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.t8 isoform g7339.t8 23112236 23114559
chr_2 g7339 g7339.t8 exon g7339.t8.exon1 23112236 23113252
chr_2 g7339 g7339.t8 TTS g7339.t8 23112244 23112244
chr_2 g7339 g7339.t8 cds g7339.t8.CDS1 23112813 23113252
chr_2 g7339 g7339.t8 exon g7339.t8.exon2 23113398 23113670
chr_2 g7339 g7339.t8 cds g7339.t8.CDS2 23113398 23113670
chr_2 g7339 g7339.t8 exon g7339.t8.exon3 23113728 23114024
chr_2 g7339 g7339.t8 cds g7339.t8.CDS3 23113728 23114016
chr_2 g7339 g7339.t8 exon g7339.t8.exon4 23114533 23114559
chr_2 g7339 g7339.t8 TSS g7339.t8 23115448 23115448

Sequences

>g7339.t8 Gene=g7339 Length=1614
ATAAAGAAACATATTTTAAATTAAAAAATCCACAAATGGCAAGTCTTAAAGATCAAATGT
TCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAA
TCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACG
TTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACG
GATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTA
ATTCACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGG
ATTTAGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACA
GTCCTGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCAT
GGAAATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCAT
CTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGGTT
GGATTATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATTGCTG
GTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTGAAAACTGGA
ATGAATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAATTGAAGGGTTATA
CATCATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATTTTCAGAAACAGTA
ATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATTGATTCAGAAGTTT
TCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAAAAAT
TGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATGGACGAAGTTCAAC
GTGGCATCAAATTGTAAACTCTAAGACACAATACATAAAGAAAATAACAACTAAAAACAG
TAATTGAATATTAAAAAATTAGCAAAATCATACTCGAATACAGAAGAAAGCGACATTTTA
TTTGCACAGCTTCTTTATGAGCACGATTGCACTAAATATTCATCCCCTGCACACACATAC
AAATGCACATTTGCACAATCAGCAATCCTTTAAGTGTCAATACCTAAACAGAATTTTTTT
AATATTATTTAATTGATTTAAGTATGGAAAAAAGCAAAATTTAACAGTAGTTGTTTGAGA
ATAGACATGAACAAAATTCGTATCATTTGTGTAGTTTTTAATTTATTTTAAATAAACTAT
GATGAAGAAATTAGTTTAAAATATACAATAGATTCATTTATTTCATTTCATTGGCACTTG
CCGATTAAGAAAAAAAGCATTTGAGGCTAATAAAATGTCTTCAATAACGACTACTACCTC
TTTAATAAGGCAAAATAAATATTTGCTTGAGAAGAAATTCGATATTGACGATGAATCAGT
AAAAAAAATAATAAAAATTCAAATTGTTTGAAAAACTCTAGATCTGAAACTTCA

>g7339.t8 Gene=g7339 Length=333
MASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLK
GEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKN
LIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLN
VAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAY
EVIKLKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANG
VVSIVKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7339.t8 CDD cd05293 LDH_1 19 330 0.0
13 g7339.t8 Gene3D G3DSA:3.40.50.720 - 1 163 1.0E-65
12 g7339.t8 Gene3D G3DSA:3.90.110.10 - 164 333 6.0E-71
4 g7339.t8 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 21 332 36.649033
3 g7339.t8 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 329 2.0E-147
14 g7339.t8 PIRSF PIRSF000102 Lac_mal_DH 18 333 1.3E-102
5 g7339.t8 PRINTS PR00086 L-lactate dehydrogenase signature 23 47 3.4E-55
8 g7339.t8 PRINTS PR00086 L-lactate dehydrogenase signature 48 72 3.4E-55
7 g7339.t8 PRINTS PR00086 L-lactate dehydrogenase signature 135 155 3.4E-55
6 g7339.t8 PRINTS PR00086 L-lactate dehydrogenase signature 159 177 3.4E-55
9 g7339.t8 PRINTS PR00086 L-lactate dehydrogenase signature 189 202 3.4E-55
2 g7339.t8 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 23 161 6.2E-45
1 g7339.t8 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 164 322 5.4E-22
16 g7339.t8 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 191 197 -
11 g7339.t8 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 161 6.95E-66
10 g7339.t8 SUPERFAMILY SSF56327 LDH C-terminal domain-like 162 331 2.1E-57
17 g7339.t8 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 26 325 4.8E-113

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