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.t18 TTS g7339.t18 23112244 23112244
chr_2 g7339 g7339.t18 isoform g7339.t18 23112472 23114735
chr_2 g7339 g7339.t18 exon g7339.t18.exon1 23112472 23113252
chr_2 g7339 g7339.t18 cds g7339.t18.CDS1 23112813 23113252
chr_2 g7339 g7339.t18 exon g7339.t18.exon2 23113398 23113670
chr_2 g7339 g7339.t18 cds g7339.t18.CDS2 23113398 23113670
chr_2 g7339 g7339.t18 exon g7339.t18.exon3 23113728 23113982
chr_2 g7339 g7339.t18 cds g7339.t18.CDS3 23113728 23113917
chr_2 g7339 g7339.t18 exon g7339.t18.exon4 23114611 23114735
chr_2 g7339 g7339.t18 TSS g7339.t18 23115448 23115448

Sequences

>g7339.t18 Gene=g7339 Length=1434
TTTCAATACTTTCTACGTTAGGAGTATATTATCCATTTGATCGCTGTTGAGAAGTACAGA
CTGTTTGCAAAAATAGAGTGAATTTGTGAATTGTAGATTTTTTAAGTAAAATTTTAATCA
AATAATCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGG
AGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGC
TCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATC
TAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTC
ACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTT
AGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCC
TGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAA
ATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCG
TTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGGTTGGAT
TATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATTGCTGGTAT
CCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTGAAAACTGGAATGA
ATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAATTGAAGGGTTATACATC
ATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATTTTCAGAAACAGTAATTC
AGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATTGATTCAGAAGTTTTCTT
GTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAAAAATTGAG
CCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATGGACGAAGTTCAACGTGG
CATCAAATTGTAAACTCTAAGACACAATACATAAAGAAAATAACAACTAAAAACAGTAAT
TGAATATTAAAAAATTAGCAAAATCATACTCGAATACAGAAGAAAGCGACATTTTATTTG
CACAGCTTCTTTATGAGCACGATTGCACTAAATATTCATCCCCTGCACACACATACAAAT
GCACATTTGCACAATCAGCAATCCTTTAAGTGTCAATACCTAAACAGAATTTTTTTAATA
TTATTTAATTGATTTAAGTATGGAAAAAAGCAAAATTTAACAGTAGTTGTTTGAGAATAG
ACATGAACAAAATTCGTATCATTTGTGTAGTTTTTAATTTATTTTAAATAAACT

>g7339.t18 Gene=g7339 Length=300
MAAAFSILAQNVSSDVALIDMFENKLKGEMMDLQHGSNFLKNAKISASTDLSVSANSRLI
IVTAGVRQKEGESRLDLVQRNADIMKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSG
LPKNRVIGSGTNLDSSRFRFLLAQRLNVAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLR
EINPSAGLDNDSENWNECHKDVVNAAYEVIKLKGYTSWAIGLSCADIASAIFRNSNSVKA
VSTLVKGIHGIDSEVFLSLPCVLNANGVVSIVKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g7339.t18 CDD cd05293 LDH_1 1 297 0.0
11 g7339.t18 Gene3D G3DSA:3.40.50.720 - 1 130 5.3E-54
10 g7339.t18 Gene3D G3DSA:3.90.110.10 - 131 300 4.6E-71
3 g7339.t18 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 1 296 1.5E-136
17 g7339.t18 PIRSF PIRSF000102 Lac_mal_DH 1 300 8.9E-96
6 g7339.t18 PRINTS PR00086 L-lactate dehydrogenase signature 15 39 6.1E-42
4 g7339.t18 PRINTS PR00086 L-lactate dehydrogenase signature 102 122 6.1E-42
5 g7339.t18 PRINTS PR00086 L-lactate dehydrogenase signature 126 144 6.1E-42
7 g7339.t18 PRINTS PR00086 L-lactate dehydrogenase signature 156 169 6.1E-42
2 g7339.t18 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 2 128 5.1E-39
1 g7339.t18 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 131 289 4.1E-22
13 g7339.t18 Phobius SIGNAL_PEPTIDE Signal peptide region 1 14 -
14 g7339.t18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
15 g7339.t18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 9 -
16 g7339.t18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 10 14 -
12 g7339.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 15 300 -
19 g7339.t18 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 158 164 -
9 g7339.t18 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 128 2.67E-55
8 g7339.t18 SUPERFAMILY SSF56327 LDH C-terminal domain-like 129 298 1.57E-57
20 g7339.t18 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 2 292 3.6E-108

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

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