General information for g8647.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L13, mitochondrial.
Parent gene
- The parent gene g8647 is located on chr_2: 32081209..32081883 (- 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 | g8647 | g8647.t3 | TTS | g8647.t3 | 32081150 | 32081150 |
| chr_2 | g8647 | g8647.t3 | isoform | g8647.t3 | 32081209 | 32081883 |
| chr_2 | g8647 | g8647.t3 | exon | g8647.t3.exon1 | 32081209 | 32081606 |
| chr_2 | g8647 | g8647.t3 | cds | g8647.t3.CDS1 | 32081209 | 32081606 |
| chr_2 | g8647 | g8647.t3 | exon | g8647.t3.exon2 | 32081659 | 32081717 |
| chr_2 | g8647 | g8647.t3 | cds | g8647.t3.CDS2 | 32081659 | 32081662 |
| chr_2 | g8647 | g8647.t3 | exon | g8647.t3.exon3 | 32081860 | 32081883 |
| chr_2 | g8647 | g8647.t3 | TSS | g8647.t3 | 32081943 | 32081943 |
Sequences
>g8647.t3 Gene=g8647 Length=481
ATGTCATCGAGGCAACGTGTACAACGCAATTGCAATAGTTAAACATCTTAAAGGTCTTCA
TAAACCTATTTATCATCCTATGAATGATTGCGGAGATCATGTTATTTGTATAAATACGAA
AGAAATTGCCCTTCCTGGCAATGAGTGGACTAAAAGAGCATATTTTCATCATACTGGTTA
TCCAGGAGGTGCATCTTGGACTCTCGCTTGGGAATTGCATTCAAAAGATCCGGTGATGAT
TATGAAAAAGGCAATCTACAGACGTCTTGGAAATAATCTTCAACGCCGGTACACAATGCA
AAGACTACACTTGTTTCCTGATGATAATGTTCCTAAAGAATTGATAGAAAATGTCACAAG
TCAAATAAGACAATTGAGAGTAGTTCCGCAAAGAATAGATCACATTGAAAAGGATGTCAT
CGATAATTATCCAAAAATCATGGATTACCCTACTGATTACTTACCTAAAACATTAAAATA
G
>g8647.t3 Gene=g8647 Length=133
MNDCGDHVICINTKEIALPGNEWTKRAYFHHTGYPGGASWTLAWELHSKDPVMIMKKAIY
RRLGNNLQRRYTMQRLHLFPDDNVPKELIENVTSQIRQLRVVPQRIDHIEKDVIDNYPKI
MDYPTDYLPKTLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8647.t3 | CDD | cd00392 | Ribosomal_L13 | 3 | 82 | 0 |
| 5 | g8647.t3 | Gene3D | G3DSA:3.90.1180.10 | - | 1 | 128 | 0 |
| 2 | g8647.t3 | PANTHER | PTHR11545:SF2 | 39S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL | 2 | 111 | 0 |
| 3 | g8647.t3 | PANTHER | PTHR11545 | RIBOSOMAL PROTEIN L13 | 2 | 111 | 0 |
| 6 | g8647.t3 | PIRSF | PIRSF002181 | RPL13p_RPL13Aa_RPL16e_RPL13o | 1 | 128 | 0 |
| 1 | g8647.t3 | Pfam | PF00572 | Ribosomal protein L13 | 2 | 85 | 0 |
| 4 | g8647.t3 | SUPERFAMILY | SSF52161 | Ribosomal protein L13 | 2 | 97 | 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:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | 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.
