General information for g10569.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L27a.
Parent gene
- The parent gene g10569 is located on chr_1: 10486175..10493295 (- 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 | g10569 | g10569.t23 | TTS | g10569.t23 | 10486114 | 10486114 |
| chr_1 | g10569 | g10569.t23 | isoform | g10569.t23 | 10486175 | 10487149 |
| chr_1 | g10569 | g10569.t23 | exon | g10569.t23.exon1 | 10486175 | 10486303 |
| chr_1 | g10569 | g10569.t23 | cds | g10569.t23.CDS1 | 10486175 | 10486303 |
| chr_1 | g10569 | g10569.t23 | exon | g10569.t23.exon2 | 10486505 | 10486742 |
| chr_1 | g10569 | g10569.t23 | cds | g10569.t23.CDS2 | 10486505 | 10486742 |
| chr_1 | g10569 | g10569.t23 | exon | g10569.t23.exon3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t23 | cds | g10569.t23.CDS3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t23 | exon | g10569.t23.exon4 | 10487140 | 10487149 |
| chr_1 | g10569 | g10569.t23 | cds | g10569.t23.CDS4 | 10487140 | 10487149 |
| chr_1 | g10569 | g10569.t23 | TSS | g10569.t23 | 10487169 | 10487169 |
Sequences
>g10569.t23 Gene=g10569 Length=444
ATGGTTGTGAAGTCTTATGAAAAGAAAGAAGACCCGAAAGCTTCGTGGTCATGTCAGCCA
TGGTCATGGTCGTATCGAAAACATCCTGGTGGTCGCGGTAATGCTGGTGGTATGCACCAT
CACAGAATAAATTACGATAAATACCATCCTGGATATTTTGGAAAAGTTGGTATGCGCAAC
TTCCATTTGAATCGTAATCACAGCTTCTGTCCAACAATTAATCTCGATAAACTTTGGTCA
TTAATTGGACAAGAAAATTACGAGAAAGCAAAGAAAGAAGGCGATAAAGTTCCAGTTATC
GATATCGTACAATTTGGATACTTTAAGCTACTTGGACATGGACATTTGCCAAAACAACCA
ATAATTGTGAAAGCAAAATATTTTTCACAGAAAGCAGAAAAGAAAATCAAGGCTGCTGGT
GGCGCATGCATCCTAAGAGCATAA
>g10569.t23 Gene=g10569 Length=147
MVVKSYEKKEDPKASWSCQPWSWSYRKHPGGRGNAGGMHHHRINYDKYHPGYFGKVGMRN
FHLNRNHSFCPTINLDKLWSLIGQENYEKAKKEGDKVPVIDIVQFGYFKLLGHGHLPKQP
IIVKAKYFSQKAEKKIKAAGGACILRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10569.t23 | Gene3D | G3DSA:3.100.10.10 | - | 58 | 147 | 6.1E-40 |
| 2 | g10569.t23 | PANTHER | PTHR11721 | 60S RIBOSOMAL PROTEIN L27A | 25 | 146 | 1.6E-52 |
| 3 | g10569.t23 | PANTHER | PTHR11721:SF13 | 60S RIBOSOMAL PROTEIN L27A | 25 | 146 | 1.6E-52 |
| 1 | g10569.t23 | Pfam | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 28 | 144 | 2.4E-23 |
| 5 | g10569.t23 | ProSitePatterns | PS00475 | Ribosomal protein L15 signature. | 109 | 140 | - |
| 4 | g10569.t23 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 26 | 145 | 2.35E-35 |
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.
