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.t7 TSS g4516.t7 2968976 2968976
chr_2 g4516 g4516.t7 isoform g4516.t7 2969079 2970881
chr_2 g4516 g4516.t7 exon g4516.t7.exon1 2969079 2969081
chr_2 g4516 g4516.t7 cds g4516.t7.CDS1 2969079 2969081
chr_2 g4516 g4516.t7 exon g4516.t7.exon2 2969516 2969867
chr_2 g4516 g4516.t7 cds g4516.t7.CDS2 2969516 2969867
chr_2 g4516 g4516.t7 exon g4516.t7.exon3 2969958 2970881
chr_2 g4516 g4516.t7 cds g4516.t7.CDS3 2969958 2970577
chr_2 g4516 g4516.t7 TTS g4516.t7 2970937 2970937

Sequences

>g4516.t7 Gene=g4516 Length=1279
ATGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTCATTG
CTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATTCTCACACTT
TTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTATCAGACTGT
GCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCATTTAAGGAT
GTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAGCGCAAAGAT
CTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTGAATACATTTGTT
GGAAATCCTGCAAATACTAATGCATTAATTTGCTCGCATTATGCACCTTCAATTCCAAAG
GAAAATTTTACAGCCATGACAAGACTCGATCAAAATCGTGCATGTGCTCAAATTGCACAA
AAAGTTGGAAGTGATATTACAAAAGTCAAGAATCTTTTCATTTGGGGTAATCATTCGGCA
ACACAATTCCCAGATTGTTCAAATGGTACGGTTGATGGTAAGCCTGTTACAGACCTTGTC
GACGCATCTTATTTGGAGAATGAATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTT
ATTGCAGCAAGAAAAATGAGTTCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTT
CGTGATTGGTGGATAGGCACACAATCAGGCAACTATGTTTCAATGGGAGTTGTTACACCG
AAAGATAATCCATATAATGTTCCAGAGGGCATCGTTTTCTCATTCCCAGTTGAGATCAAG
AATAAACAGTGGAGCATTGTTCCTGGATTCAAAATCAATGACTTTGCTCGCAGTAAATTG
GATATTACAACAAAAGAATTGTTGGAGGAAAAAGAAGAAGCAATGGCAGTCTGCAATGCA
GATGCAAAAATCTAAATACCTGAAAAGAATATTACACTATTGTTGTTGAAATTCTCCATT
TATGCTACAATTTATAAGCTGGGATGTTTAACTTACACGCATTTTTATTTGAATTCCTTA
AAATATATTTTTTTTCGTTTATAATATACATAGCATTCCTTCAAAATGTTTGTTTCTAAT
TCATCATGTACTTCCAAATTGAGATTATATTTTGTTTTATCGTTTTTATGTTAGCTTTTT
TCAAAGTCTTATTTTTTATTTTCGGAATTATCAGGAATTAAAAGATTTTATTTTTTTATT
TTGTTTTAATTAGGGATGC

>g4516.t7 Gene=g4516 Length=324
MSEPIKVVVTGAAGQIAYSLLYMIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDC
AFTLLTEVIPTTDVAVAFKDVSVVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTFV
GNPANTNALICSHYAPSIPKENFTAMTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSA
TQFPDCSNGTVDGKPVTDLVDASYLENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHV
RDWWIGTQSGNYVSMGVVTPKDNPYNVPEGIVFSFPVEIKNKQWSIVPGFKINDFARSKL
DITTKELLEEKEEAMAVCNADAKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4516.t7 Gene3D G3DSA:3.40.50.720 - 1 145 5.9E-53
7 g4516.t7 Gene3D G3DSA:3.90.110.10 - 146 322 3.3E-65
3 g4516.t7 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 318 2.8E-140
11 g4516.t7 PIRSF PIRSF000102 Lac_mal_DH 1 318 4.7E-64
2 g4516.t7 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 5 143 7.3E-30
1 g4516.t7 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 147 316 2.5E-33
6 g4516.t7 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 146 158 -
5 g4516.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 146 1.04E-39
4 g4516.t7 SUPERFAMILY SSF56327 LDH C-terminal domain-like 147 318 1.25E-56
9 g4516.t7 TIGRFAM TIGR01759 MalateDH-SF1: malate dehydrogenase 3 314 1.8E-141
10 g4516.t7 TIGRFAM TIGR01758 MDH_euk_cyt: malate dehydrogenase, NAD-dependent 6 316 5.9E-145

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:0030060 L-malate dehydrogenase activity MF
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