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.t9 TSS g4516.t9 2968976 2968976
chr_2 g4516 g4516.t9 isoform g4516.t9 2969079 2970943
chr_2 g4516 g4516.t9 exon g4516.t9.exon1 2969079 2969894
chr_2 g4516 g4516.t9 cds g4516.t9.CDS1 2969579 2969894
chr_2 g4516 g4516.t9 exon g4516.t9.exon2 2969958 2970494
chr_2 g4516 g4516.t9 cds g4516.t9.CDS2 2969958 2970494
chr_2 g4516 g4516.t9 exon g4516.t9.exon3 2970564 2970943
chr_2 g4516 g4516.t9 cds g4516.t9.CDS3 2970564 2970577
chr_2 g4516 g4516.t9 TTS g4516.t9 2970937 2970937

Sequences

>g4516.t9 Gene=g4516 Length=1733
ATGGTAAGTCAGAAAATCTATCAATATAGACTGATATTTATAGTGTATTGCGCAAAAACC
GAATGAAAAGGAAATAGAGAAAATGAAAGTGTCGTCGTCAAAACAATTCTCGGACTTTCA
TTCTTCTTTTCTTCTTACATAATCAAATTGCTCATAATGTCGCACATTTATTGCTCTGAT
AATGCTTGCGATTAAAATTATGTGACGATGAAGATTTGTTTCTATTCAATTATTTAATTT
TCAAAATGTTATTCAAATGACCTTTTTCAGTTATTAGTGTTGTATTTTATAAATATTTAC
TCACAACATTTATACAGATGTGTGTGTCTGTTTACGTTTTATATACATATACCGGTATTT
TAATGATAATATTGATGCTGGTTTTGTTACCATGTCTTTTAATATCTTTATTTTTTTCAT
ATCTTTTTTATTCATAGAGTGAACCAATCAAAGTTGTTGTTACTGGTGCAGCCGGTCAAA
TCGCTTACTCATTGCTCTACATGATTGCGAATGGCGATGTTTTTGGAAAAAATCAAAAAA
TAATTCTCACACTTTTGGATATTCCTCCTATGATGGGTGTCCTTGAAGGAGTTGTTATGG
AGTTATCAGACTGTGCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTG
TTGCATTTAAGGATGTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTA
TGGAGCGCAAAGATCTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTT
TGAATACATATGCAAAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTA
ATGCATTAATTTGCTCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGA
CAAGACTCGATCAAAATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTA
CAAAAGTCAAGAATCTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTT
CAAATGGTACGGTTGATGGTAAGCCTGTTACAGACCTTGTCGACGCATCTTATTTGGAGA
ATGAATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAAAATGA
GTTCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGATAGGCA
CACAATCAGGCAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATATAATG
TTCCAGAGGGCATCGTTTTCTCATTCCCAGTTGAGATCAAGAATAAACAGTGGAGCATTG
TTCCTGGATTCAAAATCAATGACTTTGCTCGCAATGCAAAAATCTAAATACCTGAAAAGA
ATATTACACTATTGTTGTTGAAATTCTCCATTTATGCTACAATTTATAAGCTGGGATGTT
TAACTTACACGCATTTTTATTTGAATTCCTTAAAATATATTTTTTTTCGTTTATAATATA
CATAGCATTCCTTCAAAATGTTTGTTTCTAATTCATCATGTACTTCCAAATTGAGATTAT
ATTTTGTTTTATCGTTTTTATGTTAGCTTTTTTCAAAGTCTTATTTTTTATTTTCGGAAT
TATCAGGAATTAAAAGATTTTATTTTTTTATTTTGTTTTAATTAGGGATGCAAACATCCT
ACATAAAACATGTTTTTGGAGAATTAATGAAATAAAGTTAATTAATTAAAAAA

>g4516.t9 Gene=g4516 Length=288
MIANGDVFGKNQKIILTLLDIPPMMGVLEGVVMELSDCAFTLLTEVIPTTDVAVAFKDVS
VVFLVGAMPRREGMERKDLLSANVKIFKVQGEALNTYAKKDVKVLVVGNPANTNALICSH
YAPSIPKENFTAMTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDG
KPVTDLVDASYLENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYV
SMGVVTPKDNPYNVPEGIVFSFPVEIKNKQWSIVPGFKINDFARNAKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4516.t9 Gene3D G3DSA:3.40.50.720 - 1 132 3.2E-51
7 g4516.t9 Gene3D G3DSA:3.90.110.10 - 133 287 1.1E-58
3 g4516.t9 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 285 8.4E-132
10 g4516.t9 PIRSF PIRSF000102 Lac_mal_DH 1 287 1.8E-61
2 g4516.t9 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 4 130 2.1E-29
1 g4516.t9 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 134 285 3.9E-29
6 g4516.t9 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 133 145 -
5 g4516.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 133 4.6E-35
4 g4516.t9 SUPERFAMILY SSF56327 LDH C-terminal domain-like 134 284 8.8E-51
9 g4516.t9 TIGRFAM TIGR01759 MalateDH-SF1: malate dehydrogenase 1 285 2.4E-133

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