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.t32 isoform g1576.t32 11967967 11968665
chr_3 g1576 g1576.t32 exon g1576.t32.exon1 11967967 11967996
chr_3 g1576 g1576.t32 exon g1576.t32.exon2 11968063 11968665
chr_3 g1576 g1576.t32 cds g1576.t32.CDS1 11968104 11968664
chr_3 g1576 g1576.t32 TSS g1576.t32 NA NA
chr_3 g1576 g1576.t32 TTS g1576.t32 NA NA

Sequences

>g1576.t32 Gene=g1576 Length=633
TGTAAGAGCTATTGTTGTTACTGACGGTAAGAGAAAGAATTTTAGGTTTGGGCGATCTTG
GAGCTAACGGAATGGGTATTCCAGTTGGAAAATTGGCACTCTACACTGCACTTGCTGGAA
TCAAACCTCATCAATGTTTACCAATCACACTCGATGTTGGCACAAATACTCAATCAATTC
TTGATGATCCTCTTTATATAGGATTGCGTCAAAAACGTGTAACTGGACAAGAATATGATG
ACTTTATTGAGGAATTTATGCAAGCTGCTGTTCGACGCTTCGGCCAAAGTTGTCTCATTC
AATTTGAGGACTTTGGCAATTCAAACGCTTTTAGACTTATTGAAAAATATCGCGAAGATT
ATTGCACTTTTAACGACGATATTCAGGGTACAGCTGCTGTAGCAGTTGCTGGCTTGCTTG
CTTCACTTCGAGTCACTAAAACTCGTTTATCAGATAATAAAATTTTGTTCCAAGGTAGCG
GCGAAGCTGCACTCGGAATTGCTGAATTATGTGTCATGGCAATGATTAAAGAAGGTGTTT
GTGAAGAAGACGCTCGCTCACGTGTATGGCTTGTAGATAGTAAAGGATTGATTGTCAAAG
ATCGTCCAAAAGGTGGACTCAACCATCATAAGA

>g1576.t32 Gene=g1576 Length=187
MGIPVGKLALYTALAGIKPHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIE
EFMQAAVRRFGQSCLIQFEDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLR
VTKTRLSDNKILFQGSGEAALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPK
GGLNHHK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1576.t32 Gene3D G3DSA:3.40.50.10380 - 1 101 3.6E-51
15 g1576.t32 Gene3D G3DSA:3.40.50.720 - 102 187 2.1E-31
3 g1576.t32 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 187 3.7E-101
4 g1576.t32 PANTHER PTHR23406:SF80 GH17657P-RELATED 1 187 3.7E-101
6 g1576.t32 PRINTS PR00072 Malic enzyme signature 15 37 7.1E-39
7 g1576.t32 PRINTS PR00072 Malic enzyme signature 75 93 7.1E-39
8 g1576.t32 PRINTS PR00072 Malic enzyme signature 100 116 7.1E-39
5 g1576.t32 PRINTS PR00072 Malic enzyme signature 131 147 7.1E-39
1 g1576.t32 Pfam PF00390 Malic enzyme, N-terminal domain 1 94 1.1E-38
2 g1576.t32 Pfam PF03949 Malic enzyme, NAD binding domain 104 180 3.7E-26
13 g1576.t32 ProSitePatterns PS00331 Malic enzymes signature. 100 116 -
11 g1576.t32 SMART SM01274 malic_2 1 94 4.3E-18
12 g1576.t32 SMART SM00919 Malic_M_2 104 187 8.4E-4
10 g1576.t32 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 103 7.91E-45
9 g1576.t32 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 104 180 6.13E-24

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