General information for g10569.t19
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.t19 | TTS | g10569.t19 | 10486114 | 10486114 |
| chr_1 | g10569 | g10569.t19 | isoform | g10569.t19 | 10486175 | 10487149 |
| chr_1 | g10569 | g10569.t19 | exon | g10569.t19.exon1 | 10486175 | 10486312 |
| chr_1 | g10569 | g10569.t19 | cds | g10569.t19.CDS1 | 10486175 | 10486312 |
| chr_1 | g10569 | g10569.t19 | exon | g10569.t19.exon2 | 10486514 | 10486752 |
| chr_1 | g10569 | g10569.t19 | cds | g10569.t19.CDS2 | 10486514 | 10486752 |
| chr_1 | g10569 | g10569.t19 | exon | g10569.t19.exon3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t19 | cds | g10569.t19.CDS3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t19 | exon | g10569.t19.exon4 | 10487144 | 10487149 |
| chr_1 | g10569 | g10569.t19 | cds | g10569.t19.CDS4 | 10487144 | 10487149 |
| chr_1 | g10569 | g10569.t19 | TSS | g10569.t19 | 10487169 | 10487169 |
Sequences
>g10569.t19 Gene=g10569 Length=450
ATGGTTAGTCTTATGAAAAGAAAGAAGACCCGAAAGCTTCGTGGTCATGTCAGCCATGGT
CATGGTCGTATCGGCAAACACAGAAAACATCCTGGTGGTCGCGGTAATGCTGGTGGTATG
CACCATCACAGAATAAATTACGATAAATACCATCCTGGATATTTTGGAAAAGTTGGTATG
CGCAACTTCCATTTGAATCGTAATCACAGCTTCTGTCCAACAATTAATCTCGATAAACTT
TGGTCATTAATTGGACAAGAAAATTACGAGAAAGCAAAGAAAGAAGGCGATAAAGTTCCA
GTTATCGATATCCTTTTAAAGGGATACTTTAAGCTACTTGGACATGGACATTTGCCAAAA
CAACCAATAATTGTGAAAGCAAAATATTTTTCACAGAAAGCAGAAAAGAAAATCAAGGCT
GCTGGTGGCGCATGCATCCTAAGAGCATAA
>g10569.t19 Gene=g10569 Length=149
MVSLMKRKKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINYDKYHPGYFGKVGM
RNFHLNRNHSFCPTINLDKLWSLIGQENYEKAKKEGDKVPVIDILLKGYFKLLGHGHLPK
QPIIVKAKYFSQKAEKKIKAAGGACILRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10569.t19 | Gene3D | G3DSA:3.100.10.10 | - | 60 | 149 | 1.3E-38 |
| 4 | g10569.t19 | Hamap | MF_01341 | 50S ribosomal protein L15 [rplO]. | 1 | 148 | 12.009324 |
| 7 | g10569.t19 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 2 | g10569.t19 | PANTHER | PTHR11721 | 60S RIBOSOMAL PROTEIN L27A | 6 | 148 | 2.3E-64 |
| 3 | g10569.t19 | PANTHER | PTHR11721:SF13 | 60S RIBOSOMAL PROTEIN L27A | 6 | 148 | 2.3E-64 |
| 1 | g10569.t19 | Pfam | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 30 | 146 | 5.3E-22 |
| 6 | g10569.t19 | ProSitePatterns | PS00475 | Ribosomal protein L15 signature. | 111 | 142 | - |
| 5 | g10569.t19 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 7 | 147 | 8.11E-43 |
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.
