTGCTGAGG
ATGCATATATTCATAGCGATGGAAAAGCTGTTTTTGCTTCTGGGTCACCTTTTGCGCCGG
TCACTTACAAAGGACAAAAATT
>g1576.t19 Gene=g1576 Length=281
MGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIE
EFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLR
VTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPK
GGLNHHKSKFAHAHHPVDTLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFNERPIIF
ALSNPTSKAECTAEDAYIHSDGKAVFASGSPFAPVTYKGQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g1576.t19 | Gene3D | G3DSA:3.40.50.10380 | - | 1 | 101 | 9.3E-51 |
| 13 | g1576.t19 | Gene3D | G3DSA:3.40.50.720 | - | 102 | 281 | 4.4E-78 |
| 3 | g1576.t19 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 1 | 280 | 2.4E-154 |
| 4 | g1576.t19 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 1 | 280 | 2.4E-154 |
| 14 | g1576.t19 | PIRSF | PIRSF000106 | ME | 1 | 281 | 7.9E-123 |
| 6 | g1576.t19 | PRINTS | PR00072 | Malic enzyme signature | 15 | 37 | 5.6E-49 |
| 8 | g1576.t19 | PRINTS | PR00072 | Malic enzyme signature | 75 | 93 | 5.6E-49 |
| 9 | g1576.t19 | PRINTS | PR00072 | Malic enzyme signature | 100 | 116 | 5.6E-49 |
| 5 | g1576.t19 | PRINTS | PR00072 | Malic enzyme signature | 131 | 147 | 5.6E-49 |
| 7 | g1576.t19 | PRINTS | PR00072 | Malic enzyme signature | 234 | 250 | 5.6E-49 |
| 1 | g1576.t19 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 1 | 94 | 2.7E-38 |
| 2 | g1576.t19 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 104 | 280 | 2.2E-67 |
| 15 | g1576.t19 | ProSitePatterns | PS00331 | Malic enzymes signature. | 100 | 116 | - |
| 16 | g1576.t19 | SMART | SM01274 | malic_2 | 1 | 94 | 4.3E-18 |
| 17 | g1576.t19 | SMART | SM00919 | Malic_M_2 | 104 | 281 | 1.4E-53 |
| 11 | g1576.t19 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 103 | 2.09E-44 |
| 10 | g1576.t19 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 104 | 280 | 4.92E-65 |
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:0051287 | NAD binding | 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.
