Gene loci information

Transcript annotation

  • This transcript has been annotated as L-lactate 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 g7339 g7339.t31 isoform g7339.t31 23113497 23114828
chr_2 g7339 g7339.t31 exon g7339.t31.exon1 23113497 23113670
chr_2 g7339 g7339.t31 cds g7339.t31.CDS1 23113498 23113670
chr_2 g7339 g7339.t31 exon g7339.t31.exon2 23113728 23114024
chr_2 g7339 g7339.t31 cds g7339.t31.CDS2 23113728 23114016
chr_2 g7339 g7339.t31 exon g7339.t31.exon3 23114748 23114828
chr_2 g7339 g7339.t31 TSS g7339.t31 23115448 23115448
chr_2 g7339 g7339.t31 TTS g7339.t31 NA NA

Sequences

>g7339.t31 Gene=g7339 Length=552
GGTACAAGACACATGTTTTTTTTTCTCAAAAAATTATACTTGTGAATTTTTTTCGGAGGG
GAAAAAGGTCACCTTCAAACAATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCAAG
CAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAG
CTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTC
TCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTA
ACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCAC
GTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAG
TTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTG
ATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAAT
TATCAGGATTGC

>g7339.t31 Gene=g7339 Length=154
MASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLK
GEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKN
LIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7339.t31 Gene3D G3DSA:3.40.50.720 - 1 154 0
2 g7339.t31 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 154 0
3 g7339.t31 PRINTS PR00086 L-lactate dehydrogenase signature 23 47 0
4 g7339.t31 PRINTS PR00086 L-lactate dehydrogenase signature 48 72 0
5 g7339.t31 PRINTS PR00086 L-lactate dehydrogenase signature 135 154 0
1 g7339.t31 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 23 153 0
6 g7339.t31 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 154 0

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:0019752 carboxylic acid metabolic process BP
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0055114 NA NA
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