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.t2 TTS g7339.t2 23112244 23112244
chr_2 g7339 g7339.t2 isoform g7339.t2 23112813 23115372
chr_2 g7339 g7339.t2 exon g7339.t2.exon1 23112813 23113252
chr_2 g7339 g7339.t2 cds g7339.t2.CDS1 23112813 23113252
chr_2 g7339 g7339.t2 exon g7339.t2.exon2 23113398 23113670
chr_2 g7339 g7339.t2 cds g7339.t2.CDS2 23113398 23113670
chr_2 g7339 g7339.t2 exon g7339.t2.exon3 23113728 23114024
chr_2 g7339 g7339.t2 cds g7339.t2.CDS3 23113728 23114024
chr_2 g7339 g7339.t2 exon g7339.t2.exon4 23114533 23114559
chr_2 g7339 g7339.t2 cds g7339.t2.CDS4 23114533 23114559
chr_2 g7339 g7339.t2 exon g7339.t2.exon5 23115369 23115372
chr_2 g7339 g7339.t2 cds g7339.t2.CDS5 23115369 23115372
chr_2 g7339 g7339.t2 TSS g7339.t2 23115448 23115448

Sequences

>g7339.t2 Gene=g7339 Length=1041
ATGGATAAAGAAACATATTTTAAATTAAAAAATCCACAAATGGCAAGTCTTAAAGATCAA
ATGTTCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTC
GGAATCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGT
GACGTTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAA
CACGGATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCT
GCTAATTCACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGT
TTGGATTTAGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAA
TACAGTCCTGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTT
GCATGGAAATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGAC
TCATCTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCAC
GGTTGGATTATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATT
GCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTGAAAAC
TGGAATGAATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAATTGAAGGGT
TATACATCATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATTTTCAGAAAC
AGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATTGATTCAGAA
GTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAA
AAATTGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATGGACGAAGTT
CAACGTGGCATCAAATTGTAA

>g7339.t2 Gene=g7339 Length=346
MDKETYFKLKNPQMASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSS
DVALIDMFENKLKGEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESR
LDLVQRNADIMKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLD
SSRFRFLLAQRLNVAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSEN
WNECHKDVVNAAYEVIKLKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSE
VFLSLPCVLNANGVVSIVKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7339.t2 CDD cd05293 LDH_1 32 343 0.0
13 g7339.t2 Gene3D G3DSA:3.40.50.720 - 14 176 1.1E-65
12 g7339.t2 Gene3D G3DSA:3.90.110.10 - 177 346 6.6E-71
4 g7339.t2 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 34 345 36.649033
3 g7339.t2 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 14 342 2.1E-147
14 g7339.t2 PIRSF PIRSF000102 Lac_mal_DH 31 346 1.5E-102
7 g7339.t2 PRINTS PR00086 L-lactate dehydrogenase signature 36 60 3.9E-55
5 g7339.t2 PRINTS PR00086 L-lactate dehydrogenase signature 61 85 3.9E-55
8 g7339.t2 PRINTS PR00086 L-lactate dehydrogenase signature 148 168 3.9E-55
6 g7339.t2 PRINTS PR00086 L-lactate dehydrogenase signature 172 190 3.9E-55
9 g7339.t2 PRINTS PR00086 L-lactate dehydrogenase signature 202 215 3.9E-55
2 g7339.t2 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 36 174 6.8E-45
1 g7339.t2 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 177 335 5.9E-22
16 g7339.t2 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 204 210 -
11 g7339.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 15 174 7.61E-66
10 g7339.t2 SUPERFAMILY SSF56327 LDH C-terminal domain-like 175 344 2.23E-57
17 g7339.t2 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 39 338 5.6E-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