General information for g10569.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t16 | TTS | g10569.t16 | 10486114 | 10486114 |
| chr_1 | g10569 | g10569.t16 | isoform | g10569.t16 | 10486175 | 10487149 |
| chr_1 | g10569 | g10569.t16 | exon | g10569.t16.exon1 | 10486175 | 10486303 |
| chr_1 | g10569 | g10569.t16 | cds | g10569.t16.CDS1 | 10486175 | 10486303 |
| chr_1 | g10569 | g10569.t16 | exon | g10569.t16.exon2 | 10486505 | 10486742 |
| chr_1 | g10569 | g10569.t16 | cds | g10569.t16.CDS2 | 10486505 | 10486742 |
| chr_1 | g10569 | g10569.t16 | exon | g10569.t16.exon3 | 10486844 | 10487149 |
| chr_1 | g10569 | g10569.t16 | cds | g10569.t16.CDS3 | 10486844 | 10486908 |
| chr_1 | g10569 | g10569.t16 | TSS | g10569.t16 | 10487169 | 10487169 |
Sequences
>g10569.t16 Gene=g10569 Length=673
ATGGTTGTGAGTAAAATTTTTAATTTTAATAAAATTAAATAGTATCAATGACTTTTTTAA
GATAAATAGTAATTTATTCTAATTGCCATATTATGAATTACTATTAGCATATGAAGAATT
TTAGTTAGACTTTGATAAAACTATGTAAAACTCAATGCAAAAATGTTGAAATTTTGTATT
GATCACATAAAAAATGATGTCAATTTGAGTAAATTTTTTCTTTACTTCATTTCAGAGTCT
TATGAAAAGAAAGAAGACCCGAAAGCTTCGTGGTCATGTCAGCCATGGTCATGGTCGTAT
CGGTATAAAACATCCTGGTGGTCGCGGTAATGCTGGTGGTATGCACCATCACAGAATAAA
TTACGATAAATACCATCCTGGATATTTTGGAAAAGTTGGTATGCGCAACTTCCATTTGAA
TCGTAATCACAGCTTCTGTCCAACAATTAATCTCGATAAACTTTGGTCATTAATTGGACA
AGAAAATTACGAGAAAGCAAAGAAAGAAGGCGATAAAGTTCCAGTTATCGATATCGTACA
ATTTGGATACTTTAAGCTACTTGGACATGGACATTTGCCAAAACAACCAATAATTGTGAA
AGCAAAATATTTTTCACAGAAAGCAGAAAAGAAAATCAAGGCTGCTGGTGGCGCATGCAT
CCTAAGAGCATAA
>g10569.t16 Gene=g10569 Length=143
MKRKKTRKLRGHVSHGHGRIGIKHPGGRGNAGGMHHHRINYDKYHPGYFGKVGMRNFHLN
RNHSFCPTINLDKLWSLIGQENYEKAKKEGDKVPVIDIVQFGYFKLLGHGHLPKQPIIVK
AKYFSQKAEKKIKAAGGACILRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10569.t16 | Gene3D | G3DSA:3.100.10.10 | - | 54 | 143 | 5.9E-40 |
| 4 | g10569.t16 | Hamap | MF_01341 | 50S ribosomal protein L15 [rplO]. | 1 | 142 | 10.887958 |
| 2 | g10569.t16 | PANTHER | PTHR11721 | 60S RIBOSOMAL PROTEIN L27A | 2 | 142 | 1.0E-60 |
| 3 | g10569.t16 | PANTHER | PTHR11721:SF13 | 60S RIBOSOMAL PROTEIN L27A | 2 | 142 | 1.0E-60 |
| 1 | g10569.t16 | Pfam | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 24 | 140 | 2.2E-23 |
| 6 | g10569.t16 | ProSitePatterns | PS00475 | Ribosomal protein L15 signature. | 105 | 136 | - |
| 5 | g10569.t16 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 3 | 141 | 2.22E-40 |
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:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02900 (large subunit ribosomal protein L27Ae)
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. There were no conditions that were differentially expressed