Gene loci information

Transcript annotation

  • This transcript has been annotated as Malate dehydrogenase, cytoplasmic.

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_2 g4516 g4516.t4 TSS g4516.t4 2968976 2968976
chr_2 g4516 g4516.t4 isoform g4516.t4 2969079 2970577
chr_2 g4516 g4516.t4 exon g4516.t4.exon1 2969079 2969081
chr_2 g4516 g4516.t4 cds g4516.t4.CDS1 2969079 2969081
chr_2 g4516 g4516.t4 exon g4516.t4.exon2 2969516 2969596
chr_2 g4516 g4516.t4 cds g4516.t4.CDS2 2969516 2969596
chr_2 g4516 g4516.t4 exon g4516.t4.exon3 2969681 2969894
chr_2 g4516 g4516.t4 cds g4516.t4.CDS3 2969681 2969894
chr_2 g4516 g4516.t4 exon g4516.t4.exon4 2969958 2970577
chr_2 g4516 g4516.t4 cds g4516.t4.CDS4 2969958 2970577
chr_2 g4516 g4516.t4 TTS g4516.t4 2970937 2970937

Sequences

>g4516.t4 Gene=g4516 Length=918
ATGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTCATTG
CTCTACATGATTGCGAATGGCGATTTATCAGACTGTGCTTTTACTCTTTTGACCGAAGTT
ATTCCCACAACTGACGTTGCTGTTGCATTTAAGGATGTTTCGGTTGTATTTCTCGTGGGT
GCTATGCCAAGGCGTGAAGGTATGGAGCGCAAAGATCTTTTGTCAGCGAACGTCAAGATT
TTCAAAGTTCAAGGTGAAGCTTTGAATACATATGCAAAAAAAGACGTTAAAGTTCTGGTT
GTTGGAAATCCTGCAAATACTAATGCATTAATTTGCTCGCATTATGCACCTTCAATTCCA
AAGGAAAATTTTACAGCCATGACAAGACTCGATCAAAATCGTGCATGTGCTCAAATTGCA
CAAAAAGTTGGAAGTGATATTACAAAAGTCAAGAATCTTTTCATTTGGGGTAATCATTCG
GCAACACAATTCCCAGATTGTTCAAATGGTACGGTTGATGGTAAGCCTGTTACAGACCTT
GTCGACGCATCTTATTTGGAGAATGAATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCT
GTTATTGCAGCAAGAAAAATGAGTTCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCAT
GTTCGTGATTGGTGGATAGGCACACAATCAGGCAACTATGTTTCAATGGGAGTTGTTACA
CCGAAAGATAATCCATATAATGTTCCAGAGGGCATCGTTTTCTCATTCCCAGTTGAGATC
AAGAATAAACAGTGGAGCATTGTTCCTGGATTCAAAATCAATGACTTTGCTCGCAGTAAA
TTGGATATTACAACAAAAGAATTGTTGGAGGAAAAAGAAGAAGCAATGGCAGTCTGCAAT
GCAGATGCAAAAATCTAA

>g4516.t4 Gene=g4516 Length=305
MSEPIKVVVTGAAGQIAYSLLYMIANGDLSDCAFTLLTEVIPTTDVAVAFKDVSVVFLVG
AMPRREGMERKDLLSANVKIFKVQGEALNTYAKKDVKVLVVGNPANTNALICSHYAPSIP
KENFTAMTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDGKPVTDL
VDASYLENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYVSMGVVT
PKDNPYNVPEGIVFSFPVEIKNKQWSIVPGFKINDFARSKLDITTKELLEEKEEAMAVCN
ADAKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4516.t4 Gene3D G3DSA:3.40.50.720 - 1 126 1.3E-43
8 g4516.t4 Gene3D G3DSA:3.90.110.10 - 127 303 2.8E-65
3 g4516.t4 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 29 2.0E-129
4 g4516.t4 PANTHER PTHR23382 MALATE DEHYDROGENASE 29 299 2.0E-129
11 g4516.t4 PIRSF PIRSF000102 Lac_mal_DH 1 36 8.6E-5
12 g4516.t4 PIRSF PIRSF000102 Lac_mal_DH 25 299 2.6E-60
2 g4516.t4 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 28 124 4.6E-24
1 g4516.t4 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 128 297 2.1E-33
7 g4516.t4 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 127 139 -
6 g4516.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 127 5.96E-34
5 g4516.t4 SUPERFAMILY SSF56327 LDH C-terminal domain-like 128 299 1.07E-56
10 g4516.t4 TIGRFAM TIGR01759 MalateDH-SF1: malate dehydrogenase 29 295 1.8E-122

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0006108 malate metabolic process BP
GO:0019752 carboxylic acid metabolic process BP
GO:0016615 malate dehydrogenase activity MF
GO:0005975 carbohydrate metabolic process BP
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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