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.t25 TTS g7339.t25 23112244 23112244
chr_2 g7339 g7339.t25 isoform g7339.t25 23112813 23114735
chr_2 g7339 g7339.t25 exon g7339.t25.exon1 23112813 23113228
chr_2 g7339 g7339.t25 cds g7339.t25.CDS1 23112813 23113228
chr_2 g7339 g7339.t25 exon g7339.t25.exon2 23113398 23113670
chr_2 g7339 g7339.t25 cds g7339.t25.CDS2 23113398 23113670
chr_2 g7339 g7339.t25 exon g7339.t25.exon3 23113728 23114024
chr_2 g7339 g7339.t25 cds g7339.t25.CDS3 23113728 23114016
chr_2 g7339 g7339.t25 exon g7339.t25.exon4 23114533 23114735
chr_2 g7339 g7339.t25 TSS g7339.t25 23115448 23115448

Sequences

>g7339.t25 Gene=g7339 Length=1189
TTTCAATACTTTCTACGTTAGGAGTATATTATCCATTTGATCGCTGTTGAGAAGTACAGA
CTGTTTGCAAAAATAGAGTGAATTTGTGAATTGTAGATTTTTTAAGTAAAATTTTAATCA
AATAAAATTAATTTTCTAAGCTATTTATCGAGCACTGATTTACTTTTACTGATTAGATAA
AGAAACATATTTTAAATTAAAAAATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCA
AGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGG
AGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGC
TCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATC
TAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTC
ACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTT
AGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCC
TGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAA
ATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCG
TTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGATTCATC
TGTTCCAGTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAG
TGCAGGTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTTGTAAATGC
TGCATATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTTTCATGTGC
TGATATTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGT
CAAGGGTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGC
CAACGGTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACA
CGCATCTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAA

>g7339.t25 Gene=g7339 Length=325
MASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLK
GEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKN
LIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLN
VAPTSMHDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAYEVIKLKGY
TSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANGVVSIVKQK
LSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7339.t25 CDD cd05293 LDH_1 19 322 0
11 g7339.t25 Gene3D G3DSA:3.40.50.720 - 1 163 0
10 g7339.t25 Gene3D G3DSA:3.90.110.10 - 164 325 0
3 g7339.t25 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 321 0
12 g7339.t25 PIRSF PIRSF000102 Lac_mal_DH 18 325 0
4 g7339.t25 PRINTS PR00086 L-lactate dehydrogenase signature 23 47 0
7 g7339.t25 PRINTS PR00086 L-lactate dehydrogenase signature 48 72 0
6 g7339.t25 PRINTS PR00086 L-lactate dehydrogenase signature 135 155 0
5 g7339.t25 PRINTS PR00086 L-lactate dehydrogenase signature 159 177 0
2 g7339.t25 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 23 161 0
1 g7339.t25 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 164 314 0
9 g7339.t25 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 161 0
8 g7339.t25 SUPERFAMILY SSF56327 LDH C-terminal domain-like 162 323 0
14 g7339.t25 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 26 317 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: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:0005737 cytoplasm CC
GO:0019752 carboxylic acid metabolic process BP
GO:0004459 L-lactate 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. There were no conditions that were differentially expressed