General information for g8647.t1
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.t1 | TTS | g8647.t1 | 32081150 | 32081150 |
| chr_2 | g8647 | g8647.t1 | isoform | g8647.t1 | 32081209 | 32081883 |
| chr_2 | g8647 | g8647.t1 | exon | g8647.t1.exon1 | 32081209 | 32081606 |
| chr_2 | g8647 | g8647.t1 | cds | g8647.t1.CDS1 | 32081209 | 32081606 |
| chr_2 | g8647 | g8647.t1 | exon | g8647.t1.exon2 | 32081659 | 32081782 |
| chr_2 | g8647 | g8647.t1 | cds | g8647.t1.CDS2 | 32081659 | 32081782 |
| chr_2 | g8647 | g8647.t1 | exon | g8647.t1.exon3 | 32081860 | 32081883 |
| chr_2 | g8647 | g8647.t1 | cds | g8647.t1.CDS3 | 32081860 | 32081883 |
| chr_2 | g8647 | g8647.t1 | TSS | g8647.t1 | 32081943 | 32081943 |
Sequences
>g8647.t1 Gene=g8647 Length=546
ATGTCATCGAGGCAACGTGTACAACAATGGGCAACTTTTGCTCGACAATGGCACATTTTT
GATTGTAAATGGCAAAATCCATATGAAAGCGCAATTGCAATAGTTAAACATCTTAAAGGT
CTTCATAAACCTATTTATCATCCTATGAATGATTGCGGAGATCATGTTATTTGTATAAAT
ACGAAAGAAATTGCCCTTCCTGGCAATGAGTGGACTAAAAGAGCATATTTTCATCATACT
GGTTATCCAGGAGGTGCATCTTGGACTCTCGCTTGGGAATTGCATTCAAAAGATCCGGTG
ATGATTATGAAAAAGGCAATCTACAGACGTCTTGGAAATAATCTTCAACGCCGGTACACA
ATGCAAAGACTACACTTGTTTCCTGATGATAATGTTCCTAAAGAATTGATAGAAAATGTC
ACAAGTCAAATAAGACAATTGAGAGTAGTTCCGCAAAGAATAGATCACATTGAAAAGGAT
GTCATCGATAATTATCCAAAAATCATGGATTACCCTACTGATTACTTACCTAAAACATTA
AAATAG
>g8647.t1 Gene=g8647 Length=181
MSSRQRVQQWATFARQWHIFDCKWQNPYESAIAIVKHLKGLHKPIYHPMNDCGDHVICIN
TKEIALPGNEWTKRAYFHHTGYPGGASWTLAWELHSKDPVMIMKKAIYRRLGNNLQRRYT
MQRLHLFPDDNVPKELIENVTSQIRQLRVVPQRIDHIEKDVIDNYPKIMDYPTDYLPKTL
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8647.t1 | CDD | cd00392 | Ribosomal_L13 | 17 | 130 | 0.00000 |
| 6 | g8647.t1 | Gene3D | G3DSA:3.90.1180.10 | - | 1 | 176 | 0.00000 |
| 4 | g8647.t1 | Hamap | MF_01366 | 50S ribosomal protein L13 [rplM]. | 17 | 138 | 19.57431 |
| 2 | g8647.t1 | PANTHER | PTHR11545:SF2 | 39S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL | 4 | 159 | 0.00000 |
| 3 | g8647.t1 | PANTHER | PTHR11545 | RIBOSOMAL PROTEIN L13 | 4 | 159 | 0.00000 |
| 7 | g8647.t1 | PIRSF | PIRSF002181 | RPL13p_RPL13Aa_RPL16e_RPL13o | 1 | 176 | 0.00000 |
| 1 | g8647.t1 | Pfam | PF00572 | Ribosomal protein L13 | 15 | 133 | 0.00000 |
| 5 | g8647.t1 | SUPERFAMILY | SSF52161 | Ribosomal protein L13 | 7 | 145 | 0.00000 |
| 9 | g8647.t1 | TIGRFAM | TIGR01066 | rplM_bact: ribosomal protein uL13 | 10 | 139 | 0.00000 |
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 transcript has been annotated with K02871 (large subunit ribosomal protein L13)
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.
