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.t14 TSS g4516.t14 2968976 2968976
chr_2 g4516 g4516.t14 isoform g4516.t14 2969517 2970944
chr_2 g4516 g4516.t14 exon g4516.t14.exon1 2969517 2969849
chr_2 g4516 g4516.t14 cds g4516.t14.CDS1 2969579 2969849
chr_2 g4516 g4516.t14 exon g4516.t14.exon2 2969958 2970944
chr_2 g4516 g4516.t14 cds g4516.t14.CDS2 2969958 2970577
chr_2 g4516 g4516.t14 TTS g4516.t14 2970937 2970937

Sequences

>g4516.t14 Gene=g4516 Length=1320
GTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAATCGCTTACTCATTGCTCT
ACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAATAATTCTCACACTTTTGG
ATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGGAGTTATCAGACTGTGCTT
TTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTTGCATTTAAGGATGTTT
CGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATGGAGCGCAAAGATCTTT
TGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGTTGTTGGAAATCCTGCAAATACTAATG
CATTAATTTGCTCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACAA
GACTCGATCAAAATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTACAA
AAGTCAAGAATCTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTTCAA
ATGGTACGGTTGATGGTAAGCCTGTTACAGACCTTGTCGACGCATCTTATTTGGAGAATG
AATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAAAATGAGTT
CAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGATAGGCACAC
AATCAGGCAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATATAATGTTC
CAGAGGGCATCGTTTTCTCATTCCCAGTTGAGATCAAGAATAAACAGTGGAGCATTGTTC
CTGGATTCAAAATCAATGACTTTGCTCGCAGTAAATTGGATATTACAACAAAAGAATTGT
TGGAGGAAAAAGAAGAAGCAATGGCAGTCTGCAATGCAGATGCAAAAATCTAAATACCTG
AAAAGAATATTACACTATTGTTGTTGAAATTCTCCATTTATGCTACAATTTATAAGCTGG
GATGTTTAACTTACACGCATTTTTATTTGAATTCCTTAAAATATATTTTTTTTCGTTTAT
AATATACATAGCATTCCTTCAAAATGTTTGTTTCTAATTCATCATGTACTTCCAAATTGA
GATTATATTTTGTTTTATCGTTTTTATGTTAGCTTTTTTCAAAGTCTTATTTTTTATTTT
CGGAATTATCAGGAATTAAAAGATTTTATTTTTTTATTTTGTTTTAATTAGGGATGCAAA
CATCCTACATAAAACATGTTTTTGGAGAATTAATGAAATAAAGTTAATTAATTAAAAAAA

>g4516.t14 Gene=g4516 Length=296
MIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDCAFTLLTEVIPTTDVAVAFKDVS
VVFLVGAMPRREGMERKDLLSANVKIFKVQVVGNPANTNALICSHYAPSIPKENFTAMTR
LDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDGKPVTDLVDASYLENE
FVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYVSMGVVTPKDNPYNVP
EGIVFSFPVEIKNKQWSIVPGFKINDFARSKLDITTKELLEEKEEAMAVCNADAKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4516.t14 Gene3D G3DSA:3.40.50.720 - 1 117 1.2E-37
7 g4516.t14 Gene3D G3DSA:3.90.110.10 - 118 294 2.6E-65
3 g4516.t14 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 290 3.4E-125
10 g4516.t14 PIRSF PIRSF000102 Lac_mal_DH 1 290 3.1E-51
2 g4516.t14 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 4 115 9.4E-19
1 g4516.t14 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 119 288 1.9E-33
6 g4516.t14 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 118 130 -
5 g4516.t14 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 118 2.27E-28
4 g4516.t14 SUPERFAMILY SSF56327 LDH C-terminal domain-like 119 290 9.73E-57
9 g4516.t14 TIGRFAM TIGR01759 MalateDH-SF1: malate dehydrogenase 1 286 8.2E-124

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

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