Gene loci information

Transcript annotation

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

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.t18 isoform g3335.t18 24725121 24726455
chr_3 g3335 g3335.t18 exon g3335.t18.exon1 24725121 24725263
chr_3 g3335 g3335.t18 cds g3335.t18.CDS1 24725254 24725263
chr_3 g3335 g3335.t18 exon g3335.t18.exon2 24725319 24725466
chr_3 g3335 g3335.t18 cds g3335.t18.CDS2 24725319 24725466
chr_3 g3335 g3335.t18 exon g3335.t18.exon3 24725537 24725582
chr_3 g3335 g3335.t18 cds g3335.t18.CDS3 24725537 24725582
chr_3 g3335 g3335.t18 exon g3335.t18.exon4 24726089 24726166
chr_3 g3335 g3335.t18 cds g3335.t18.CDS4 24726089 24726166
chr_3 g3335 g3335.t18 exon g3335.t18.exon5 24726241 24726265
chr_3 g3335 g3335.t18 cds g3335.t18.CDS5 24726241 24726265
chr_3 g3335 g3335.t18 exon g3335.t18.exon6 24726323 24726455
chr_3 g3335 g3335.t18 cds g3335.t18.CDS6 24726323 24726453
chr_3 g3335 g3335.t18 TSS g3335.t18 NA NA
chr_3 g3335 g3335.t18 TTS g3335.t18 NA NA

Sequences

>g3335.t18 Gene=g3335 Length=573
TCGTAATGGGTCGTTTGCGCGATCATATCCAAATCTTGCAATATGTGGTACGACTTCTTC
ACCGAAAAAGTCAACACCCAATCAGCAAATTCGCTTGCATCATGAAGTTACAGGCGACAT
AATTGTTCCGTCTATGGTTATGGGAATTGATCATTTAAGAGATCCGCGTTTAAATAAAGG
TCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCATTCATGGTCTTCAACCAGCACG
AATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAATTTCAATTATGAGATATCAAGA
AGATTTAAATAAATATCAATATCTTGTAGACTTACAGGATCGAAATGAACGTCTATTTTT
TCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCATCATTTATACACCAACTGTTGG
TTCAGCTTGCCAAAAATTCGGCTTAATTTATCGAAGACCAAGAGGTCTTTTCGTAACATT
CAATGACAAAGGACACGTGTTTGATGTATTAAAGAACTGGCCAGAGCCAGATGTAAGAGC
TATCGTTGTTACCGATGGTGAACGTATTTTAGG

>g3335.t18 Gene=g3335 Length=146
MVMGIDHLRDPRLNKGLAFSLQERQVLGIHGLQPARIKTQEEQLELCKISIMRYQEDLNK
YQYLVDLQDRNERLFFRLVSENVEMMMPIIYTPTVGSACQKFGLIYRRPRGLFVTFNDKG
HVFDVLKNWPEPDVRAIVVTDGERIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3335.t18 Coils Coil Coil 37 57 -
9 g3335.t18 Gene3D G3DSA:1.20.1370.30 - 4 109 2.2E-66
8 g3335.t18 Gene3D G3DSA:3.40.50.10380 - 110 146 2.2E-66
2 g3335.t18 PANTHER PTHR23406 MALIC ENZYME-RELATED 3 146 1.9E-59
3 g3335.t18 PANTHER PTHR23406:SF80 GH17657P-RELATED 3 146 1.9E-59
4 g3335.t18 PRINTS PR00072 Malic enzyme signature 74 98 3.2E-16
5 g3335.t18 PRINTS PR00072 Malic enzyme signature 134 146 3.2E-16
1 g3335.t18 Pfam PF00390 Malic enzyme, N-terminal domain 68 146 2.1E-26
7 g3335.t18 SMART SM01274 malic_2 68 146 1.4E-7
6 g3335.t18 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 3 146 7.19E-48

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: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