General information for g1576.t21
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.t21 | isoform | g1576.t21 | 11964183 | 11969410 |
| chr_3 | g1576 | g1576.t21 | exon | g1576.t21.exon1 | 11964183 | 11964464 |
| chr_3 | g1576 | g1576.t21 | cds | g1576.t21.CDS1 | 11964219 | 11964464 |
| chr_3 | g1576 | g1576.t21 | exon | g1576.t21.exon2 | 11967614 | 11967992 |
| chr_3 | g1576 | g1576.t21 | cds | g1576.t21.CDS2 | 11967614 | 11967992 |
| chr_3 | g1576 | g1576.t21 | exon | g1576.t21.exon3 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t21 | cds | g1576.t21.CDS3 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t21 | exon | g1576.t21.exon4 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t21 | cds | g1576.t21.CDS4 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t21 | exon | g1576.t21.exon5 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t21 | cds | g1576.t21.CDS5 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t21 | TTS | g1576.t21 | 11969767 | 11969767 |
| chr_3 | g1576 | g1576.t21 | TSS | g1576.t21 | NA | NA |
Sequences
>g1576.t21 Gene=g1576 Length=1887
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGAC
GGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGA
AAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACA
CTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGT
CAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCT
GTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCT
TTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGT
ACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTA
TCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTA
TGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGG
CTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATCAT
AAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGATATT
TTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAATT
ATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAACA
AGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGTTTTT
GCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATTCTATCCAGGACAA
GGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGTTTCC
AAAATTCCAGAAGATATCTTTTTGATTTCCGCTAAAGCTCTTGCTGATTTAGTTACTGAT
GATGATTTAAATAAAGGAGCTTTATATCCACCATTAGAAACAATTCAAGATTGTTCATTT
GAAATTGCTGTTAAAGTTATGGAATATGCTTATGATAATGGATTGGCTACGGTTCGTCCT
AAACCAAAAAATATGCGTACTTTCATCAAGGCCCAAATGTATGACCCATCTTACAAACCA
GCCATCCCACCCGTATATAAATTATAA
>g1576.t21 Gene=g1576 Length=616
MSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKITILSPFGLNTKSNIMSESRDRLGQWP
VESEAELTGQGLQRLKNNHYNKGLAFTHEERQILGIHGLLAPGIKSIDEQIKHAHILLER
CATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLY
ISIYDKGHIYDVIKNWPEFDVRAIVVTDGERILGLGDLGANGMGIPVGKLALYTALAGIK
PHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIEEFMQAAVRRFGQSCLIQF
EDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLRVTKTRLSDNKILFQGSGE
AALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPKGGLNHHKSKFAHAHHPVD
TLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFNERPIIFALSNPTSKAECTAEDAYI
HSDGKAVFASGSPFAPVTYKGQKFYPGQGNNSYIFPGVALGVIAGAVSKIPEDIFLISAK
ALADLVTDDDLNKGALYPPLETIQDCSFEIAVKVMEYAYDNGLATVRPKPKNMRTFIKAQ
MYDPSYKPAIPPVYKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g1576.t21 | CDD | cd05312 | NAD_bind_1_malic_enz | 326 | 604 | 1.12724E-145 |
| 17 | g1576.t21 | Gene3D | G3DSA:1.20.1370.30 | - | 70 | 176 | 2.2E-255 |
| 14 | g1576.t21 | Gene3D | G3DSA:3.40.50.10380 | - | 177 | 582 | 2.2E-255 |
| 15 | g1576.t21 | Gene3D | G3DSA:3.40.50.720 | - | 324 | 510 | 2.2E-255 |
| 16 | g1576.t21 | Gene3D | G3DSA:3.30.2330.30 | - | 583 | 615 | 2.2E-255 |
| 23 | g1576.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 3 | g1576.t21 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 40 | 615 | 2.0E-297 |
| 4 | g1576.t21 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 40 | 615 | 2.0E-297 |
| 18 | g1576.t21 | PIRSF | PIRSF000106 | ME | 18 | 611 | 1.3E-224 |
| 10 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 141 | 165 | 1.3E-76 |
| 7 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 201 | 230 | 1.3E-76 |
| 11 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 237 | 259 | 1.3E-76 |
| 5 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 297 | 315 | 1.3E-76 |
| 6 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 322 | 338 | 1.3E-76 |
| 9 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 353 | 369 | 1.3E-76 |
| 8 | g1576.t21 | PRINTS | PR00072 | Malic enzyme signature | 456 | 472 | 1.3E-76 |
| 1 | g1576.t21 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 135 | 316 | 3.7E-78 |
| 2 | g1576.t21 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 326 | 579 | 9.1E-98 |
| 22 | g1576.t21 | ProSitePatterns | PS00331 | Malic enzymes signature. | 322 | 338 | - |
| 20 | g1576.t21 | SMART | SM01274 | malic_2 | 135 | 316 | 4.5E-104 |
| 21 | g1576.t21 | SMART | SM00919 | Malic_M_2 | 326 | 579 | 1.9E-118 |
| 13 | g1576.t21 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 65 | 325 | 2.81E-106 |
| 12 | g1576.t21 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 326 | 612 | 6.3E-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 K00029 (malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+))
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.
