General information for g1576.t1
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.t1 | TSS | g1576.t1 | 11963117 | 11963117 |
| chr_3 | g1576 | g1576.t1 | isoform | g1576.t1 | 11963299 | 11969410 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon1 | 11963299 | 11963336 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS1 | 11963299 | 11963336 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon2 | 11964182 | 11964464 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS2 | 11964182 | 11964464 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon3 | 11967614 | 11967992 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS3 | 11967614 | 11967992 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon4 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS4 | 11968063 | 11968962 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon5 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS5 | 11969024 | 11969118 |
| chr_3 | g1576 | g1576.t1 | exon | g1576.t1.exon6 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t1 | cds | g1576.t1.CDS6 | 11969180 | 11969410 |
| chr_3 | g1576 | g1576.t1 | TTS | g1576.t1 | 11969767 | 11969767 |
Sequences
>g1576.t1 Gene=g1576 Length=1926
ATGTCTTTAATCAATGGAAAATTGCAGAATGGTCATGCAGTCGCAACGGAAAATGGAAAT
GAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAATATAAAACGCAAACGAATGAA
AATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACATCGTTCGTAGAAAAAATTACA
ATTCTTTCACCATTTGGATTGAATACTAAATCAAACATTATGAGTGAAAGCCGAGATAGA
CTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACAGGACAAGGATTGCAACGTTTG
AAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCATGAAGAACGACAAATTTTGGGA
ATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGATGAACAAATTAAGCATGCCCAT
ATTTTATTGGAACGATGTGCGACTGATTTAGACAAATATATTTATTTGATGGGACTTCAA
GACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCCGATATTGCAAACATGATGCCT
TTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAGTATTCGATGATTTACACTAAT
CCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCATATTTACGATGTCATCAAAAAT
TGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGACGGAGAAAGAATTTTAGGTTTG
GGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGAAAATTGGCACTCTACACTGCA
CTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACACTCGATGTTGGCACAAATACT
CAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGACAA
GAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAAAGT
TGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAATAT
CGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTTGCT
GGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTATCAGATAATAAAATTTTGTTC
CAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTATGTGTCATGGCAATGATTAAA
GAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGGCTTGTAGATAGTAAAGGATTG
ATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATCATAAGAGTAAATTTGCTCACGCT
CATCACCCAGTTGATACATTAGCAGAAGCTGTAGATATTTTGAAACCAACAGTCTTGATT
GGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAATTATCAAAGCAATGGCTAGTTTT
AATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAACAAGCAAGGCTGAATGTACTGCT
GAGGATGCATATATTCATAGCGATGGAAAAGCTGTTTTTGCTTCTGGGTCACCTTTTGCG
CCGGTCACTTACAAAGGACAAAAATTCTATCCAGGACAAGGCAATAATTCTTATATTTTC
CCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGTTTCCAAAATTCCAGAAGATATCTTT
TTGATTTCCGCTAAAGCTCTTGCTGATTTAGTTACTGATGATGATTTAAATAAAGGAGCT
TTATATCCACCATTAGAAACAATTCAAGATTGTTCATTTGAAATTGCTGTTAAAGTTATG
GAATATGCTTATGATAATGGATTGGCTACGGTTCGTCCTAAACCAAAAAATATGCGTACT
TTCATCAAGGCCCAAATGTATGACCCATCTTACAAACCAGCCATCCCACCCGTATATAAA
TTATAA
>g1576.t1 Gene=g1576 Length=641
MSLINGKLQNGHAVATENGNENHDVMSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKIT
ILSPFGLNTKSNIMSESRDRLGQWPVESEAELTGQGLQRLKNNHYNKGLAFTHEERQILG
IHGLLAPGIKSIDEQIKHAHILLERCATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMP
LVYTPTVGLACQKYSMIYTNPKGLYISIYDKGHIYDVIKNWPEFDVRAIVVTDGERILGL
GDLGANGMGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQ
EYDDFIEEFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVA
GLLASLRVTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGL
IVKDRPKGGLNHHKSKFAHAHHPVDTLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASF
NERPIIFALSNPTSKAECTAEDAYIHSDGKAVFASGSPFAPVTYKGQKFYPGQGNNSYIF
PGVALGVIAGAVSKIPEDIFLISAKALADLVTDDDLNKGALYPPLETIQDCSFEIAVKVM
EYAYDNGLATVRPKPKNMRTFIKAQMYDPSYKPAIPPVYKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g1576.t1 | CDD | cd05312 | NAD_bind_1_malic_enz | 351 | 629 | 2.00431E-145 |
| 17 | g1576.t1 | Gene3D | G3DSA:1.20.1370.30 | - | 95 | 201 | 2.5E-255 |
| 14 | g1576.t1 | Gene3D | G3DSA:3.40.50.10380 | - | 202 | 607 | 2.5E-255 |
| 15 | g1576.t1 | Gene3D | G3DSA:3.40.50.720 | - | 349 | 535 | 2.5E-255 |
| 16 | g1576.t1 | Gene3D | G3DSA:3.30.2330.30 | - | 608 | 640 | 2.5E-255 |
| 23 | g1576.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 24 | g1576.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 3 | g1576.t1 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 61 | 640 | 1.6E-297 |
| 4 | g1576.t1 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 61 | 640 | 1.6E-297 |
| 18 | g1576.t1 | PIRSF | PIRSF000106 | ME | 37 | 636 | 1.4E-224 |
| 6 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 166 | 190 | 1.6E-76 |
| 8 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 226 | 255 | 1.6E-76 |
| 7 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 262 | 284 | 1.6E-76 |
| 5 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 322 | 340 | 1.6E-76 |
| 9 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 347 | 363 | 1.6E-76 |
| 10 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 378 | 394 | 1.6E-76 |
| 11 | g1576.t1 | PRINTS | PR00072 | Malic enzyme signature | 481 | 497 | 1.6E-76 |
| 1 | g1576.t1 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 160 | 341 | 4.0E-78 |
| 2 | g1576.t1 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 351 | 604 | 9.9E-98 |
| 22 | g1576.t1 | ProSitePatterns | PS00331 | Malic enzymes signature. | 347 | 363 | - |
| 20 | g1576.t1 | SMART | SM01274 | malic_2 | 160 | 341 | 4.5E-104 |
| 21 | g1576.t1 | SMART | SM00919 | Malic_M_2 | 351 | 604 | 1.9E-118 |
| 13 | g1576.t1 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 90 | 350 | 3.09E-106 |
| 12 | g1576.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 351 | 637 | 6.7E-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.
