General information for g10871.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L12.
Parent gene
- The parent gene g10871 is located on chr_1: 12375655..12376316 (- 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 | g10871 | g10871.t16 | TTS | g10871.t16 | 12375274 | 12375274 |
| chr_1 | g10871 | g10871.t16 | isoform | g10871.t16 | 12375365 | 12376314 |
| chr_1 | g10871 | g10871.t16 | exon | g10871.t16.exon1 | 12375365 | 12375570 |
| chr_1 | g10871 | g10871.t16 | cds | g10871.t16.CDS1 | 12375567 | 12375570 |
| chr_1 | g10871 | g10871.t16 | exon | g10871.t16.exon2 | 12375628 | 12375939 |
| chr_1 | g10871 | g10871.t16 | cds | g10871.t16.CDS2 | 12375628 | 12375923 |
| chr_1 | g10871 | g10871.t16 | exon | g10871.t16.exon3 | 12376291 | 12376314 |
| chr_1 | g10871 | g10871.t16 | TSS | g10871.t16 | 12376347 | 12376347 |
Sequences
>g10871.t16 Gene=g10871 Length=542
CATTGAATTAATTTTTATTAAAAATTAATAAAGCAACAAAATGCCACCAAAATTTGATCC
AACAGAAATCAAGCTCGTCTATTTGAGATGCGTTGGCGGCGAGGTTGGTGCAACATCCTC
ACTTGCTCCTAAAATCGGTCCACTCGGTTTATCACCAAAAAAAGTTGGTGACGATATTGC
AAAAGCCACTGGTGACTGGAAAGGACTCAAGATCACAGTTTGTCTCACCATTCAAAATCG
TCAGGCCACTATCTCAGTCGTTCCATCAGCTGCTTCAATGATCATTAAGGCATTGAAAGA
ACCACCAAGAGACAGAAAGAAGGTGAAAAACAGTAATTAAACACAGTGGTAACATCACCT
TTGATGAAGTTATTAGCATTGCTCGCGTAATGAGACCACGTTCAATGGCTAAGGACCTCT
CTGGCACAATCAAAGAAATTTTAGGTACAGCTCACAGTGTTGGATGCACAATTGATGGAC
GTGCACCACATGACATTATCGATGACGTTAATTCAGGAGCTATCGAATGTCCAGACTCTT
AA
>g10871.t16 Gene=g10871 Length=99
MPPKFDPTEIKLVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV
CLTIQNRQATISVVPSAASMIIKALKEPPRDRKKVKNSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10871.t16 | Gene3D | G3DSA:1.10.10.250 | - | 1 | 99 | 0 |
| 2 | g10871.t16 | PANTHER | PTHR11661:SF23 | - | 1 | 97 | 0 |
| 3 | g10871.t16 | PANTHER | PTHR11661 | 60S RIBOSOMAL PROTEIN L12 | 1 | 97 | 0 |
| 1 | g10871.t16 | Pfam | PF03946 | Ribosomal protein L11, N-terminal domain | 9 | 69 | 0 |
| 5 | g10871.t16 | SMART | SM00649 | rl11c | 13 | 99 | 0 |
| 4 | g10871.t16 | SUPERFAMILY | SSF54747 | Ribosomal L11/L12e N-terminal domain | 1 | 86 | 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.
