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 g6243 g6243.t1 TSS g6243.t1 15593118 15593118
chr_2 g6243 g6243.t1 isoform g6243.t1 15593340 15594391
chr_2 g6243 g6243.t1 exon g6243.t1.exon1 15593340 15593901
chr_2 g6243 g6243.t1 cds g6243.t1.CDS1 15593340 15593901
chr_2 g6243 g6243.t1 exon g6243.t1.exon2 15593952 15594391
chr_2 g6243 g6243.t1 cds g6243.t1.CDS2 15593952 15594391
chr_2 g6243 g6243.t1 TTS g6243.t1 NA NA

Sequences

>g6243.t1 Gene=g6243 Length=1002
ATGCCAATACTTAAAGAAGAACTCTTTCAAGAATTGCTTGACAATGATAATACTAAGTCT
TCAAATAAAATAACAATTGTCGGAATCGGAGCTGTAGGAATGGCTGCCGCTTTCTCTATT
CTTACACAAAATGTTTCAAGTGACGTTGCACTAGTCGATATTTTTGAAGACAAGCTAAAA
GGTGAATTGATGGATTTGCAGCATGGTTCAAATTTTCTTAAAAATGCAAAGATTTCTGCA
AGCAGTGATTTGGCAGTGTCAGCTGGATCTCGTTTAATCGTCGTTACCGCAGGCGTTCGT
CAGAAAGAAGGCGAATCGAGATTGAATCTCGTTCAGAGAAATGTTGATGTAATGAAAACA
ATAATTCCAAAATTGGTTGAATACAGCCCTGAAACGACACTTTTGATTGTCTCAAATCCT
TGCGATATTCTAACTTATGTTGCATGGAAGCTTTCAGGATTGCCCAAAAATCGTGTCATT
GGATCTGGAACAAATTTAGATTCTTCAAGATTTCGATTTTTGCTTGCACAGAGATTAAAA
ATTGCACCAACATCAATGCATGGTTGGATAATTGGGGAACATGGTGATTCATCTGTTCCT
GTTTGGTCTGGTGTCAATGTTGCTGGTGTTTGCTTGCGTGATTTCAATCCAAATATAGGA
AAAGAAGATGATTCAGAAAATTGGAATCAATGCCATGATGAAGTTGTCAATGCAGCTTAT
GAAGTTATCAAATTGAAAGGTTATACTTCTTGGGCTATTGGACTTTCAATTTCAGACATT
GCTTCAGCATTTCTATGCAATACAAATTCAGTTAAAGCTGTATCAACACTTGTTAAAGGA
ATTCATGGAATTGACAAAGAAGTTTTTCTATCTCTGCCTTGTGTTGTGAATTCAAATGGA
ATTTCTTCTATTGTTATACAGAAATTAAGTGCAGATGAATTAAAGAAACTTCAAGCTTCA
GCAAATTTGATTGATGAAATTCAAAAAGGAATTAAATTTTAA

>g6243.t1 Gene=g6243 Length=333
MPILKEELFQELLDNDNTKSSNKITIVGIGAVGMAAAFSILTQNVSSDVALVDIFEDKLK
GELMDLQHGSNFLKNAKISASSDLAVSAGSRLIVVTAGVRQKEGESRLNLVQRNVDVMKT
IIPKLVEYSPETTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLK
IAPTSMHGWIIGEHGDSSVPVWSGVNVAGVCLRDFNPNIGKEDDSENWNQCHDEVVNAAY
EVIKLKGYTSWAIGLSISDIASAFLCNTNSVKAVSTLVKGIHGIDKEVFLSLPCVVNSNG
ISSIVIQKLSADELKKLQASANLIDEIQKGIKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6243.t1 CDD cd05293 LDH_1 19 330 0.0
13 g6243.t1 Gene3D G3DSA:3.40.50.720 - 2 163 5.1E-65
12 g6243.t1 Gene3D G3DSA:3.90.110.10 - 164 333 2.3E-69
4 g6243.t1 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 21 332 36.038162
3 g6243.t1 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 3 329 1.2E-145
14 g6243.t1 PIRSF PIRSF000102 Lac_mal_DH 18 333 7.2E-99
5 g6243.t1 PRINTS PR00086 L-lactate dehydrogenase signature 23 47 5.7E-56
8 g6243.t1 PRINTS PR00086 L-lactate dehydrogenase signature 48 72 5.7E-56
7 g6243.t1 PRINTS PR00086 L-lactate dehydrogenase signature 135 155 5.7E-56
6 g6243.t1 PRINTS PR00086 L-lactate dehydrogenase signature 159 177 5.7E-56
9 g6243.t1 PRINTS PR00086 L-lactate dehydrogenase signature 189 202 5.7E-56
2 g6243.t1 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 23 161 1.9E-43
1 g6243.t1 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 164 333 1.1E-20
16 g6243.t1 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 191 197 -
11 g6243.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 4 161 1.74E-66
10 g6243.t1 SUPERFAMILY SSF56327 LDH C-terminal domain-like 162 331 2.23E-55
17 g6243.t1 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 26 325 3.9E-112

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. There were no conditions that were differentially expressed