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.t14 TTS g7339.t14 23112244 23112244
chr_2 g7339 g7339.t14 isoform g7339.t14 23112250 23115372
chr_2 g7339 g7339.t14 exon g7339.t14.exon1 23112250 23113252
chr_2 g7339 g7339.t14 cds g7339.t14.CDS1 23112813 23113252
chr_2 g7339 g7339.t14 exon g7339.t14.exon2 23113398 23113670
chr_2 g7339 g7339.t14 cds g7339.t14.CDS2 23113398 23113670
chr_2 g7339 g7339.t14 exon g7339.t14.exon3 23113728 23114000
chr_2 g7339 g7339.t14 cds g7339.t14.CDS3 23113728 23114000
chr_2 g7339 g7339.t14 exon g7339.t14.exon4 23115369 23115372
chr_2 g7339 g7339.t14 cds g7339.t14.CDS4 23115369 23115372
chr_2 g7339 g7339.t14 TSS g7339.t14 23115448 23115448

Sequences

>g7339.t14 Gene=g7339 Length=1553
ATGGATCAAATGTTCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTC
ACCGTTGTCGGAATCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAAT
GTTTCAAGTGACGTTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATG
GATTTGCAACACGGATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTG
TCAGTCTCTGCTAATTCACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGC
GAGTCACGTTTGGATTTAGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAA
CTCGTCGAATACAGTCCTGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTG
ACATATGTTGCATGGAAATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACT
AATTTGGACTCATCTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACA
TCTATGCACGGTTGGATTATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGT
GTCAATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGAC
AGTGAAAACTGGAATGAATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAA
TTGAAGGGTTATACATCATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATT
TTCAGAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATT
GATTCAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATT
GTCAAGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATG
GACGAAGTTCAACGTGGCATCAAATTGTAAACTCTAAGACACAATACATAAAGAAAATAA
CAACTAAAAACAGTAATTGAATATTAAAAAATTAGCAAAATCATACTCGAATACAGAAGA
AAGCGACATTTTATTTGCACAGCTTCTTTATGAGCACGATTGCACTAAATATTCATCCCC
TGCACACACATACAAATGCACATTTGCACAATCAGCAATCCTTTAAGTGTCAATACCTAA
ACAGAATTTTTTTAATATTATTTAATTGATTTAAGTATGGAAAAAAGCAAAATTTAACAG
TAGTTGTTTGAGAATAGACATGAACAAAATTCGTATCATTTGTGTAGTTTTTAATTTATT
TTAAATAAACTATGATGAAGAAATTAGTTTAAAATATACAATAGATTCATTTATTTCATT
TCATTGGCACTTGCCGATTAAGAAAAAAAGCATTTGAGGCTAATAAAATGTCTTCAATAA
CGACTACTACCTCTTTAATAAGGCAAAATAAATATTTGCTTGAGAAGAAATTCGATATTG
ACGATGAATCAGTAAAAAAAATAATAAAAATTCAAATTGTTTGAAAAACTCTA

>g7339.t14 Gene=g7339 Length=329
MDQMFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLKGEMM
DLQHGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKNLIPK
LVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQRLNVAPT
SMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAYEVIK
LKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANGVVSI
VKQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g7339.t14 CDD cd05293 LDH_1 15 326 0.0
13 g7339.t14 Gene3D G3DSA:3.40.50.720 - 1 159 1.8E-64
12 g7339.t14 Gene3D G3DSA:3.90.110.10 - 160 329 5.8E-71
4 g7339.t14 Hamap MF_00488 L-lactate dehydrogenase [ldh]. 17 328 36.649033
3 g7339.t14 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 2 325 2.3E-146
17 g7339.t14 PIRSF PIRSF000102 Lac_mal_DH 14 329 1.3E-102
6 g7339.t14 PRINTS PR00086 L-lactate dehydrogenase signature 19 43 3.2E-55
9 g7339.t14 PRINTS PR00086 L-lactate dehydrogenase signature 44 68 3.2E-55
7 g7339.t14 PRINTS PR00086 L-lactate dehydrogenase signature 131 151 3.2E-55
5 g7339.t14 PRINTS PR00086 L-lactate dehydrogenase signature 155 173 3.2E-55
8 g7339.t14 PRINTS PR00086 L-lactate dehydrogenase signature 185 198 3.2E-55
2 g7339.t14 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 19 157 6.1E-45
1 g7339.t14 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 160 318 5.2E-22
14 g7339.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
16 g7339.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 38 -
15 g7339.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 39 329 -
20 g7339.t14 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 187 193 -
11 g7339.t14 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 157 8.55E-65
10 g7339.t14 SUPERFAMILY SSF56327 LDH C-terminal domain-like 158 327 1.97E-57
21 g7339.t14 TIGRFAM TIGR01771 L-LDH-NAD: L-lactate dehydrogenase 22 321 4.6E-113
19 g7339.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -

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