General information for g11401.t26
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L13a.
Parent gene
- The parent gene g11401 is located on chr_1: 15971204..15980307 (+ 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 | g11401 | g11401.t26 | TSS | g11401.t26 | 15970763 | 15970763 |
| chr_1 | g11401 | g11401.t26 | isoform | g11401.t26 | 15971100 | 15975720 |
| chr_1 | g11401 | g11401.t26 | exon | g11401.t26.exon1 | 15971100 | 15971674 |
| chr_1 | g11401 | g11401.t26 | cds | g11401.t26.CDS1 | 15971192 | 15971614 |
| chr_1 | g11401 | g11401.t26 | exon | g11401.t26.exon2 | 15975706 | 15975720 |
| chr_1 | g11401 | g11401.t26 | TTS | g11401.t26 | NA | NA |
Sequences
>g11401.t26 Gene=g11401 Length=590
CTAGAAACAAAATTAAGTTCTTGTCGTTCCTTCGCAAGCGCTGTAATGTCAACCCAGCTC
GTGGTCCATTCCATTTCCGCGCACCAAGTCGTATGTTTTGGAAAGCTGTTCGCGGAATGG
TTCCACATAAAACACGCCGTGGAAAGCTTGCATTAGCTCGTTTAAAGGTCTTTGAAGGAA
TTCCACCACCATATGACAAGCAAAAGCGAGTTTGTGTTCCTCTTGCTATGAAAATTTTGT
GCTTACGATCAGACAGAAAGTATTGCCAAGTAGGACGTGTAGCTCATGAAGTTGGTTGGC
AATATAAAGATGTTGTAAGCAGTCTTGAAGCAAAGAGAAAGATCAAGGCACGCTTGTATT
ACAACCATAAACAACGTTTGGAAAAACTTCGTCTACGTGCTACACAAAAAGTTTCAAAAG
GAATCGCCAAACAAAATTCCATTCTCAAAAAGTTCGGATATATCACATCAGAAAATGAAG
TGAAGCCAGTCGCCGCCGTCGCAGCAAAGGCATAAACTTTTGACCGAAAACATGAAATAA
AGAAGTTAAAAAGGATTCAATAAAATCAATGAACCTATTACAAATAATTT
>g11401.t26 Gene=g11401 Length=140
MFWKAVRGMVPHKTRRGKLALARLKVFEGIPPPYDKQKRVCVPLAMKILCLRSDRKYCQV
GRVAHEVGWQYKDVVSSLEAKRKIKARLYYNHKQRLEKLRLRATQKVSKGIAKQNSILKK
FGYITSENEVKPVAAVAAKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11401.t26 | Gene3D | G3DSA:3.90.1180.10 | - | 1 | 71 | 1.7E-27 |
| 2 | g11401.t26 | PANTHER | PTHR11545:SF3 | 60S RIBOSOMAL PROTEIN L13A-RELATED | 1 | 123 | 4.2E-45 |
| 3 | g11401.t26 | PANTHER | PTHR11545 | RIBOSOMAL PROTEIN L13 | 1 | 123 | 4.2E-45 |
| 1 | g11401.t26 | Pfam | PF00572 | Ribosomal protein L13 | 1 | 32 | 9.9E-6 |
| 5 | g11401.t26 | ProSitePatterns | PS00783 | Ribosomal protein L13 signature. | 6 | 29 | - |
| 4 | g11401.t26 | SUPERFAMILY | SSF52161 | Ribosomal protein L13 | 1 | 71 | 4.97E-19 |
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 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.
