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.t27 TTS g7339.t27 23112244 23112244
chr_2 g7339 g7339.t27 isoform g7339.t27 23112813 23114735
chr_2 g7339 g7339.t27 exon g7339.t27.exon1 23112813 23113252
chr_2 g7339 g7339.t27 cds g7339.t27.CDS1 23112813 23113252
chr_2 g7339 g7339.t27 exon g7339.t27.exon2 23113398 23113670
chr_2 g7339 g7339.t27 cds g7339.t27.CDS2 23113398 23113670
chr_2 g7339 g7339.t27 exon g7339.t27.exon3 23113728 23114008
chr_2 g7339 g7339.t27 cds g7339.t27.CDS3 23113728 23113995
chr_2 g7339 g7339.t27 exon g7339.t27.exon4 23114533 23114735
chr_2 g7339 g7339.t27 TSS g7339.t27 23114705 23114705

Sequences

>g7339.t27 Gene=g7339 Length=1197
TTTCAATACTTTCTACGTTAGGAGTATATTATCCATTTGATCGCTGTTGAGAAGTACAGA
CTGTTTGCAAAAATAGAGTGAATTTGTGAATTGTAGATTTTTTAAGTAAAATTTTAATCA
AATAAAATTAATTTTCTAAGCTATTTATCGAGCACTGATTTACTTTTACTGATTAGATAA
AGAAACATATTTTAAATTAAAAATCTTAAAGATCAAATGTTCCAAGCAGTCGCTGAGGAT
GTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAGCTGTTGGAATGGCT
GCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTCTCATCGATATGTTT
GAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTAACTTTTTGAAGAAT
GCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCACGTTTAATCATTGTT
ACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCA
GACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACACTTTTG
ATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGATTGCCT
AAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTCTTGCTT
GCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGGTTGGATTATCGGTGAACACGGT
GATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATT
AATCCAAGTGCAGGTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTT
GTAAATGCTGCATATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTT
TCATGTGCTGATATTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCC
ACATTGGTCAAGGGTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTT
CTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCT
AAATTACACGCATCTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAA

>g7339.t27 Gene=g7339 Length=326
MFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLKGEMMDLQ
HGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKNLIPKLVE
YSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLNVAPTSMH
GWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAYEVIKLKG
YTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANGVVSIVKQ
KLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7339.t27 CDD cd05293 LDH_1 12 323 0.0
13 g7339.t27 Gene3D G3DSA:3.40.50.720 - 1 156 7.9E-64
12 g7339.t27 Gene3D G3DSA:3.90.110.10 - 157 326 5.7E-71
4 g7339.t27 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 14 325 36.649033
3 g7339.t27 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 2 322 9.5E-146
14 g7339.t27 PIRSF PIRSF000102 Lac_mal_DH 11 326 1.2E-102
6 g7339.t27 PRINTS PR00086 L-lactate dehydrogenase signature 16 40 3.1E-55
8 g7339.t27 PRINTS PR00086 L-lactate dehydrogenase signature 41 65 3.1E-55
5 g7339.t27 PRINTS PR00086 L-lactate dehydrogenase signature 128 148 3.1E-55
7 g7339.t27 PRINTS PR00086 L-lactate dehydrogenase signature 152 170 3.1E-55
9 g7339.t27 PRINTS PR00086 L-lactate dehydrogenase signature 182 195 3.1E-55
2 g7339.t27 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 16 154 5.9E-45
1 g7339.t27 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 157 315 5.1E-22
17 g7339.t27 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 184 190 -
11 g7339.t27 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 154 2.63E-64
10 g7339.t27 SUPERFAMILY SSF56327 LDH C-terminal domain-like 155 324 1.97E-57
18 g7339.t27 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 19 318 4.5E-113
16 g7339.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 17 39 -

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

Pathway

  • This transcript belongs to the following pathways

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