General information for g1576.t25
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.t25 | isoform | g1576.t25 | 11964183 | 11969918 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon1 | 11964183 | 11964464 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS1 | 11964219 | 11964464 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon2 | 11967614 | 11967728 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS2 | 11967614 | 11967728 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon3 | 11967837 | 11967992 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS3 | 11967837 | 11967992 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon4 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS4 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon5 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS5 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t25 | exon | g1576.t25.exon6 | 11969180 | 11969918 |
| chr_3 | g1576 | g1576.t25 | cds | g1576.t25.CDS6 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t25 | TSS | g1576.t25 | NA | NA |
| chr_3 | g1576 | g1576.t25 | TTS | g1576.t25 | NA | NA |
Sequences
>g1576.t25 Gene=g1576 Length=2287
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATTTTATACACCAACTGTTGGTCTT
GCATGTCAAAAGTATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTAT
GATAAGGGTCATATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATT
GTTGTTACTGACGGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGT
ATTCCAGTTGGAAAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGT
TTACCAATCACACTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTAT
ATAGGATTGCGTCAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTT
ATGCAAGCTGCTGTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGC
AATTCAAACGCTTTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGAC
GATATTCAGGGTACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACT
AAAACTCGTTTATCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGA
ATTGCTGAATTATGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGACGCTCGC
TCACGTGTATGGCTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGA
CTCAACCATCATAAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAA
GCTGTAGATATTTTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTT
ACACCCGAAATTATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTG
TCAAATCCAACAAGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGA
AAAGCTGTTTTTGCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATTC
TATCCAGGACAAGGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGTCATTGCT
GGTGCCGTTTCCAAAATTCCAGAAGATATCTTTTTGATTTCCGCTAAAGCTCTTGCTGAT
TTAGTTACTGATGATGATTTAAATAAAGGAGCTTTATATCCACCATTAGAAACAATTCAA
GATTGTTCATTTGAAATTGCTGTTAAAGTTATGGAATATGCTTATGATAATGGATTGGCT
ACGGTTCGTCCTAAACCAAAAAATATGCGTACTTTCATCAAGGCCCAAATGTATGACCCA
TCTTACAAACCAGCCATCCCACCCGTATATAAATTATAAAACAATTTCATTTTTATCAAT
TCTCATTTTCCAATTCTATCGTTCTATTGTTTTATGTAATTTATATCTCATGACAAGCAA
TTTCAAAGGAAAAAAGTATATTTTTTATGTTTTTGCGTGTAAATCATGCAAACTATTCGG
AAAAATTTAGTAAAAAGTCTTTTAATTATTTATTAATGCAATAAATTAATTTCACTTGCC
AACCTTCTTTGAATTTTCGCATTTGTCGACTCATTTGTAATATCTGGAACAAAATTACAA
ATGACTTTACATATGTGTAGAATAATCGATATCTTATTTAAAGTTATAAAAATGGTTTAC
AATAAAAATTCATCCATGCAAAGTATTTATAAAAATCAATAATCAATGTTTTATTTAAAT
CTCTTTATTAGTTTTTTCTCATTGTTAGTTTATACTACAAACAAATATGTTTTTTGTTCT
CTTATCAAAATAATCAATAGCATTATACAAACAATAGATAAAAAATAATTATTAAATGTT
TAAAGTT
>g1576.t25 Gene=g1576 Length=580
MSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKITILSPFGLNTKSNIMSESRDRLGQWP
VESEAELTGQGLQRLKNNHYNKGLAFTHEERQILGIHGLLAPGIKSIDEQIKHAHILLER
FYTPTVGLACQKYSMIYTNPKGLYISIYDKGHIYDVIKNWPEFDVRAIVVTDGERILGLG
DLGANGMGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQE
YDDFIEEFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAG
LLASLRVTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLI
VKDRPKGGLNHHKSKFAHAHHPVDTLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFN
ERPIIFALSNPTSKAECTAEDAYIHSDGKAVFASGSPFAPVTYKGQKFYPGQGNNSYIFP
GVALGVIAGAVSKIPEDIFLISAKALADLVTDDDLNKGALYPPLETIQDCSFEIAVKVME
YAYDNGLATVRPKPKNMRTFIKAQMYDPSYKPAIPPVYKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g1576.t25 | CDD | cd05312 | NAD_bind_1_malic_enz | 290 | 568 | 6.97637E-146 |
| 19 | g1576.t25 | Gene3D | G3DSA:1.20.1370.30 | - | 69 | 116 | 1.8E-8 |
| 20 | g1576.t25 | Gene3D | G3DSA:1.20.1370.30 | - | 117 | 140 | 2.0E-222 |
| 16 | g1576.t25 | Gene3D | G3DSA:3.40.50.10380 | - | 141 | 546 | 2.0E-222 |
| 17 | g1576.t25 | Gene3D | G3DSA:3.40.50.720 | - | 288 | 474 | 2.0E-222 |
| 18 | g1576.t25 | Gene3D | G3DSA:3.30.2330.30 | - | 547 | 579 | 2.0E-222 |
| 27 | g1576.t25 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 4 | g1576.t25 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 41 | 121 | 2.4E-270 |
| 6 | g1576.t25 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 41 | 121 | 2.4E-270 |
| 3 | g1576.t25 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 122 | 579 | 2.4E-270 |
| 5 | g1576.t25 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 122 | 579 | 2.4E-270 |
| 22 | g1576.t25 | PIRSF | PIRSF000106 | ME | 39 | 121 | 9.5E-12 |
| 21 | g1576.t25 | PIRSF | PIRSF000106 | ME | 111 | 575 | 9.3E-195 |
| 13 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 105 | 129 | 3.1E-66 |
| 11 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 165 | 194 | 3.1E-66 |
| 12 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 201 | 223 | 3.1E-66 |
| 8 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 261 | 279 | 3.1E-66 |
| 9 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 286 | 302 | 3.1E-66 |
| 10 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 317 | 333 | 3.1E-66 |
| 7 | g1576.t25 | PRINTS | PR00072 | Malic enzyme signature | 420 | 436 | 3.1E-66 |
| 1 | g1576.t25 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 115 | 280 | 3.8E-71 |
| 2 | g1576.t25 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 290 | 543 | 7.9E-98 |
| 26 | g1576.t25 | ProSitePatterns | PS00331 | Malic enzymes signature. | 286 | 302 | - |
| 24 | g1576.t25 | SMART | SM01274 | malic_2 | 107 | 280 | 9.9E-88 |
| 25 | g1576.t25 | SMART | SM00919 | Malic_M_2 | 290 | 543 | 1.9E-118 |
| 15 | g1576.t25 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 65 | 289 | 1.29E-89 |
| 14 | g1576.t25 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 290 | 576 | 5.51E-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.
