General information for g13382.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13382 is located on chr_1: 29617560..29619496 (- 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_1 | g13382 | g13382.t1 | TTS | g13382.t1 | 29616883 | 29616883 |
| chr_1 | g13382 | g13382.t1 | isoform | g13382.t1 | 29616934 | 29617560 |
| chr_1 | g13382 | g13382.t1 | exon | g13382.t1.exon1 | 29616934 | 29617351 |
| chr_1 | g13382 | g13382.t1 | cds | g13382.t1.CDS1 | 29616934 | 29617351 |
| chr_1 | g13382 | g13382.t1 | exon | g13382.t1.exon2 | 29617406 | 29617560 |
| chr_1 | g13382 | g13382.t1 | cds | g13382.t1.CDS2 | 29617406 | 29617560 |
| chr_1 | g13382 | g13382.t1 | TSS | g13382.t1 | 29617572 | 29617572 |
Sequences
>g13382.t1 Gene=g13382 Length=573
ATGTTTTCGCTTAAGAAATTTGTAAAAGTTATTGAATTTCCGCTTTTAACCTTAAGTAGA
GGTACAGCTCGATATAATCCACGCCATAATAAGAACCCACTCTACAAGAAAGAGGACAAG
CAACAGATTGAGAAATACATTACATATTATCCTCGTAAAAATGCAACTGATTCAGAACAA
CAATTAGCAGAACCATCAAAACTCTTTAGAGTAAGCAGAATTAAGAAGCTGAAAAATCTT
CCTTATTGGGAGAAACGATTACTTCGAGATTTTTGCCTTTTTGATAGAGGTGCAGTTTCA
ATTGTGAAAAATATCCCTGAAAACAACCAGAGACTTTGGAAAATTAAACATTTGGTTAAA
ATTGAACCGATTAATTTTGTGAATGGTGAGCCAACAGAAAAAGATATCAATTACACCTTC
CTCAAAGAAAACGGTGATTGTATTGTAATTAAAAATATCGAATGTGTTGAGAAACGACTG
GATGCCACAGAGAAATTTGAAAAGAATGAGAAAAATCTTAATAGTGAAATATTAAAGAGA
GACTCACGTTTGAAATGGGTTAATAATTATTAA
>g13382.t1 Gene=g13382 Length=190
MFSLKKFVKVIEFPLLTLSRGTARYNPRHNKNPLYKKEDKQQIEKYITYYPRKNATDSEQ
QLAEPSKLFRVSRIKKLKNLPYWEKRLLRDFCLFDRGAVSIVKNIPENNQRLWKIKHLVK
IEPINFVNGEPTEKDINYTFLKENGDCIVIKNIECVEKRLDATEKFEKNEKNLNSEILKR
DSRLKWVNNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13382.t1 | CDD | cd00355 | Ribosomal_L30_like | 70 | 122 | 0.0001334 |
| 5 | g13382.t1 | Gene3D | G3DSA:3.30.1390.20 | - | 67 | 122 | 0.0000000 |
| 2 | g13382.t1 | PANTHER | PTHR15892:SF2 | 39S RIBOSOMAL PROTEIN L30, MITOCHONDRIAL | 35 | 167 | 0.0000000 |
| 3 | g13382.t1 | PANTHER | PTHR15892 | MITOCHONDRIAL RIBOSOMAL PROTEIN L30 | 35 | 167 | 0.0000000 |
| 1 | g13382.t1 | Pfam | PF00327 | Ribosomal protein L30p/L7e | 70 | 119 | 0.0000007 |
| 4 | g13382.t1 | SUPERFAMILY | SSF55129 | Ribosomal protein L30p/L7e | 67 | 124 | 0.0000000 |
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:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02907 (large subunit ribosomal protein L30)
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.
