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.t28 TTS g7339.t28 23112244 23112244
chr_2 g7339 g7339.t28 isoform g7339.t28 23112813 23115372
chr_2 g7339 g7339.t28 exon g7339.t28.exon1 23112813 23113238
chr_2 g7339 g7339.t28 cds g7339.t28.CDS1 23113228 23113238
chr_2 g7339 g7339.t28 exon g7339.t28.exon2 23113398 23113670
chr_2 g7339 g7339.t28 cds g7339.t28.CDS2 23113398 23113670
chr_2 g7339 g7339.t28 exon g7339.t28.exon3 23113728 23114024
chr_2 g7339 g7339.t28 cds g7339.t28.CDS3 23113728 23114024
chr_2 g7339 g7339.t28 exon g7339.t28.exon4 23115369 23115372
chr_2 g7339 g7339.t28 cds g7339.t28.CDS4 23115369 23115372
chr_2 g7339 g7339.t28 TSS g7339.t28 23115448 23115448

Sequences

>g7339.t28 Gene=g7339 Length=1000
ATGGATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCAAGCAGTCGCTGAGGATGTG
GACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAGCTGTTGGAATGGCTGCC
GCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTCTCATCGATATGTTTGAG
AACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTAACTTTTTGAAGAATGCT
AAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCACGTTTAATCATTGTTACC
GCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCAGAC
ATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACACTTTTGATT
GTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGATTGCCTAAG
AACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTCTTGCTTGCT
CAACGTTTGAACGTTGCTCCAACATCTATGCACGGAACACGGTGATTCATCTGTTCCAGT
TTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTT
GGATAATGACAGTGAAAACTGGAATGAATGTCATAAGGATGTTGTAAATGCTGCATATGA
AGTCATTAAATTGAAGGGTTATACATCATGGGCCATTGGACTTTCATGTGCTGATATTGC
ATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTAT
TCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGT
TGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGC
CGCATTGATGGACGAAGTTCAACGTGGCATCAAATTGTAA

>g7339.t28 Gene=g7339 Length=194
MDPQMASLKDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFE
NKLKGEMMDLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNAD
IMKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLA
QRLNVAPTSMHGTR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7339.t28 Gene3D G3DSA:3.40.50.720 - 5 166 0.00e+00
9 g7339.t28 Gene3D G3DSA:3.90.110.10 - 167 193 3.60e-06
2 g7339.t28 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 5 192 0.00e+00
4 g7339.t28 PRINTS PR00086 L-lactate dehydrogenase signature 27 51 0.00e+00
6 g7339.t28 PRINTS PR00086 L-lactate dehydrogenase signature 52 76 0.00e+00
3 g7339.t28 PRINTS PR00086 L-lactate dehydrogenase signature 139 159 0.00e+00
5 g7339.t28 PRINTS PR00086 L-lactate dehydrogenase signature 163 181 0.00e+00
1 g7339.t28 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 27 165 0.00e+00
8 g7339.t28 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 6 165 0.00e+00
7 g7339.t28 SUPERFAMILY SSF56327 LDH C-terminal domain-like 166 192 4.01e-05

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: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