General information for g7339.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as L-lactate dehydrogenase.
Parent gene
- The parent gene g7339 is located on chr_2: 23114611..23115372 (- strand)
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.t11 | isoform | g7339.t11 | 23112236 | 23114735 |
| chr_2 | g7339 | g7339.t11 | exon | g7339.t11.exon1 | 23112236 | 23113252 |
| chr_2 | g7339 | g7339.t11 | TTS | g7339.t11 | 23112244 | 23112244 |
| chr_2 | g7339 | g7339.t11 | cds | g7339.t11.CDS1 | 23112813 | 23113252 |
| chr_2 | g7339 | g7339.t11 | exon | g7339.t11.exon2 | 23113398 | 23113656 |
| chr_2 | g7339 | g7339.t11 | cds | g7339.t11.CDS2 | 23113398 | 23113608 |
| chr_2 | g7339 | g7339.t11 | exon | g7339.t11.exon3 | 23113728 | 23114024 |
| chr_2 | g7339 | g7339.t11 | exon | g7339.t11.exon4 | 23114529 | 23114735 |
| chr_2 | g7339 | g7339.t11 | TSS | g7339.t11 | 23115448 | 23115448 |
Sequences
>g7339.t11 Gene=g7339 Length=1780
TTTCAATACTTTCTACGTTAGGAGTATATTATCCATTTGATCGCTGTTGAGAAGTACAGA
CTGTTTGCAAAAATAGAGTGAATTTGTGAATTGTAGATTTTTTAAGTAAAATTTTAATCA
AATAAAATTAATTTTCTAAGCTATTTATCGAGCACTGATTTACTTTTACTGATTAGATAA
AGAAACATATTTTAAATTAAAAAGTAAATCCACAAATGGCAAGTCTTAAAGATCAAATGT
TCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCGTTGTCGGAA
TCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTTCAAGTGACG
TTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATTTGCAACACG
GATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAGTCTCTGCTA
ATTCACGTTTAATCATTGTTACCGAAGGAAGGCGAGTCACGTTTGGATTTAGTTCAACGT
AATGCAGACATCATGAAGAATTTGATTCCAAAACTCGTCGAATACAGTCCTGATACTACA
CTTTTGATTGTCTCAAATCCATGTGATATCTTGACATATGTTGCATGGAAATTATCAGGA
TTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATTTGGACTCATCTCGTTTCCGTTTC
TTGCTTGCTCAACGTTTGAACGTTGCTCCAACATCTATGCACGGTTGGATTATCGGTGAA
CACGGTGATTCATCTGTTCCAGTTTGGTCTGGTGTCAATATTGCTGGTATCCGTTTGCGA
GAAATTAATCCAAGTGCAGGTTTGGATAATGACAGTGAAAACTGGAATGAATGTCATAAG
GATGTTGTAAATGCTGCATATGAAGTCATTAAATTGAAGGGTTATACATCATGGGCCATT
GGACTTTCATGTGCTGATATTGCATCAGCTATTTTCAGAAACAGTAATTCAGTCAAAGCT
GTCTCCACATTGGTCAAGGGTATTCATGGAATTGATTCAGAAGTTTTCTTGTCACTTCCT
TGCGTTCTTAACGCCAACGGTGTTGTTTCGATTGTCAAGCAAAAATTGAGCCCAGATGAG
TTGGCTAAATTACACGCATCTGCCGCATTGATGGACGAAGTTCAACGTGGCATCAAATTG
TAAACTCTAAGACACAATACATAAAGAAAATAACAACTAAAAACAGTAATTGAATATTAA
AAAATTAGCAAAATCATACTCGAATACAGAAGAAAGCGACATTTTATTTGCACAGCTTCT
TTATGAGCACGATTGCACTAAATATTCATCCCCTGCACACACATACAAATGCACATTTGC
ACAATCAGCAATCCTTTAAGTGTCAATACCTAAACAGAATTTTTTTAATATTATTTAATT
GATTTAAGTATGGAAAAAAGCAAAATTTAACAGTAGTTGTTTGAGAATAGACATGAACAA
AATTCGTATCATTTGTGTAGTTTTTAATTTATTTTAAATAAACTATGATGAAGAAATTAG
TTTAAAATATACAATAGATTCATTTATTTCATTTCATTGGCACTTGCCGATTAAGAAAAA
AAGCATTTGAGGCTAATAAAATGTCTTCAATAACGACTACTACCTCTTTAATAAGGCAAA
ATAAATATTTGCTTGAGAAGAAATTCGATATTGACGATGAATCAGTAAAAAAAATAATAA
AAATTCAAATTGTTTGAAAAACTCTAGATCTGAAACTTCA
>g7339.t11 Gene=g7339 Length=216
MKNLIPKLVEYSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQ
RLNVAPTSMHGWIIGEHGDSSVPVWSGVNIAGIRLREINPSAGLDNDSENWNECHKDVVN
AAYEVIKLKGYTSWAIGLSCADIASAIFRNSNSVKAVSTLVKGIHGIDSEVFLSLPCVLN
ANGVVSIVKQKLSPDELAKLHASAALMDEVQRGIKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g7339.t11 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 46 | 2.6E-18 |
| 10 | g7339.t11 | Gene3D | G3DSA:3.90.110.10 | - | 47 | 216 | 1.7E-71 |
| 3 | g7339.t11 | PANTHER | PTHR43128 | L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) | 1 | 212 | 7.3E-97 |
| 5 | g7339.t11 | PRINTS | PR00086 | L-lactate dehydrogenase signature | 18 | 38 | 7.9E-29 |
| 6 | g7339.t11 | PRINTS | PR00086 | L-lactate dehydrogenase signature | 42 | 60 | 7.9E-29 |
| 4 | g7339.t11 | PRINTS | PR00086 | L-lactate dehydrogenase signature | 72 | 85 | 7.9E-29 |
| 2 | g7339.t11 | Pfam | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 1 | 44 | 4.0E-10 |
| 1 | g7339.t11 | Pfam | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 47 | 205 | 1.5E-22 |
| 9 | g7339.t11 | ProSitePatterns | PS00064 | L-lactate dehydrogenase active site. | 74 | 80 | - |
| 8 | g7339.t11 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 44 | 9.13E-17 |
| 7 | g7339.t11 | 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. There were no conditions that were differentially expressed