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 g3335 g3335.t31 isoform g3335.t31 24726455 24727292
chr_3 g3335 g3335.t31 exon g3335.t31.exon1 24726455 24727292
chr_3 g3335 g3335.t31 cds g3335.t31.CDS1 24726481 24727290
chr_3 g3335 g3335.t31 TTS g3335.t31 24727926 24727926
chr_3 g3335 g3335.t31 TSS g3335.t31 NA NA

Sequences

>g3335.t31 Gene=g3335 Length=838
GTTTAGGCGATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACA
CTGCCCTTGCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAA
ATAATAAAGATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAG
GACAAGCCTATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGAC
AAAATACTTTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACA
AATACCGTGACACTTATTGCACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTG
TTGCAGGACTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTC
TTTTCCTCGGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGA
TGACAGAAGGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATG
GACTTTTAGCAAAAGGACGACCAGAAGGGCAGTTAGGTGGTCACAAATGGTTTTATGCTA
AAGAGCATGAAGTTATGAAAGATTTTACTGAAATTGTAAAAGAAGTAAGGCCATCAATTT
TAATTGGTGCAAGTGCTGTTGGTGGTGCTTTTACACCTGAAATTTTGCAAATGATGGCAG
AATTCAATGAACGACCTATTATTTTTGCATTATCAAATCCAACAATTAAAGCTGAATATA
CTACAGAAGCAGCTTATACACATACAAAAGGAAAATGCATTTTTGCTTCAGGTTCACC

>g3335.t31 Gene=g3335 Length=270
MGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNKDLLEDPLYVGLRQPRVSGQAYDDFID
EFMEAVVKRYGQNTLIQFEDFGNHNAFRFLDKYRDTYCTFNDDIQGTASVAVAGLLASKR
VTGKKLSDNKILFLGAGEAAIGIADLCVKAMMTEGVSQDEARDKIWMVDIDGLLAKGRPE
GQLGGHKWFYAKEHEVMKDFTEIVKEVRPSILIGASAVGGAFTPEILQMMAEFNERPIIF
ALSNPTIKAEYTTEAAYTHTKGKCIFASGS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3335.t31 Gene3D G3DSA:3.40.50.10380 - 1 101 6.7E-52
13 g3335.t31 Gene3D G3DSA:3.40.50.720 - 102 270 5.0E-69
3 g3335.t31 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 270 3.3E-132
4 g3335.t31 PANTHER PTHR23406:SF80 GH17657P-RELATED 1 270 3.3E-132
14 g3335.t31 PIRSF PIRSF000106 ME 1 270 4.2E-117
6 g3335.t31 PRINTS PR00072 Malic enzyme signature 15 37 2.1E-50
8 g3335.t31 PRINTS PR00072 Malic enzyme signature 75 93 2.1E-50
9 g3335.t31 PRINTS PR00072 Malic enzyme signature 100 116 2.1E-50
5 g3335.t31 PRINTS PR00072 Malic enzyme signature 131 147 2.1E-50
7 g3335.t31 PRINTS PR00072 Malic enzyme signature 234 250 2.1E-50
1 g3335.t31 Pfam PF00390 Malic enzyme, N-terminal domain 1 94 4.4E-40
2 g3335.t31 Pfam PF03949 Malic enzyme, NAD binding domain 104 270 2.4E-60
15 g3335.t31 ProSitePatterns PS00331 Malic enzymes signature. 100 116 -
16 g3335.t31 SMART SM01274 malic_2 1 94 3.3E-22
17 g3335.t31 SMART SM00919 Malic_M_2 104 270 1.7E-38
11 g3335.t31 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 103 1.01E-45
10 g3335.t31 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 104 269 2.33E-58

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.

Raw TPM values