General information for g1576.t30
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.t30 | isoform | g1576.t30 | 11967613 | 11969918 |
| chr_3 | g1576 | g1576.t30 | exon | g1576.t30.exon1 | 11967613 | 11967992 |
| chr_3 | g1576 | g1576.t30 | cds | g1576.t30.CDS1 | 11967761 | 11967992 |
| chr_3 | g1576 | g1576.t30 | exon | g1576.t30.exon2 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t30 | cds | g1576.t30.CDS2 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t30 | exon | g1576.t30.exon3 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t30 | cds | g1576.t30.CDS3 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t30 | exon | g1576.t30.exon4 | 11969180 | 11969918 |
| chr_3 | g1576 | g1576.t30 | cds | g1576.t30.CDS4 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t30 | TSS | g1576.t30 | NA | NA |
| chr_3 | g1576 | g1576.t30 | TTS | g1576.t30 | NA | NA |
Sequences
>g1576.t30 Gene=g1576 Length=2114
GGGCCTTGCTTTCACTCATGAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACC
AGGCATTAAATCTATTGATGAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGC
GACTGATTTAGACAAATATATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATT
TTATCGCGTTCTTGCATCCGATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGT
TGGTCTTGCATGTCAAAAGTATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATC
AATTTATGATAAGGGTCATATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAG
AGCTATTGTTGTTACTGACGGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGG
AATGGGTATTCCAGTTGGAAAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCA
TCAATGTTTACCAATCACACTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCC
TCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGA
GGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGA
CTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTT
TAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCG
AGTCACTAAAACTCGTTTATCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGC
ACTCGGAATTGCTGAATTATGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGA
CGCTCGCTCACGTGTATGGCTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAA
AGGTGGACTCAACCATCATAAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATT
AGCAGAAGCTGTAGATATTTTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGG
AGCTTTTACACCCGAAATTATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTT
TGCTTTGTCAAATCCAACAAGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAG
CGATGGAAAAGCTGTTTTTGCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACA
AAAATTCTATCCAGGACAAGGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGT
CATTGCTGGTGCCGTTTCCAAAATTCCAGAAGATATCTTTTTGATTTCCGCTAAAGCTCT
TGCTGATTTAGTTACTGATGATGATTTAAATAAAGGAGCTTTATATCCACCATTAGAAAC
AATTCAAGATTGTTCATTTGAAATTGCTGTTAAAGTTATGGAATATGCTTATGATAATGG
ATTGGCTACGGTTCGTCCTAAACCAAAAAATATGCGTACTTTCATCAAGGCCCAAATGTA
TGACCCATCTTACAAACCAGCCATCCCACCCGTATATAAATTATAAAACAATTTCATTTT
TATCAATTCTCATTTTCCAATTCTATCGTTCTATTGTTTTATGTAATTTATATCTCATGA
CAAGCAATTTCAAAGGAAAAAAGTATATTTTTTATGTTTTTGCGTGTAAATCATGCAAAC
TATTCGGAAAAATTTAGTAAAAAGTCTTTTAATTATTTATTAATGCAATAAATTAATTTC
ACTTGCCAACCTTCTTTGAATTTTCGCATTTGTCGACTCATTTGTAATATCTGGAACAAA
ATTACAAATGACTTTACATATGTGTAGAATAATCGATATCTTATTTAAAGTTATAAAAAT
GGTTTACAATAAAAATTCATCCATGCAAAGTATTTATAAAAATCAATAATCAATGTTTTA
TTTAAATCTCTTTATTAGTTTTTTCTCATTGTTAGTTTATACTACAAACAAATATGTTTT
TTGTTCTCTTATCAAAATAATCAATAGCATTATACAAACAATAGATAAAAAATAATTATT
AAATGTTTAAAGTT
>g1576.t30 Gene=g1576 Length=485
MGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLYISIYDKGHIYD
VIKNWPEFDVRAIVVTDGERILGLGDLGANGMGIPVGKLALYTALAGIKPHQCLPITLDV
GTNTQSILDDPLYIGLRQKRVTGQEYDDFIEEFMQAAVRRFGQSCLIQFEDFGNSNAFRL
IEKYREDYCTFNDDIQGTAAVAVAGLLASLRVTKTRLSDNKILFQGSGEAALGIAELCVM
AMIKEGVCEEDARSRVWLVDSKGLIVKDRPKGGLNHHKSKFAHAHHPVDTLAEAVDILKP
TVLIGAAAIGGAFTPEIIKAMASFNERPIIFALSNPTSKAECTAEDAYIHSDGKAVFASG
SPFAPVTYKGQKFYPGQGNNSYIFPGVALGVIAGAVSKIPEDIFLISAKALADLVTDDDL
NKGALYPPLETIQDCSFEIAVKVMEYAYDNGLATVRPKPKNMRTFIKAQMYDPSYKPAIP
PVYKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g1576.t30 | CDD | cd05312 | NAD_bind_1_malic_enz | 195 | 473 | 2.88105E-146 |
| 17 | g1576.t30 | Gene3D | G3DSA:1.20.1370.30 | - | 2 | 45 | 6.9E-234 |
| 14 | g1576.t30 | Gene3D | G3DSA:3.40.50.10380 | - | 46 | 451 | 6.9E-234 |
| 15 | g1576.t30 | Gene3D | G3DSA:3.40.50.720 | - | 193 | 379 | 6.9E-234 |
| 16 | g1576.t30 | Gene3D | G3DSA:3.30.2330.30 | - | 452 | 484 | 6.9E-234 |
| 3 | g1576.t30 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 1 | 484 | 7.2E-268 |
| 4 | g1576.t30 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 1 | 484 | 7.2E-268 |
| 18 | g1576.t30 | PIRSF | PIRSF000106 | ME | 1 | 480 | 2.0E-202 |
| 7 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 10 | 34 | 3.7E-77 |
| 9 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 70 | 99 | 3.7E-77 |
| 8 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 106 | 128 | 3.7E-77 |
| 6 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 166 | 184 | 3.7E-77 |
| 5 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 191 | 207 | 3.7E-77 |
| 10 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 222 | 238 | 3.7E-77 |
| 11 | g1576.t30 | PRINTS | PR00072 | Malic enzyme signature | 325 | 341 | 3.7E-77 |
| 1 | g1576.t30 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 4 | 185 | 2.3E-78 |
| 2 | g1576.t30 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 195 | 448 | 5.1E-98 |
| 22 | g1576.t30 | ProSitePatterns | PS00331 | Malic enzymes signature. | 191 | 207 | - |
| 23 | g1576.t30 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 35 | 5.0 |
| 20 | g1576.t30 | SMART | SM01274 | malic_2 | 4 | 185 | 4.5E-104 |
| 21 | g1576.t30 | SMART | SM00919 | Malic_M_2 | 195 | 448 | 1.9E-118 |
| 13 | g1576.t30 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 2 | 194 | 1.15E-85 |
| 12 | g1576.t30 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 195 | 482 | 3.35E-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 transcript has been annotated with K00027 (malate dehydrogenase (oxaloacetate-decarboxylating))
Pathway
- This transcript belongs to the following pathways
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.
