General information for g10569.t20
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.t20 | TTS | g10569.t20 | 10486114 | 10486114 |
| chr_1 | g10569 | g10569.t20 | isoform | g10569.t20 | 10486175 | 10487149 |
| chr_1 | g10569 | g10569.t20 | exon | g10569.t20.exon1 | 10486175 | 10486303 |
| chr_1 | g10569 | g10569.t20 | cds | g10569.t20.CDS1 | 10486293 | 10486303 |
| chr_1 | g10569 | g10569.t20 | exon | g10569.t20.exon2 | 10486501 | 10486752 |
| chr_1 | g10569 | g10569.t20 | cds | g10569.t20.CDS2 | 10486501 | 10486752 |
| chr_1 | g10569 | g10569.t20 | exon | g10569.t20.exon3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t20 | cds | g10569.t20.CDS3 | 10486848 | 10486914 |
| chr_1 | g10569 | g10569.t20 | exon | g10569.t20.exon4 | 10487144 | 10487149 |
| chr_1 | g10569 | g10569.t20 | cds | g10569.t20.CDS4 | 10487144 | 10487149 |
| chr_1 | g10569 | g10569.t20 | TSS | g10569.t20 | 10487169 | 10487169 |
Sequences
>g10569.t20 Gene=g10569 Length=454
ATGGTTAGTCTTATGAAAAGAAAGAAGACCCGAAAGCTTCGTGGTCATGTCAGCCATGGT
CATGGTCGTATCGGCAAACACAGAAAACATCCTGGTGGTCGCGGTAATGCTGGTGGTATG
CACCATCACAGAATAAATTACGATAAATACCATCCTGGATATTTTGGAAAAGTTGGTATG
CGCAACTTCCATTTGAATCGTAATCACAGCTTCTGTCCAACAATTAATCTCGATAAACTT
TGGTCATTAATTGGACAAGAAAATTACGAGAAAGCAAAGAAAGAAGGCGATAAAGTTCCA
GTTATCGATATCGTACAATTTGTAAGGATACTTTAAGCTACTTGGACATGGACATTTGCC
AAAACAACCAATAATTGTGAAAGCAAAATATTTTTCACAGAAAGCAGAAAAGAAAATCAA
GGCTGCTGGTGGCGCATGCATCCTAAGAGCATAA
>g10569.t20 Gene=g10569 Length=111
MVSLMKRKKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINYDKYHPGYFGKVGM
RNFHLNRNHSFCPTINLDKLWSLIGQENYEKAKKEGDKVPVIDIVQFVRIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10569.t20 | Gene3D | G3DSA:3.100.10.10 | - | 60 | 110 | 8.6E-15 |
| 5 | g10569.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 2 | g10569.t20 | PANTHER | PTHR11721 | 60S RIBOSOMAL PROTEIN L27A | 6 | 106 | 2.5E-46 |
| 3 | g10569.t20 | PANTHER | PTHR11721:SF13 | 60S RIBOSOMAL PROTEIN L27A | 6 | 106 | 2.5E-46 |
| 1 | g10569.t20 | Pfam | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 30 | 107 | 2.1E-9 |
| 4 | g10569.t20 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 7 | 107 | 9.42E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
