General information for g10224.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L21.
Parent gene
- The parent gene g10224 is located on chr_1: 8346808..8347094 (+ 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 | g10224 | g10224.t3 | isoform | g10224.t3 | 8346268 | 8347036 |
| chr_1 | g10224 | g10224.t3 | exon | g10224.t3.exon1 | 8346268 | 8346345 |
| chr_1 | g10224 | g10224.t3 | exon | g10224.t3.exon2 | 8346469 | 8346620 |
| chr_1 | g10224 | g10224.t3 | cds | g10224.t3.CDS1 | 8346492 | 8346620 |
| chr_1 | g10224 | g10224.t3 | exon | g10224.t3.exon3 | 8346686 | 8347036 |
| chr_1 | g10224 | g10224.t3 | cds | g10224.t3.CDS2 | 8346686 | 8347036 |
| chr_1 | g10224 | g10224.t3 | TTS | g10224.t3 | 8347087 | 8347087 |
| chr_1 | g10224 | g10224.t3 | TSS | g10224.t3 | NA | NA |
Sequences
>g10224.t3 Gene=g10224 Length=581
TGCGTTTCGTATCGCATGTAAGTAAATAATTTTTAATAATTTTTAATGGTTCTAAATATT
ATAATAACTCAAATACTAAGATTTCTTAATACCATTAAAAGATGACTCGCACTCACGGTT
ATCGTCGCGGTACACGCGACATGTTCTCGCGTCAATTCCGCAGACATGGAGCTATCCCTC
TTGCAACATACATGAAAGTATACAAAGCTGGCGATTATGTTGATGTTAAGGGTAATGGTG
CAGTTCACAAAGGTATGCCATTTAAAGCATATCACGGCAAAACTGGTCGTGTCTACAATG
TAACACAACACGCACTCGGTGTTATTGTAAACAAAAGACATCGTGGTAAAATCCTTGCCA
AGAGAATTAATGTTCGTATTGAACATGTTAAACCATCAAAGTGTCGCGAAGAATTTTTGG
CACGAGTAAAGAGCAACGATGAGAAGCGTCGTGAAGCCAGAGCTCAAGGAAAACGCGTTA
TGCTTAAGCGTAAACCAGTGGAACCATTGAAAGCTCGCGTTATCGAAAATCCACCACAGC
CTGTTTTTCTCGCTCCAATTCCATATGAGTTTGTCGCGTAA
>g10224.t3 Gene=g10224 Length=159
MTRTHGYRRGTRDMFSRQFRRHGAIPLATYMKVYKAGDYVDVKGNGAVHKGMPFKAYHGK
TGRVYNVTQHALGVIVNKRHRGKILAKRINVRIEHVKPSKCREEFLARVKSNDEKRREAR
AQGKRVMLKRKPVEPLKARVIENPPQPVFLAPIPYEFVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10224.t3 | Gene3D | G3DSA:2.30.30.70 | - | 1 | 97 | 2.8E-48 |
| 2 | g10224.t3 | PANTHER | PTHR20981 | 60S RIBOSOMAL PROTEIN L21 | 1 | 158 | 3.0E-68 |
| 1 | g10224.t3 | Pfam | PF01157 | Ribosomal protein L21e | 1 | 101 | 5.5E-47 |
| 4 | g10224.t3 | ProSitePatterns | PS01171 | Ribosomal protein L21e signature. | 37 | 62 | - |
| 3 | g10224.t3 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 3 | 100 | 4.11E-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 transcript has been annotated with K02889 (large subunit ribosomal protein L21e)
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.
