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.t5 isoform g7339.t5 23112236 23113661
chr_2 g7339 g7339.t5 exon g7339.t5.exon1 23112236 23113252
chr_2 g7339 g7339.t5 TTS g7339.t5 23112244 23112244
chr_2 g7339 g7339.t5 cds g7339.t5.CDS1 23112813 23113252
chr_2 g7339 g7339.t5 exon g7339.t5.exon2 23113398 23113661
chr_2 g7339 g7339.t5 cds g7339.t5.CDS2 23113398 23113608
chr_2 g7339 g7339.t5 TSS g7339.t5 NA NA

Sequences

>g7339.t5 Gene=g7339 Length=1281
GCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCAGACATCATGAAGA
ATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACACTTTTGATTGTCTCAAATC
CATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGATTGCCTAAGAACAGAGTTA
TTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGA
ACGTTGCTCCAACATCTATGCACGGTTGGATTATCGGTGAACACGGTGATTCATCTGTTC
CAGTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAG
GTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTTGTAAATGCTGCAT
ATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTTTCATGTGCTGATA
TTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGG
GTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACG
GTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACACGCAT
CTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAAACTCTAAGACACAATA
CATAAAGAAAATAACAACTAAAAACAGTAATTGAATATTAAAAAATTAGCAAAATCATAC
TCGAATACAGAAGAAAGCGACATTTTATTTGCACAGCTTCTTTATGAGCACGATTGCACT
AAATATTCATCCCCTGCACACACATACAAATGCACATTTGCACAATCAGCAATCCTTTAA
GTGTCAATACCTAAACAGAATTTTTTTAATATTATTTAATTGATTTAAGTATGGAAAAAA
GCAAAATTTAACAGTAGTTGTTTGAGAATAGACATGAACAAAATTCGTATCATTTGTGTA
GTTTTTAATTTATTTTAAATAAACTATGATGAAGAAATTAGTTTAAAATATACAATAGAT
TCATTTATTTCATTTCATTGGCACTTGCCGATTAAGAAAAAAAGCATTTGAGGCTAATAA
AATGTCTTCAATAACGACTACTACCTCTTTAATAAGGCAAAATAAATATTTGCTTGAGAA
GAAATTCGATATTGACGATGAATCAGTAAAAAAAATAATAAAAATTCAAATTGTTTGAAA
AACTCTAGATCTGAAACTTCA

>g7339.t5 Gene=g7339 Length=216
MKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQ
RLNVAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVN
AAYEVIKLKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLN
ANGVVSIVKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7339.t5 Gene3D G3DSA:3.40.50.720 - 1 46 2.6E-18
10 g7339.t5 Gene3D G3DSA:3.90.110.10 - 47 216 1.7E-71
3 g7339.t5 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 212 7.3E-97
5 g7339.t5 PRINTS PR00086 L-lactate dehydrogenase signature 18 38 7.9E-29
6 g7339.t5 PRINTS PR00086 L-lactate dehydrogenase signature 42 60 7.9E-29
4 g7339.t5 PRINTS PR00086 L-lactate dehydrogenase signature 72 85 7.9E-29
2 g7339.t5 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 1 44 4.0E-10
1 g7339.t5 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 47 205 1.5E-22
9 g7339.t5 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 74 80 -
8 g7339.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 44 9.13E-17
7 g7339.t5 SUPERFAMILY SSF56327 LDH C-terminal domain-like 45 214 5.77E-58

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:0019752 carboxylic acid metabolic process BP
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0005975 carbohydrate metabolic process BP
GO:0004459 L-lactate dehydrogenase activity MF
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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