Gene loci information

Transcript annotation

  • This transcript has been annotated as NADP-dependent malic enzyme.

Parent gene

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.t26 TSS g1576.t26 11964272 11964272
chr_3 g1576 g1576.t26 isoform g1576.t26 11964749 11969410
chr_3 g1576 g1576.t26 exon g1576.t26.exon1 11964749 11964772
chr_3 g1576 g1576.t26 exon g1576.t26.exon2 11967614 11967992
chr_3 g1576 g1576.t26 cds g1576.t26.CDS1 11967761 11967992
chr_3 g1576 g1576.t26 exon g1576.t26.exon3 11968063 11968962
chr_3 g1576 g1576.t26 cds g1576.t26.CDS2 11968063 11968962
chr_3 g1576 g1576.t26 exon g1576.t26.exon4 11969024 11969118
chr_3 g1576 g1576.t26 cds g1576.t26.CDS3 11969024 11969118
chr_3 g1576 g1576.t26 exon g1576.t26.exon5 11969180 11969410
chr_3 g1576 g1576.t26 cds g1576.t26.CDS4 11969180 11969410
chr_3 g1576 g1576.t26 TTS g1576.t26 11969767 11969767

Sequences

>g1576.t26 Gene=g1576 Length=1629
TGAAAGTATTTTAAAATTGTGAAGGGCCTTGCTTTCACTCATGAAGAACGACAAATTTTG
GGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGATGAACAAATTAAGCATGCC
CATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATATATTTATTTGATGGGACTT
CAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCCGATATTGCAAACATGATG
CCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAGTATTCGATGATTTACACT
AATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCATATTTACGATGTCATCAAA
AATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGACGGAGAAAGAATTTTAGGT
TTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGAAAATTGGCACTCTACACT
GCACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACACTCGATGTTGGCACAAAT
ACTCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGA
CAAGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAA
AGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAA
TATCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTT
GCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTATCAGATAATAAAATTTTG
TTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTATGTGTCATGGCAATGATT
AAAGAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGGCTTGTAGATAGTAAAGGA
TTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATCATAAGAGTAAATTTGCTCAC
GCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGATATTTTGAAACCAACAGTCTTG
ATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAATTATCAAAGCAATGGCTAGT
TTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAACAAGCAAGGCTGAATGTACT
GCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGTTTTTGCTTCTGGGTCACCTTTT
GCGCCGGTCACTTACAAAGGACAAAAATTCTATCCAGGACAAGGCAATAATTCTTATATT
TTCCCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGTTTCCAAAATTCCAGAAGATATC
TTTTTGATTTCCGCTAAAGCTCTTGCTGATTTAGTTACTGATGATGATTTAAATAAAGGA
GCTTTATATCCACCATTAGAAACAATTCAAGATTGTTCATTTGAAATTGCTGTTAAAGTT
ATGGAATATGCTTATGATAATGGATTGGCTACGGTTCGTCCTAAACCAAAAAATATGCGT
ACTTTCATCAAGGCCCAAATGTATGACCCATCTTACAAACCAGCCATCCCACCCGTATAT
AAATTATAA

>g1576.t26 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.t26 CDD cd05312 NAD_bind_1_malic_enz 195 473 2.88105E-146
17 g1576.t26 Gene3D G3DSA:1.20.1370.30 - 2 45 6.9E-234
14 g1576.t26 Gene3D G3DSA:3.40.50.10380 - 46 451 6.9E-234
15 g1576.t26 Gene3D G3DSA:3.40.50.720 - 193 379 6.9E-234
16 g1576.t26 Gene3D G3DSA:3.30.2330.30 - 452 484 6.9E-234
3 g1576.t26 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 484 7.2E-268
4 g1576.t26 PANTHER PTHR23406:SF80 GH17657P-RELATED 1 484 7.2E-268
18 g1576.t26 PIRSF PIRSF000106 ME 1 480 1.9E-202
7 g1576.t26 PRINTS PR00072 Malic enzyme signature 10 34 3.7E-77
9 g1576.t26 PRINTS PR00072 Malic enzyme signature 70 99 3.7E-77
8 g1576.t26 PRINTS PR00072 Malic enzyme signature 106 128 3.7E-77
6 g1576.t26 PRINTS PR00072 Malic enzyme signature 166 184 3.7E-77
5 g1576.t26 PRINTS PR00072 Malic enzyme signature 191 207 3.7E-77
10 g1576.t26 PRINTS PR00072 Malic enzyme signature 222 238 3.7E-77
11 g1576.t26 PRINTS PR00072 Malic enzyme signature 325 341 3.7E-77
1 g1576.t26 Pfam PF00390 Malic enzyme, N-terminal domain 4 185 2.3E-78
2 g1576.t26 Pfam PF03949 Malic enzyme, NAD binding domain 195 448 5.1E-98
22 g1576.t26 ProSitePatterns PS00331 Malic enzymes signature. 191 207 -
23 g1576.t26 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 35 5.0
20 g1576.t26 SMART SM01274 malic_2 4 185 4.5E-104
21 g1576.t26 SMART SM00919 Malic_M_2 195 448 1.9E-118
13 g1576.t26 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 2 194 1.15E-85
12 g1576.t26 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

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.

Raw TPM values