General information for g5102.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L18, mitochondrial.
Parent gene
- The parent gene g5102 is located on chr_2: 6879006..6880878 (- 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 | g5102 | g5102.t1 | TTS | g5102.t1 | 6878294 | 6878294 |
| chr_2 | g5102 | g5102.t1 | isoform | g5102.t1 | 6878385 | 6879006 |
| chr_2 | g5102 | g5102.t1 | exon | g5102.t1.exon1 | 6878385 | 6878754 |
| chr_2 | g5102 | g5102.t1 | cds | g5102.t1.CDS1 | 6878385 | 6878754 |
| chr_2 | g5102 | g5102.t1 | exon | g5102.t1.exon2 | 6878813 | 6879006 |
| chr_2 | g5102 | g5102.t1 | cds | g5102.t1.CDS2 | 6878813 | 6879006 |
| chr_2 | g5102 | g5102.t1 | TSS | g5102.t1 | 6879063 | 6879063 |
Sequences
>g5102.t1 Gene=g5102 Length=564
ATGGTTAGACCAAGAGTATTTCCTCATAATAAACAAATTTTAAAACGAATTAAAAACACT
GTAAGTCCAGTTGAAAGTGAAAAATATATTATCAACCGAAATCCAAGGAATTTAGAATTT
CTTAGAATTGCTGCAAAACCAAAAGGCTATCATTTAGATACACCATTCTCAAAAGAATGC
AATTATTGGCATAAATTAGTTGTGACACCTTCAGCTAAATTTGTAACCGCTCAGTTAGTG
CATCATCAAAATGGTCCTGTAATTGAAGCATCAACAAAAGAATGGGCTATAAAAAAACAA
CTTTATAAAACTTCAGACCTATCTGCTTATACGAATCTTGCAAAAGTATTTGCACAACGA
TGTCTCGAGAGTGGAATTCATGAGATGTCAACTAAACCATATTCAGGAACAAAAATTGAA
AAGTTTATGGAAATATTGCAAGAAAATGGCTTAAACTTAAATGAATCGCCTGAAATAAAT
AGTAAACCAGATCCTAATATCAACAGATATCAAGGCAGAAAAATGACACCAATTGACTGG
AAAGATATTGTTGAACATCACTAA
>g5102.t1 Gene=g5102 Length=187
MVRPRVFPHNKQILKRIKNTVSPVESEKYIINRNPRNLEFLRIAAKPKGYHLDTPFSKEC
NYWHKLVVTPSAKFVTAQLVHHQNGPVIEASTKEWAIKKQLYKTSDLSAYTNLAKVFAQR
CLESGIHEMSTKPYSGTKIEKFMEILQENGLNLNESPEINSKPDPNINRYQGRKMTPIDW
KDIVEHH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5102.t1 | CDD | cd00432 | Ribosomal_L18_L5e | 61 | 151 | 0 |
| 4 | g5102.t1 | Gene3D | G3DSA:3.30.420.80 | - | 23 | 161 | 0 |
| 1 | g5102.t1 | PANTHER | PTHR12899:SF3 | 39S RIBOSOMAL PROTEIN L18, MITOCHONDRIAL | 19 | 153 | 0 |
| 2 | g5102.t1 | PANTHER | PTHR12899 | 39S RIBOSOMAL PROTEIN L18, MITOCHONDRIAL | 19 | 153 | 0 |
| 3 | g5102.t1 | SUPERFAMILY | SSF53137 | Translational machinery components | 65 | 151 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5102/g5102.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5102.t1.fa.iupred3.txt does not exist
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 K02881 (large subunit ribosomal protein L18)
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.
