General information for g5988.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ragulator complex protein LAMTOR3-like protein.
Parent gene
- The parent gene g5988 is located on chr_2: 13174094..13174635 (+ 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 | g5988 | g5988.t1 | TSS | g5988.t1 | 13174001 | 13174001 |
| chr_2 | g5988 | g5988.t1 | isoform | g5988.t1 | 13174094 | 13174635 |
| chr_2 | g5988 | g5988.t1 | exon | g5988.t1.exon1 | 13174094 | 13174137 |
| chr_2 | g5988 | g5988.t1 | cds | g5988.t1.CDS1 | 13174094 | 13174137 |
| chr_2 | g5988 | g5988.t1 | exon | g5988.t1.exon2 | 13174242 | 13174437 |
| chr_2 | g5988 | g5988.t1 | cds | g5988.t1.CDS2 | 13174242 | 13174437 |
| chr_2 | g5988 | g5988.t1 | exon | g5988.t1.exon3 | 13174492 | 13174635 |
| chr_2 | g5988 | g5988.t1 | cds | g5988.t1.CDS3 | 13174492 | 13174635 |
| chr_2 | g5988 | g5988.t1 | TTS | g5988.t1 | 13174662 | 13174662 |
Sequences
>g5988.t1 Gene=g5988 Length=384
ATGAGTGATGAAGTGAAAAGATTTTTTACATCTATACTAAATAAAGTAAACGGATTAAAT
TGCGTTTTGATTAGTGACAGAGATGGTGTGCCATTATTAAAACTATCTAAAGACAACAAG
TTTCCTGAGCTTGGAACAAAACAATCATTTCTTTCAACTTTCTCAATAGCCACAGTTCAA
TCTTCAAAGATGATGCTGGGAAAAAATAAGCAGATTATACTTTGTTATAAGTCATCGACC
ATTGTACAATTGAATAAGGCACCATTAATCATTACTTTTGTTGGAACAGAATCAACAAAT
ATTGGACACTTGTTAACATATGCAAATGAAGTTGATAAATATTTGGAGGAATATAAGATT
GTATTAGAACAAAACCTAATCTGA
>g5988.t1 Gene=g5988 Length=127
MSDEVKRFFTSILNKVNGLNCVLISDRDGVPLLKLSKDNKFPELGTKQSFLSTFSIATVQ
SSKMMLGKNKQIILCYKSSTIVQLNKAPLIITFVGTESTNIGHLLTYANEVDKYLEEYKI
VLEQNLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5988.t1 | Gene3D | G3DSA:3.30.450.30 | Dynein light chain 2a | 1 | 124 | 0 |
| 2 | g5988.t1 | PANTHER | PTHR13378 | REGULATOR COMPLEX PROTEIN LAMTOR3 | 3 | 123 | 0 |
| 1 | g5988.t1 | Pfam | PF08923 | Mitogen-activated protein kinase kinase 1 interacting | 3 | 119 | 0 |
| 4 | g5988.t1 | SMART | SM01278 | MAPKK1_Int_3 | 3 | 122 | 0 |
| 3 | g5988.t1 | SUPERFAMILY | SSF103196 | Roadblock/LC7 domain | 3 | 123 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5988/g5988.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5988.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0032006 | regulation of TOR signaling | BP |
KEGG
Orthology
- This transcript has been annotated with K04370 (ragulator complex protein LAMTOR3)
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.
