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.t5 TSS g4516.t5 2968976 2968976
chr_2 g4516 g4516.t5 isoform g4516.t5 2969079 2970577
chr_2 g4516 g4516.t5 exon g4516.t5.exon1 2969079 2969081
chr_2 g4516 g4516.t5 cds g4516.t5.CDS1 2969079 2969081
chr_2 g4516 g4516.t5 exon g4516.t5.exon2 2969516 2969894
chr_2 g4516 g4516.t5 cds g4516.t5.CDS2 2969516 2969894
chr_2 g4516 g4516.t5 exon g4516.t5.exon3 2969958 2970187
chr_2 g4516 g4516.t5 cds g4516.t5.CDS3 2969958 2970187
chr_2 g4516 g4516.t5 exon g4516.t5.exon4 2970270 2970577
chr_2 g4516 g4516.t5 cds g4516.t5.CDS4 2970270 2970281
chr_2 g4516 g4516.t5 TTS g4516.t5 2970937 2970937

Sequences

>g4516.t5 Gene=g4516 Length=920
ATGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTCATTG
CTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATTCTCACACTT
TTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTATCAGACTGT
GCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCATTTAAGGAT
GTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAGCGCAAAGAT
CTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTGAATACATATGCA
AAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTAATGCATTAATTTGC
TCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACAAGACTCGATCAA
AATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTACAAAAGTCAAGAAT
CTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTTCAAATGGTACGGTT
GATGGTAAGCCTCAAGAAAAATGAGTTCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATC
ATGTTCGTGATTGGTGGATAGGCACACAATCAGGCAACTATGTTTCAATGGGAGTTGTTA
CACCGAAAGATAATCCATATAATGTTCCAGAGGGCATCGTTTTCTCATTCCCAGTTGAGA
TCAAGAATAAACAGTGGAGCATTGTTCCTGGATTCAAAATCAATGACTTTGCTCGCAGTA
AATTGGATATTACAACAAAAGAATTGTTGGAGGAAAAAGAAGAAGCAATGGCAGTCTGCA
ATGCAGATGCAAAAATCTAA

>g4516.t5 Gene=g4516 Length=207
MSEPIKVVVTGAAGQIAYSLLYMIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDC
AFTLLTEVIPTTDVAVAFKDVSVVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTYA
KKDVKVLVVGNPANTNALICSHYAPSIPKENFTAMTRLDQNRACAQIAQKVGSDITKVKN
LFIWGNHSATQFPDCSNGTVDGKPQEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4516.t5 Gene3D G3DSA:3.40.50.720 - 1 154 2.5E-63
7 g4516.t5 Gene3D G3DSA:3.90.110.10 - 155 207 1.5E-16
3 g4516.t5 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 204 2.1E-99
2 g4516.t5 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 5 152 3.1E-38
1 g4516.t5 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 156 190 6.0E-6
6 g4516.t5 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 155 167 -
5 g4516.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 155 1.07E-46
4 g4516.t5 SUPERFAMILY SSF56327 LDH C-terminal domain-like 156 205 9.42E-16

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:0016615 malate dehydrogenase activity MF
GO:0005975 carbohydrate metabolic process BP
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF
GO:0006108 malate metabolic process BP

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