General information for g1576.t23
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.t23 | isoform | g1576.t23 | 11964183 | 11969918 |
| chr_3 | g1576 | g1576.t23 | exon | g1576.t23.exon1 | 11964183 | 11964464 |
| chr_3 | g1576 | g1576.t23 | exon | g1576.t23.exon2 | 11967614 | 11967996 |
| chr_3 | g1576 | g1576.t23 | exon | g1576.t23.exon3 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t23 | cds | g1576.t23.CDS1 | 11968104 | 11968962 |
| chr_3 | g1576 | g1576.t23 | exon | g1576.t23.exon4 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t23 | cds | g1576.t23.CDS2 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t23 | exon | g1576.t23.exon5 | 11969180 | 11969918 |
| chr_3 | g1576 | g1576.t23 | cds | g1576.t23.CDS3 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t23 | TSS | g1576.t23 | NA | NA |
| chr_3 | g1576 | g1576.t23 | TTS | g1576.t23 | NA | NA |
Sequences
>g1576.t23 Gene=g1576 Length=2399
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGAC
GGTAAGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGT
TGGAAAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAAT
CACACTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATT
GCGTCAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTTATGCAAGC
TGCTGTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAA
CGCTTTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGACGATATTCA
GGGTACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCG
TTTATCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGA
ATTATGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGT
ATGGCTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCA
TCATAAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGA
TATTTTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGA
AATTATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCC
AACAAGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGT
TTTTGCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATTCTATCCAGG
ACAAGGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGT
TTCCAAAATTCCAGAAGATATCTTTTTGATTTCCGCTAAAGCTCTTGCTGATTTAGTTAC
TGATGATGATTTAAATAAAGGAGCTTTATATCCACCATTAGAAACAATTCAAGATTGTTC
ATTTGAAATTGCTGTTAAAGTTATGGAATATGCTTATGATAATGGATTGGCTACGGTTCG
TCCTAAACCAAAAAATATGCGTACTTTCATCAAGGCCCAAATGTATGACCCATCTTACAA
ACCAGCCATCCCACCCGTATATAAATTATAAAACAATTTCATTTTTATCAATTCTCATTT
TCCAATTCTATCGTTCTATTGTTTTATGTAATTTATATCTCATGACAAGCAATTTCAAAG
GAAAAAAGTATATTTTTTATGTTTTTGCGTGTAAATCATGCAAACTATTCGGAAAAATTT
AGTAAAAAGTCTTTTAATTATTTATTAATGCAATAAATTAATTTCACTTGCCAACCTTCT
TTGAATTTTCGCATTTGTCGACTCATTTGTAATATCTGGAACAAAATTACAAATGACTTT
ACATATGTGTAGAATAATCGATATCTTATTTAAAGTTATAAAAATGGTTTACAATAAAAA
TTCATCCATGCAAAGTATTTATAAAAATCAATAATCAATGTTTTATTTAAATCTCTTTAT
TAGTTTTTTCTCATTGTTAGTTTATACTACAAACAAATATGTTTTTTGTTCTCTTATCAA
AATAATCAATAGCATTATACAAACAATAGATAAAAAATAATTATTAAATGTTTAAAGTT
>g1576.t23 Gene=g1576 Length=394
MGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIE
EFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLR
VTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPK
GGLNHHKSKFAHAHHPVDTLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFNERPIIF
ALSNPTSKAECTAEDAYIHSDGKAVFASGSPFAPVTYKGQKFYPGQGNNSYIFPGVALGV
IAGAVSKIPEDIFLISAKALADLVTDDDLNKGALYPPLETIQDCSFEIAVKVMEYAYDNG
LATVRPKPKNMRTFIKAQMYDPSYKPAIPPVYKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g1576.t23 | CDD | cd05312 | NAD_bind_1_malic_enz | 104 | 382 | 6.7701E-147 |
| 12 | g1576.t23 | Gene3D | G3DSA:3.40.50.10380 | - | 1 | 360 | 4.2E-183 |
| 13 | g1576.t23 | Gene3D | G3DSA:3.40.50.720 | - | 102 | 288 | 4.2E-183 |
| 14 | g1576.t23 | Gene3D | G3DSA:3.30.2330.30 | - | 361 | 393 | 4.2E-183 |
| 3 | g1576.t23 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 1 | 393 | 5.5E-211 |
| 4 | g1576.t23 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 1 | 393 | 5.5E-211 |
| 15 | g1576.t23 | PIRSF | PIRSF000106 | ME | 1 | 389 | 1.6E-160 |
| 6 | g1576.t23 | PRINTS | PR00072 | Malic enzyme signature | 15 | 37 | 2.3E-48 |
| 8 | g1576.t23 | PRINTS | PR00072 | Malic enzyme signature | 75 | 93 | 2.3E-48 |
| 9 | g1576.t23 | PRINTS | PR00072 | Malic enzyme signature | 100 | 116 | 2.3E-48 |
| 5 | g1576.t23 | PRINTS | PR00072 | Malic enzyme signature | 131 | 147 | 2.3E-48 |
| 7 | g1576.t23 | PRINTS | PR00072 | Malic enzyme signature | 234 | 250 | 2.3E-48 |
| 1 | g1576.t23 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 1 | 94 | 5.1E-38 |
| 2 | g1576.t23 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 104 | 357 | 2.9E-98 |
| 17 | g1576.t23 | ProSitePatterns | PS00331 | Malic enzymes signature. | 100 | 116 | - |
| 18 | g1576.t23 | SMART | SM01274 | malic_2 | 1 | 94 | 4.3E-18 |
| 19 | g1576.t23 | SMART | SM00919 | Malic_M_2 | 104 | 357 | 1.9E-118 |
| 11 | g1576.t23 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 103 | 4.03E-44 |
| 10 | g1576.t23 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 104 | 391 | 1.77E-100 |
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. There were no conditions that were differentially expressed