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.t33 isoform g1576.t33 11968062 11968948
chr_3 g1576 g1576.t33 exon g1576.t33.exon1 11968062 11968948
chr_3 g1576 g1576.t33 cds g1576.t33.CDS1 11968104 11968946
chr_3 g1576 g1576.t33 TTS g1576.t33 11969767 11969767
chr_3 g1576 g1576.t33 TSS g1576.t33 NA NA

Sequences

>g1576.t33 Gene=g1576 Length=887
GGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGA
AAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACA
CTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGT
CAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCT
GTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCT
TTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGT
ACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTA
TCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTA
TGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGG
CTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATCAT
AAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGATATT
TTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAATT
ATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAACA
AGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGTTTTT
GCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATT

>g1576.t33 Gene=g1576 Length=281
MGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIE
EFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLR
VTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPK
GGLNHHKSKFAHAHHPVDTLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFNERPIIF
ALSNPTSKAECTAEDAYIHSDGKAVFASGSPFAPVTYKGQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1576.t33 Gene3D G3DSA:3.40.50.10380 - 1 101 9.3E-51
13 g1576.t33 Gene3D G3DSA:3.40.50.720 - 102 281 4.4E-78
3 g1576.t33 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 280 2.4E-154
4 g1576.t33 PANTHER PTHR23406:SF80 GH17657P-RELATED 1 280 2.4E-154
14 g1576.t33 PIRSF PIRSF000106 ME 1 281 7.9E-123
6 g1576.t33 PRINTS PR00072 Malic enzyme signature 15 37 5.6E-49
8 g1576.t33 PRINTS PR00072 Malic enzyme signature 75 93 5.6E-49
9 g1576.t33 PRINTS PR00072 Malic enzyme signature 100 116 5.6E-49
5 g1576.t33 PRINTS PR00072 Malic enzyme signature 131 147 5.6E-49
7 g1576.t33 PRINTS PR00072 Malic enzyme signature 234 250 5.6E-49
1 g1576.t33 Pfam PF00390 Malic enzyme, N-terminal domain 1 94 2.7E-38
2 g1576.t33 Pfam PF03949 Malic enzyme, NAD binding domain 104 280 2.2E-67
15 g1576.t33 ProSitePatterns PS00331 Malic enzymes signature. 100 116 -
16 g1576.t33 SMART SM01274 malic_2 1 94 4.3E-18
17 g1576.t33 SMART SM00919 Malic_M_2 104 281 1.4E-53
11 g1576.t33 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 103 2.09E-44
10 g1576.t33 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 104 280 4.92E-65

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed