General information for g10918.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L6.
Parent gene
- The parent gene g10918 is located on chr_1: 12701957..12702601 (+ 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 | g10918 | g10918.t4 | isoform | g10918.t4 | 12701280 | 12702487 |
| chr_1 | g10918 | g10918.t4 | exon | g10918.t4.exon1 | 12701280 | 12701431 |
| chr_1 | g10918 | g10918.t4 | exon | g10918.t4.exon2 | 12701684 | 12702487 |
| chr_1 | g10918 | g10918.t4 | cds | g10918.t4.CDS1 | 12701696 | 12702487 |
| chr_1 | g10918 | g10918.t4 | TTS | g10918.t4 | 12702600 | 12702600 |
| chr_1 | g10918 | g10918.t4 | TSS | g10918.t4 | NA | NA |
Sequences
>g10918.t4 Gene=g10918 Length=956
ATGAGTAATTAAAGTGAAATATTGAGAACAGAAAATTTTTCAAGTAGCAGTCTCCATAAT
GTCGTTAAATTTTAAAAATATTTTTTGAACTTGAAGTAAGTTCAATTTTTGAACTTAATC
GTTCTTTTCTGCCTCGATTTTCAATTTCGCATTCGGAGTATATAATGGCACCAACAGCTA
CTAAAAAGAAGGCAACCAAACAGGTTGTGAACAAGAAAGTTAAAAACCGTGATTTGGGAA
ATGGCGTTCTCCGATGGTCACGATTCAAGCTCAAGCAAAAGAATTCGTATCGCTTGAAAA
ATGTTAAAGCAAAGAAACCAGTTAGGCCCAAGAAGCAACCAGCTAAAGTTGCAATCACAG
TTGTGAAGCAAATCGGCGGAGCTAAAAATGGTGGAACCCGCGTTGTTCGTGTTAAGAAGA
ATCGCGCTTCGTATGCTACAAAAGCAAAAGTCACACCACGTCCATCAAAGAATTATTTCG
CCAAACACACTCGTTACACTCGCCGTACATTGGTTCCAGGAAAAGTGTTGATTCTTTTGG
CTGGTCGTCATAAGGGCAAGCGTGTTGTATTGTTGAAAGTCTTGAAATCTGGTTTGCTTC
TTGTCAATGGTCCATTCTACTTGAATAGCTGTCCATTGAGACGTATCTCTCAGCGATATG
TAATCTGCACAAAGACTCGTGTCAACTTGAAAGGCGTCACCATTCCTGAACACATCAATG
ACACTTACTTCAAGCGAGCTGAGAAGAAAAAGCCACGTAAAACCGAAGGCGATATTTTTG
CTAAACAAGAAGAAAAGTATGCACCATCAGAGCAACGCAAGAAGGATCAAATCACAGTTG
ATAAACTTGTTCGTGAAGCAATTAAGAAGACACACCAAGGTTTGCTCGTTAGCAAATACC
TTAAATCAAACTTTGCATTGAGAAGCCATCAATATCCACATCGTATGCGCTTCTAA
>g10918.t4 Gene=g10918 Length=263
MAPTATKKKATKQVVNKKVKNRDLGNGVLRWSRFKLKQKNSYRLKNVKAKKPVRPKKQPA
KVAITVVKQIGGAKNGGTRVVRVKKNRASYATKAKVTPRPSKNYFAKHTRYTRRTLVPGK
VLILLAGRHKGKRVVLLKVLKSGLLLVNGPFYLNSCPLRRISQRYVICTKTRVNLKGVTI
PEHINDTYFKRAEKKKPRKTEGDIFAKQEEKYAPSEQRKKDQITVDKLVREAIKKTHQGL
LVSKYLKSNFALRSHQYPHRMRF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10918.t4 | CDD | cd13156 | KOW_RPL6 | 108 | 263 | 0 |
| 5 | g10918.t4 | Gene3D | G3DSA:2.30.30.30 | - | 115 | 196 | 0 |
| 2 | g10918.t4 | PANTHER | PTHR10715 | 60S RIBOSOMAL PROTEIN L6 | 17 | 263 | 0 |
| 3 | g10918.t4 | PANTHER | PTHR10715:SF0 | 60S RIBOSOMAL PROTEIN L6 | 17 | 263 | 0 |
| 1 | g10918.t4 | Pfam | PF01159 | Ribosomal protein L6e | 153 | 263 | 0 |
| 4 | g10918.t4 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 113 | 208 | 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 transcript has been annotated with K02934 (large subunit ribosomal protein L6e)
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.
