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.t1 TTS g7339.t1 23112244 23112244
chr_2 g7339 g7339.t1 isoform g7339.t1 23112813 23115372
chr_2 g7339 g7339.t1 exon g7339.t1.exon1 23112813 23113252
chr_2 g7339 g7339.t1 cds g7339.t1.CDS1 23112813 23113252
chr_2 g7339 g7339.t1 exon g7339.t1.exon2 23113398 23113670
chr_2 g7339 g7339.t1 cds g7339.t1.CDS2 23113398 23113670
chr_2 g7339 g7339.t1 exon g7339.t1.exon3 23113728 23114024
chr_2 g7339 g7339.t1 cds g7339.t1.CDS3 23113728 23114024
chr_2 g7339 g7339.t1 exon g7339.t1.exon4 23115369 23115372
chr_2 g7339 g7339.t1 cds g7339.t1.CDS4 23115369 23115372
chr_2 g7339 g7339.t1 TSS g7339.t1 23115448 23115448

Sequences

>g7339.t1 Gene=g7339 Length=1014
ATGGATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCAAGCAGTCGCTGAGGATGTG
GACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAGCTGTTGGAATGGCTGCC
GCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTCTCATCGATATGTTTGAG
AACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTAACTTTTTGAAGAATGCT
AAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCACGTTTAATCATTGTTACC
GCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCAGAC
ATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACACTTTTGATT
GTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGATTGCCTAAG
AACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTCTTGCTTGCT
CAACGTTTGAACGTTGCTCCAACATCTATGCACGGTTGGATTATCGGTGAACACGGTGAT
TCATCTGTTCCAGTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATTAAT
CCAAGTGCAGGTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTTGTA
AATGCTGCATATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTTTCA
TGTGCTGATATTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACA
TTGGTCAAGGGTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTT
AACGCCAACGGTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAA
TTACACGCATCTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAA

>g7339.t1 Gene=g7339 Length=337
MDPQMASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFE
NKLKGEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNAD
IMKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLA
QRLNVAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVV
NAAYEVIKLKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVL
NANGVVSIVKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7339.t1 CDD cd05293 LDH_1 23 334 0.0
13 g7339.t1 Gene3D G3DSA:3.40.50.720 - 5 167 1.1E-65
12 g7339.t1 Gene3D G3DSA:3.90.110.10 - 168 337 6.2E-71
4 g7339.t1 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 25 336 36.649033
3 g7339.t1 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 5 333 1.9E-147
14 g7339.t1 PIRSF PIRSF000102 Lac_mal_DH 22 337 1.4E-102
6 g7339.t1 PRINTS PR00086 L-lactate dehydrogenase signature 27 51 3.5E-55
9 g7339.t1 PRINTS PR00086 L-lactate dehydrogenase signature 52 76 3.5E-55
5 g7339.t1 PRINTS PR00086 L-lactate dehydrogenase signature 139 159 3.5E-55
8 g7339.t1 PRINTS PR00086 L-lactate dehydrogenase signature 163 181 3.5E-55
7 g7339.t1 PRINTS PR00086 L-lactate dehydrogenase signature 193 206 3.5E-55
2 g7339.t1 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 27 165 6.4E-45
1 g7339.t1 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 168 326 5.5E-22
16 g7339.t1 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 195 201 -
11 g7339.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 6 165 7.14E-66
10 g7339.t1 SUPERFAMILY SSF56327 LDH C-terminal domain-like 166 335 2.1E-57
17 g7339.t1 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 30 329 5.1E-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