Gene loci information

Transcript annotation

  • This transcript has been annotated as Malate dehydrogenase.

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.t15 TSS g4516.t15 2968976 2968976
chr_2 g4516 g4516.t15 isoform g4516.t15 2969681 2970943
chr_2 g4516 g4516.t15 exon g4516.t15.exon1 2969681 2969894
chr_2 g4516 g4516.t15 cds g4516.t15.CDS1 2969780 2969894
chr_2 g4516 g4516.t15 exon g4516.t15.exon2 2969958 2970415
chr_2 g4516 g4516.t15 cds g4516.t15.CDS2 2969958 2970415
chr_2 g4516 g4516.t15 exon g4516.t15.exon3 2970552 2970943
chr_2 g4516 g4516.t15 cds g4516.t15.CDS3 2970552 2970611
chr_2 g4516 g4516.t15 TTS g4516.t15 2970937 2970937

Sequences

>g4516.t15 Gene=g4516 Length=1064
TTATCAGACTGTGCTTTTACTCTTTTGACCGAAGTTATTCCCACAACTGACGTTGCTGTT
GCATTTAAGGATGTTTCGGTTGTATTTCTCGTGGGTGCTATGCCAAGGCGTGAAGGTATG
GAGCGCAAAGATCTTTTGTCAGCGAACGTCAAGATTTTCAAAGTTCAAGGTGAAGCTTTG
AATACATATGCAAAAAAAGACGTTAAAGTTCTGGTTGTTGGAAATCCTGCAAATACTAAT
GCATTAATTTGCTCGCATTATGCACCTTCAATTCCAAAGGAAAATTTTACAGCCATGACA
AGACTCGATCAAAATCGTGCATGTGCTCAAATTGCACAAAAAGTTGGAAGTGATATTACA
AAAGTCAAGAATCTTTTCATTTGGGGTAATCATTCGGCAACACAATTCCCAGATTGTTCA
AATGGTACGGTTGATGGTAAGCCTGTTACAGACCTTGTCGACGCATCTTATTTGGAGAAT
GAATTTGTCACAACTGTCCAAAAGAGAGGTGCAGCTGTTATTGCAGCAAGAAAAATGAGT
TCAGCAATGAGTGCTGCTAAAGCTGCTGCTGATCATGTTCGTGATTGGTGGATAGGCACA
CAATCAGGCAACTATGTTTCAATGGGAGTTGTTACACCGAAAGATAATCCATATAATGTT
CCAGAGGGCATCTCTGCAATGCAGATGCAAAAATCTAAATACCTGAAAAGAATATTACAC
TATTGTTGTTGAAATTCTCCATTTATGCTACAATTTATAAGCTGGGATGTTTAACTTACA
CGCATTTTTATTTGAATTCCTTAAAATATATTTTTTTTCGTTTATAATATACATAGCATT
CCTTCAAAATGTTTGTTTCTAATTCATCATGTACTTCCAAATTGAGATTATATTTTGTTT
TATCGTTTTTATGTTAGCTTTTTTCAAAGTCTTATTTTTTATTTTCGGAATTATCAGGAA
TTAAAAGATTTTATTTTTTTATTTTGTTTTAATTAGGGATGCAAACATCCTACATAAAAC
ATGTTTTTGGAGAATTAATGAAATAAAGTTAATTAATTAAAAAA

>g4516.t15 Gene=g4516 Length=210
MPRREGMERKDLLSANVKIFKVQGEALNTYAKKDVKVLVVGNPANTNALICSHYAPSIPK
ENFTAMTRLDQNRACAQIAQKVGSDITKVKNLFIWGNHSATQFPDCSNGTVDGKPVTDLV
DASYLENEFVTTVQKRGAAVIAARKMSSAMSAAKAAADHVRDWWIGTQSGNYVSMGVVTP
KDNPYNVPEGISAMQMQKSKYLKRILHYCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4516.t15 Gene3D G3DSA:3.40.50.720 - 1 65 5.2E-25
7 g4516.t15 Gene3D G3DSA:3.90.110.10 - 66 195 4.0E-47
3 g4516.t15 PANTHER PTHR23382 MALATE DEHYDROGENASE 1 191 4.7E-85
2 g4516.t15 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 1 63 5.9E-16
1 g4516.t15 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 67 187 1.4E-22
6 g4516.t15 ProSitePatterns PS00068 Malate dehydrogenase active site signature. 66 78 -
5 g4516.t15 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 66 9.11E-16
4 g4516.t15 SUPERFAMILY SSF56327 LDH C-terminal domain-like 67 191 3.55E-41

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