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.t20 TTS g7339.t20 23112244 23112244
chr_2 g7339 g7339.t20 isoform g7339.t20 23112472 23115372
chr_2 g7339 g7339.t20 exon g7339.t20.exon1 23112472 23113252
chr_2 g7339 g7339.t20 cds g7339.t20.CDS1 23112813 23113252
chr_2 g7339 g7339.t20 exon g7339.t20.exon2 23113398 23113486
chr_2 g7339 g7339.t20 cds g7339.t20.CDS2 23113398 23113404
chr_2 g7339 g7339.t20 exon g7339.t20.exon3 23113575 23113670
chr_2 g7339 g7339.t20 exon g7339.t20.exon4 23113728 23114024
chr_2 g7339 g7339.t20 exon g7339.t20.exon5 23115369 23115372
chr_2 g7339 g7339.t20 TSS g7339.t20 23115448 23115448

Sequences

>g7339.t20 Gene=g7339 Length=1267
ATGGATCCACAAATGGCAAGTCTTAAAGATCAAATGTTCCAAGCAGTCGCTGAGGATGTG
GACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAATCGGAGCTGTTGGAATGGCTGCC
GCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACGTTGCTCTCATCGATATGTTTGAG
AACAAATTGAAAGGAGAGATGATGGATTTGCAACACGGATCTAACTTTTTGAAGAATGCT
AAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTAATTCACGTTTAATCATTGTTACC
GCTGGTGTACGCCAGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGTAATGCAGAC
ATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAAGTTATTGGATCAGGAACTAATT
TGGACTCATCTCGTTTCCGTTTCTTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTA
TGCACGGTTGGATTATCGGTGAACACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCA
ATATTGCTGGTATCCGTTTGCGAGAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTG
AAAACTGGAATGAATGTCATAAGGATGTTGTAAATGCTGCATATGAAGTCATTAAATTGA
AGGGTTATACATCATGGGCCATTGGACTTTCATGTGCTGATATTGCATCAGCTATTTTCA
GAAACAGTAATTCAGTCAAAGCTGTCTCCACATTGGTCAAGGGTATTCATGGAATTGATT
CAGAAGTTTTCTTGTCACTTCCTTGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCA
AGCAAAAATTGAGCCCAGATGAGTTGGCTAAATTACACGCATCTGCCGCATTGATGGACG
AAGTTCAACGTGGCATCAAATTGTAAACTCTAAGACACAATACATAAAGAAAATAACAAC
TAAAAACAGTAATTGAATATTAAAAAATTAGCAAAATCATACTCGAATACAGAAGAAAGC
GACATTTTATTTGCACAGCTTCTTTATGAGCACGATTGCACTAAATATTCATCCCCTGCA
CACACATACAAATGCACATTTGCACAATCAGCAATCCTTTAAGTGTCAATACCTAAACAG
AATTTTTTTAATATTATTTAATTGATTTAAGTATGGAAAAAAGCAAAATTTAACAGTAGT
TGTTTGAGAATAGACATGAACAAAATTCGTATCATTTGTGTAGTTTTTAATTTATTTTAA
ATAAACT

>g7339.t20 Gene=g7339 Length=148
MHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVNAAYEVIKL
KGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLNANGVVSIV
KQKLSPDELAKLHASAALMDEVQRGIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7339.t20 Gene3D G3DSA:3.90.110.10 - 1 148 1.3E-60
2 g7339.t20 PANTHER PTHR43128:SF8 L-LACTATE DEHYDROGENASE A-LIKE 6B 2 148 2.1E-55
3 g7339.t20 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 2 148 2.1E-55
1 g7339.t20 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain 5 138 1.7E-15
5 g7339.t20 ProSitePatterns PS00064 L-lactate dehydrogenase active site. 6 12 -
4 g7339.t20 SUPERFAMILY SSF56327 LDH C-terminal domain-like 2 146 3.01E-47

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:0005975 carbohydrate metabolic process BP
GO:0004459 L-lactate dehydrogenase activity MF
GO:0003824 catalytic activity MF
GO:0055114 NA NA

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