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.t9 TSS g3335.t9 24723961 24723961
chr_3 g3335 g3335.t9 isoform g3335.t9 24724136 24726697
chr_3 g3335 g3335.t9 exon g3335.t9.exon1 24724136 24724155
chr_3 g3335 g3335.t9 cds g3335.t9.CDS1 24724136 24724155
chr_3 g3335 g3335.t9 exon g3335.t9.exon2 24725121 24725263
chr_3 g3335 g3335.t9 cds g3335.t9.CDS2 24725121 24725263
chr_3 g3335 g3335.t9 exon g3335.t9.exon3 24725319 24725466
chr_3 g3335 g3335.t9 cds g3335.t9.CDS3 24725319 24725466
chr_3 g3335 g3335.t9 exon g3335.t9.exon4 24725537 24725582
chr_3 g3335 g3335.t9 cds g3335.t9.CDS4 24725537 24725582
chr_3 g3335 g3335.t9 exon g3335.t9.exon5 24726089 24726191
chr_3 g3335 g3335.t9 cds g3335.t9.CDS5 24726089 24726175
chr_3 g3335 g3335.t9 exon g3335.t9.exon6 24726323 24726697
chr_3 g3335 g3335.t9 TTS g3335.t9 NA NA

Sequences

>g3335.t9 Gene=g3335 Length=835
ATGTCTCTTAGACTTTTAATTCGTAATGGGTCGTTTGCGCGATCATATCCAAATCTTGCA
ATATGTGGTACGACTTCTTCACCGAAAAAGTCAACACCCAATCAGCAAATTCGCTTGCAT
CATGAAGTTACAGGCGACATAATTGTTCCGTCTATGGTTATGGGAATTGATCATTTAAGA
GATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCATT
CATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAATT
TCAATTATGAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACTTACAGGAT
CGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCATC
ATTTATACACCAACTGTAATTTAAACCCTTTATTATTTGTGCTTAATTTATCGAAGACCA
AGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAAAGAACTGG
CCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAGGTTTAGGC
GATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACACTGCCCTT
GCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAAATAATAAA
GATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAGGACAAGCC
TATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGACAAA

>g3335.t9 Gene=g3335 Length=147
MSLRLLIRNGSFARSYPNLAICGTTSSPKKSTPNQQIRLHHEVTGDIIVPSMVMGIDHLR
DPRLNKGLAFSLQERQVLGIHGLQPARIKTQEEQLELCKISIMRYQEDLNKYQYLVDLQD
RNERLFFRLVSENVEMMMPIIYTPTVI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3335.t9 Coils Coil Coil 88 108 -
5 g3335.t9 Gene3D G3DSA:1.20.1370.30 - 54 147 9.3E-33
2 g3335.t9 PANTHER PTHR23406 MALIC ENZYME-RELATED 50 146 6.0E-31
3 g3335.t9 PANTHER PTHR23406:SF34 MALIC ENZYME-RELATED 50 146 6.0E-31
1 g3335.t9 Pfam PF00390 Malic enzyme, N-terminal domain 119 146 3.4E-5
4 g3335.t9 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 38 146 4.24E-28

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: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