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.t10 TSS g3335.t10 24723961 24723961
chr_3 g3335 g3335.t10 isoform g3335.t10 24724136 24727000
chr_3 g3335 g3335.t10 exon g3335.t10.exon1 24724136 24724155
chr_3 g3335 g3335.t10 exon g3335.t10.exon2 24725121 24725263
chr_3 g3335 g3335.t10 exon g3335.t10.exon3 24725319 24725582
chr_3 g3335 g3335.t10 exon g3335.t10.exon4 24726089 24726189
chr_3 g3335 g3335.t10 exon g3335.t10.exon5 24726323 24727000
chr_3 g3335 g3335.t10 cds g3335.t10.CDS1 24726481 24726999
chr_3 g3335 g3335.t10 TTS g3335.t10 24727926 24727926

Sequences

>g3335.t10 Gene=g3335 Length=1206
ATGTCTCTTAGACTTTTAATTCGTAATGGGTCGTTTGCGCGATCATATCCAAATCTTGCA
ATATGTGGTACGACTTCTTCACCGAAAAAGTCAACACCCAATCAGCAAATTCGCTTGCAT
CATGAAGTTACAGGCGACATAATTGTTCCGTCTATGGTTATGGGAATTGATCATTTAAGA
GATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCATT
CATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAATT
TCAATTATGAGGTGAGGCAAATCCAATTAATATAAGTTTGTCACATATGAGTCACTATAA
AATTCTTATTGATTCTTATAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGA
CTTACAGGATCGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGAT
GATGCCCATCATTTATACACCAACTGTAATTTAAACCCTTTATTATTTGCTTAATTTATC
GAAGACCAAGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAA
AGAACTGGCCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAG
GTTTAGGCGATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACA
CTGCCCTTGCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAA
ATAATAAAGATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAG
GACAAGCCTATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGAC
AAAATACTTTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACA
AATACCGTGACACTTATTGCACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTG
TTGCAGGACTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTC
TTTTCCTCGGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGA
TGACAGAAGGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATG
GACTTT

>g3335.t10 Gene=g3335 Length=173
MGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNKDLLEDPLYVGLRQPRVSGQAYDDFID
EFMEAVVKRYGQNTLIQFEDFGNHNAFRFLDKYRDTYCTFNDDIQGTASVAVAGLLASKR
VTGKKLSDNKILFLGAGEAAIGIADLCVKAMMTEGVSQDEARDKIWMVDIDGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3335.t10 Gene3D G3DSA:3.40.50.10380 - 1 101 2.3E-52
14 g3335.t10 Gene3D G3DSA:3.40.50.720 - 102 173 5.5E-28
3 g3335.t10 PANTHER PTHR23406:SF27 NAD-DEPENDENT MALIC ENZYME, MITOCHONDRIAL 1 173 2.0E-88
4 g3335.t10 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 173 2.0E-88
6 g3335.t10 PRINTS PR00072 Malic enzyme signature 15 37 4.4E-41
7 g3335.t10 PRINTS PR00072 Malic enzyme signature 75 93 4.4E-41
8 g3335.t10 PRINTS PR00072 Malic enzyme signature 100 116 4.4E-41
5 g3335.t10 PRINTS PR00072 Malic enzyme signature 131 147 4.4E-41
1 g3335.t10 Pfam PF00390 Malic enzyme, N-terminal domain 1 94 1.6E-40
2 g3335.t10 Pfam PF03949 Malic enzyme, NAD binding domain 104 173 2.7E-25
12 g3335.t10 ProSitePatterns PS00331 Malic enzymes signature. 100 116 -
11 g3335.t10 SMART SM01274 malic_2 1 94 3.3E-22
10 g3335.t10 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 103 3.31E-46
9 g3335.t10 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 104 173 1.15E-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.

Raw TPM values