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.t27 isoform g3335.t27 24725537 24727000
chr_3 g3335 g3335.t27 exon g3335.t27.exon1 24725537 24725582
chr_3 g3335 g3335.t27 exon g3335.t27.exon2 24726089 24726166
chr_3 g3335 g3335.t27 cds g3335.t27.CDS1 24726137 24726166
chr_3 g3335 g3335.t27 exon g3335.t27.exon3 24726241 24726265
chr_3 g3335 g3335.t27 cds g3335.t27.CDS2 24726241 24726265
chr_3 g3335 g3335.t27 exon g3335.t27.exon4 24726323 24727000
chr_3 g3335 g3335.t27 cds g3335.t27.CDS3 24726323 24726999
chr_3 g3335 g3335.t27 TTS g3335.t27 24727926 24727926
chr_3 g3335 g3335.t27 TSS g3335.t27 NA NA

Sequences

>g3335.t27 Gene=g3335 Length=827
ATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACTTACAGGATCGAAATGAACG
TCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCATCATTTATACACC
AACTGTTGGTTCAGCTTGCCAAAAATTCGGCTTAATTTATCGAAGACCAAGAGGTCTTTT
CGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAAAGAACTGGCCAGAGCCAGA
TGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAGGTTTAGGCGATTTAGGAGC
TCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACACTGCCCTTGCTGGTATCAA
ACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAAATAATAAAGATCTTCTCGA
AGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAGGACAAGCCTATGACGATTT
TATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGACAAAATACTTTGATTCAATT
TGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACAAATACCGTGACACTTATTG
CACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTGTTGCAGGACTTCTTGCTTC
AAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTCTTTTCCTCGGTGCTGGTGA
AGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGATGACAGAAGGAGTTTCACA
AGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATGGACTTT

>g3335.t27 Gene=g3335 Length=244
MMMPIIYTPTVGSACQKFGLIYRRPRGLFVTFNDKGHVFDVLKNWPEPDVRAIVVTDGER
ILGLGDLGAQGMGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNKDLLEDPLYVGLRQPR
VSGQAYDDFIDEFMEAVVKRYGQNTLIQFEDFGNHNAFRFLDKYRDTYCTFNDDIQGTAS
VAVAGLLASKRVTGKKLSDNKILFLGAGEAAIGIADLCVKAMMTEGVSQDEARDKIWMVD
IDGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3335.t27 Gene3D G3DSA:3.40.50.10380 - 1 172 2.8E-92
13 g3335.t27 Gene3D G3DSA:3.40.50.720 - 173 244 1.1E-27
3 g3335.t27 PANTHER PTHR23406 MALIC ENZYME-RELATED 2 244 2.2E-129
4 g3335.t27 PANTHER PTHR23406:SF80 GH17657P-RELATED 2 244 2.2E-129
14 g3335.t27 PIRSF PIRSF000106 ME 1 244 3.5E-118
8 g3335.t27 PRINTS PR00072 Malic enzyme signature 50 79 8.7E-57
9 g3335.t27 PRINTS PR00072 Malic enzyme signature 86 108 8.7E-57
7 g3335.t27 PRINTS PR00072 Malic enzyme signature 146 164 8.7E-57
6 g3335.t27 PRINTS PR00072 Malic enzyme signature 171 187 8.7E-57
5 g3335.t27 PRINTS PR00072 Malic enzyme signature 202 218 8.7E-57
1 g3335.t27 Pfam PF00390 Malic enzyme, N-terminal domain 2 165 9.4E-76
2 g3335.t27 Pfam PF03949 Malic enzyme, NAD binding domain 175 244 5.5E-25
15 g3335.t27 ProSitePatterns PS00331 Malic enzymes signature. 171 187 -
16 g3335.t27 SMART SM01274 malic_2 1 165 1.3E-92
11 g3335.t27 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 2 174 2.52E-80
10 g3335.t27 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 175 244 2.76E-22

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