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.t9 isoform g7339.t9 23112236 23114559
chr_2 g7339 g7339.t9 exon g7339.t9.exon1 23112236 23113252
chr_2 g7339 g7339.t9 TTS g7339.t9 23112244 23112244
chr_2 g7339 g7339.t9 cds g7339.t9.CDS1 23113237 23113252
chr_2 g7339 g7339.t9 exon g7339.t9.exon2 23113394 23113670
chr_2 g7339 g7339.t9 cds g7339.t9.CDS2 23113394 23113670
chr_2 g7339 g7339.t9 exon g7339.t9.exon3 23113728 23114024
chr_2 g7339 g7339.t9 cds g7339.t9.CDS3 23113728 23114016
chr_2 g7339 g7339.t9 exon g7339.t9.exon4 23114533 23114559
chr_2 g7339 g7339.t9 TSS g7339.t9 23115448 23115448

Sequences

>g7339.t9 Gene=g7339 Length=1618
ATAAAGAAACATATTTTAAATTAAAAAATCCACAAATGGCAAGTCTTAAAGATCAAATGT
TCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAA
TCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACG
TTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACG
GATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTA
ATTCACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGG
ATTTAGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACA
GTCCTGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCAT
GGAAATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCAT
CTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGGTA
GGTTGGATTATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATT
GCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTGAAAAC
TGGAATGAATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAATTGAAGGGT
TATACATCATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATTTTCAGAAAC
AGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATTGATTCAGAA
GTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAA
AAATTGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATGGACGAAGTT
CAACGTGGCATCAAATTGTAAACTCTAAGACACAATACATAAAGAAAATAACAACTAAAA
ACAGTAATTGAATATTAAAAAATTAGCAAAATCATACTCGAATACAGAAGAAAGCGACAT
TTTATTTGCACAGCTTCTTTATGAGCACGATTGCACTAAATATTCATCCCCTGCACACAC
ATACAAATGCACATTTGCACAATCAGCAATCCTTTAAGTGTCAATACCTAAACAGAATTT
TTTTAATATTATTTAATTGATTTAAGTATGGAAAAAAGCAAAATTTAACAGTAGTTGTTT
GAGAATAGACATGAACAAAATTCGTATCATTTGTGTAGTTTTTAATTTATTTTAAATAAA
CTATGATGAAGAAATTAGTTTAAAATATACAATAGATTCATTTATTTCATTTCATTGGCA
CTTGCCGATTAAGAAAAAAAGCATTTGAGGCTAATAAAATGTCTTCAATAACGACTACTA
CCTCTTTAATAAGGCAAAATAAATATTTGCTTGAGAAGAAATTCGATATTGACGATGAAT
CAGTAAAAAAAATAATAAAAATTCAAATTGTTTGAAAAACTCTAGATCTGAAACTTCA

>g7339.t9 Gene=g7339 Length=193
MASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLK
GEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKN
LIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLN
VAPTSMHGRLDYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7339.t9 Gene3D G3DSA:3.40.50.720 - 1 162 0.0e+00
9 g7339.t9 Gene3D G3DSA:3.90.110.10 - 163 190 3.9e-06
2 g7339.t9 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 188 0.0e+00
3 g7339.t9 PRINTS PR00086 L-lactate dehydrogenase signature 23 47 0.0e+00
6 g7339.t9 PRINTS PR00086 L-lactate dehydrogenase signature 48 72 0.0e+00
5 g7339.t9 PRINTS PR00086 L-lactate dehydrogenase signature 135 155 0.0e+00
4 g7339.t9 PRINTS PR00086 L-lactate dehydrogenase signature 159 177 0.0e+00
1 g7339.t9 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 23 161 0.0e+00
8 g7339.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 161 0.0e+00
7 g7339.t9 SUPERFAMILY SSF56327 LDH C-terminal domain-like 162 188 3.4e-05

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