General information for g6396.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein mago nashi-like protein.
Parent gene
- The parent gene g6396 is located on chr_2: 16858307..16858812 (- 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 | g6396 | g6396.t1 | TTS | g6396.t1 | 16858118 | 16858118 |
| chr_2 | g6396 | g6396.t1 | isoform | g6396.t1 | 16858307 | 16858812 |
| chr_2 | g6396 | g6396.t1 | exon | g6396.t1.exon1 | 16858307 | 16858649 |
| chr_2 | g6396 | g6396.t1 | cds | g6396.t1.CDS1 | 16858307 | 16858649 |
| chr_2 | g6396 | g6396.t1 | exon | g6396.t1.exon2 | 16858706 | 16858812 |
| chr_2 | g6396 | g6396.t1 | cds | g6396.t1.CDS2 | 16858706 | 16858812 |
| chr_2 | g6396 | g6396.t1 | TSS | g6396.t1 | 16858912 | 16858912 |
Sequences
>g6396.t1 Gene=g6396 Length=450
ATGGCGTCTGGCACTCAAGACTTTTATTTAAGATATTATATAGGACATAAAGGCAAATTT
GGACATGAATTTCTTGAATTTGAATTTCGACCGGATGGAAAGTTGAGATATGCAAATAAC
TCAAATTATAAGAACGACACGATGATCAGGAAAGAAGCATACGTTCATACATCGGTTTTA
CAAGAGCTCAAGAGAATTATTCAAGATTCTGAAATTATGGCTGAAGATGACTCACTTTGG
CCGCCTGCAGATCGAGTTGGCAGACAAGAACTCGAGATTTTAATTGGTGATGAACACATT
TCATTCACAACATCAAAGATTGGTTCACTATTAGACGTAGATCAGTCAAAAGATCCAGAA
GGCTTGAGATTGTTTTATTATCTTGTTCAGGATCTGAAATGTTTAGTATTTTCACTCATC
GGATTGCATTTTAAAATTAAGCCAATTTAA
>g6396.t1 Gene=g6396 Length=149
MASGTQDFYLRYYIGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAYVHTSVL
QELKRIIQDSEIMAEDDSLWPPADRVGRQELEILIGDEHISFTTSKIGSLLDVDQSKDPE
GLRLFYYLVQDLKCLVFSLIGLHFKIKPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6396.t1 | CDD | cd11295 | Mago_nashi | 7 | 149 | 0 |
| 5 | g6396.t1 | Gene3D | G3DSA:3.30.1560.10 | Mago nashi protein | 4 | 149 | 0 |
| 2 | g6396.t1 | PANTHER | PTHR12638:SF1 | PROTEIN MAGO NASHI HOMOLOG 2 | 6 | 149 | 0 |
| 3 | g6396.t1 | PANTHER | PTHR12638 | PROTEIN MAGO NASHI HOMOLOG | 6 | 149 | 0 |
| 1 | g6396.t1 | Pfam | PF02792 | Mago nashi protein | 8 | 149 | 0 |
| 4 | g6396.t1 | SUPERFAMILY | SSF89817 | Mago nashi protein | 7 | 149 | 0 |
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:0005634 | nucleus | CC |
| GO:0035145 | exon-exon junction complex | CC |
| GO:0008380 | RNA splicing | BP |
KEGG
Orthology
- This transcript has been annotated with K12877 (protein mago nashi)
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.
