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.t7 TSS g3335.t7 24723961 24723961
chr_3 g3335 g3335.t7 isoform g3335.t7 24724136 24726697
chr_3 g3335 g3335.t7 exon g3335.t7.exon1 24724136 24724155
chr_3 g3335 g3335.t7 cds g3335.t7.CDS1 24724136 24724155
chr_3 g3335 g3335.t7 exon g3335.t7.exon2 24725121 24725263
chr_3 g3335 g3335.t7 cds g3335.t7.CDS2 24725121 24725263
chr_3 g3335 g3335.t7 exon g3335.t7.exon3 24725319 24725466
chr_3 g3335 g3335.t7 cds g3335.t7.CDS3 24725319 24725466
chr_3 g3335 g3335.t7 exon g3335.t7.exon4 24725537 24725582
chr_3 g3335 g3335.t7 cds g3335.t7.CDS4 24725537 24725582
chr_3 g3335 g3335.t7 exon g3335.t7.exon5 24726089 24726166
chr_3 g3335 g3335.t7 cds g3335.t7.CDS5 24726089 24726166
chr_3 g3335 g3335.t7 exon g3335.t7.exon6 24726241 24726265
chr_3 g3335 g3335.t7 cds g3335.t7.CDS6 24726241 24726265
chr_3 g3335 g3335.t7 exon g3335.t7.exon7 24726323 24726697
chr_3 g3335 g3335.t7 cds g3335.t7.CDS7 24726323 24726696
chr_3 g3335 g3335.t7 TTS g3335.t7 NA NA

Sequences

>g3335.t7 Gene=g3335 Length=835
ATGTCTCTTAGACTTTTAATTCGTAATGGGTCGTTTGCGCGATCATATCCAAATCTTGCA
ATATGTGGTACGACTTCTTCACCGAAAAAGTCAACACCCAATCAGCAAATTCGCTTGCAT
CATGAAGTTACAGGCGACATAATTGTTCCGTCTATGGTTATGGGAATTGATCATTTAAGA
GATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCATT
CATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAATT
TCAATTATGAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACTTACAGGAT
CGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCATC
ATTTATACACCAACTGTTGGTTCAGCTTGCCAAAAATTCGGCTTAATTTATCGAAGACCA
AGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAAAGAACTGG
CCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAGGTTTAGGC
GATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACACTGCCCTT
GCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAAATAATAAA
GATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAGGACAAGCC
TATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGACAAA

>g3335.t7 Gene=g3335 Length=278
MSLRLLIRNGSFARSYPNLAICGTTSSPKKSTPNQQIRLHHEVTGDIIVPSMVMGIDHLR
DPRLNKGLAFSLQERQVLGIHGLQPARIKTQEEQLELCKISIMRYQEDLNKYQYLVDLQD
RNERLFFRLVSENVEMMMPIIYTPTVGSACQKFGLIYRRPRGLFVTFNDKGHVFDVLKNW
PEPDVRAIVVTDGERILGLGDLGAQGMGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNK
DLLEDPLYVGLRQPRVSGQAYDDFIDEFMEAVVKRYGQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3335.t7 Coils Coil Coil 88 108 -
8 g3335.t7 Gene3D G3DSA:3.40.50.10380 - 54 278 3.7E-104
2 g3335.t7 PANTHER PTHR23406 MALIC ENZYME-RELATED 44 278 8.8E-111
3 g3335.t7 PANTHER PTHR23406:SF80 GH17657P-RELATED 44 278 8.8E-111
10 g3335.t7 PIRSF PIRSF000106 ME 25 278 8.0E-97
6 g3335.t7 PRINTS PR00072 Malic enzyme signature 125 149 6.6E-38
5 g3335.t7 PRINTS PR00072 Malic enzyme signature 185 214 6.6E-38
4 g3335.t7 PRINTS PR00072 Malic enzyme signature 221 243 6.6E-38
1 g3335.t7 Pfam PF00390 Malic enzyme, N-terminal domain 119 277 1.8E-69
11 g3335.t7 SMART SM01274 malic_2 119 276 1.6E-83
7 g3335.t7 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 38 277 3.02E-92

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.

Raw TPM values