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.t19 TTS g7339.t19 23112244 23112244
chr_2 g7339 g7339.t19 isoform g7339.t19 23112472 23115372
chr_2 g7339 g7339.t19 exon g7339.t19.exon1 23112472 23113213
chr_2 g7339 g7339.t19 cds g7339.t19.CDS1 23112813 23113213
chr_2 g7339 g7339.t19 exon g7339.t19.exon2 23113428 23113670
chr_2 g7339 g7339.t19 cds g7339.t19.CDS2 23113428 23113670
chr_2 g7339 g7339.t19 exon g7339.t19.exon3 23113728 23114024
chr_2 g7339 g7339.t19 cds g7339.t19.CDS3 23113728 23114024
chr_2 g7339 g7339.t19 exon g7339.t19.exon4 23115369 23115372
chr_2 g7339 g7339.t19 cds g7339.t19.CDS4 23115369 23115372
chr_2 g7339 g7339.t19 TSS g7339.t19 23115448 23115448

Sequences

>g7339.t19 Gene=g7339 Length=1286
ATGGATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCAAGCAGTCGCTGAGGATGTG
GACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAGCTGTTGGAATGGCTGCC
GCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTCTCATCGATATGTTTGAG
AACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTAACTTTTTGAAGAATGCT
AAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCACGTTTAATCATTGTTACC
GCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCAGAC
ATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACACTTTTGATT
GTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGATTGCCTAAG
AACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTCTTGCTTGCT
CAACTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCA
GGTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTTGTAAATGCTGCA
TATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTTTCATGTGCTGAT
ATTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAG
GGTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAAC
GGTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACACGCA
TCTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAAACTCTAAGACACAAT
ACATAAAGAAAATAACAACTAAAAACAGTAATTGAATATTAAAAAATTAGCAAAATCATA
CTCGAATACAGAAGAAAGCGACATTTTATTTGCACAGCTTCTTTATGAGCACGATTGCAC
TAAATATTCATCCCCTGCACACACATACAAATGCACATTTGCACAATCAGCAATCCTTTA
AGTGTCAATACCTAAACAGAATTTTTTTAATATTATTTAATTGATTTAAGTATGGAAAAA
AGCAAAATTTAACAGTAGTTGTTTGAGAATAGACATGAACAAAATTCGTATCATTTGTGT
AGTTTTTAATTTATTTTAAATAAACT

>g7339.t19 Gene=g7339 Length=314
MDPQMASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFE
NKLKGEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNAD
IMKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLA
QLWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAYEVIKLKGYTSWAIGLSCAD
IASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANGVVSIVKQKLSPDELAKLHA
SAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g7339.t19 CDD cd05293 LDH_1 23 311 0
11 g7339.t19 Gene3D G3DSA:3.40.50.720 - 5 167 0
10 g7339.t19 Gene3D G3DSA:3.90.110.10 - 168 314 0
3 g7339.t19 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 5 310 0
12 g7339.t19 PIRSF PIRSF000102 Lac_mal_DH 22 182 0
13 g7339.t19 PIRSF PIRSF000102 Lac_mal_DH 180 314 0
5 g7339.t19 PRINTS PR00086 L-lactate dehydrogenase signature 27 51 0
7 g7339.t19 PRINTS PR00086 L-lactate dehydrogenase signature 52 76 0
4 g7339.t19 PRINTS PR00086 L-lactate dehydrogenase signature 139 159 0
6 g7339.t19 PRINTS PR00086 L-lactate dehydrogenase signature 163 181 0
2 g7339.t19 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 27 165 0
1 g7339.t19 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 205 303 0
9 g7339.t19 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 6 165 0
8 g7339.t19 SUPERFAMILY SSF56327 LDH C-terminal domain-like 166 312 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:0005975 carbohydrate metabolic process BP
GO:0003824 catalytic activity 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