General information for g10884.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L30.
Parent gene
- The parent gene g10884 is located on chr_1: 12444618..12445292 (+ 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 | g10884 | g10884.t4 | isoform | g10884.t4 | 12444252 | 12445226 |
| chr_1 | g10884 | g10884.t4 | exon | g10884.t4.exon1 | 12444252 | 12444261 |
| chr_1 | g10884 | g10884.t4 | exon | g10884.t4.exon2 | 12444341 | 12444395 |
| chr_1 | g10884 | g10884.t4 | cds | g10884.t4.CDS1 | 12444375 | 12444395 |
| chr_1 | g10884 | g10884.t4 | exon | g10884.t4.exon3 | 12444618 | 12444763 |
| chr_1 | g10884 | g10884.t4 | cds | g10884.t4.CDS2 | 12444618 | 12444763 |
| chr_1 | g10884 | g10884.t4 | exon | g10884.t4.exon4 | 12445046 | 12445226 |
| chr_1 | g10884 | g10884.t4 | cds | g10884.t4.CDS3 | 12445046 | 12445226 |
| chr_1 | g10884 | g10884.t4 | TTS | g10884.t4 | 12445286 | 12445286 |
| chr_1 | g10884 | g10884.t4 | TSS | g10884.t4 | NA | NA |
Sequences
>g10884.t4 Gene=g10884 Length=392
TTTGAATCAAGTTTAAAGTTAGTAGCCAACGCTAATCTTCAAAAATGGTCACCCAAAAGA
AGCAAAAAAAGGCTTTAGAATCTATCAACTCTCGCTTGGCTTTGGTGATGAAGTCAGGCA
AATATTGCTTAGGATATAAGCAGACTTTAAAAACACTCCGTCAAGGCAAGGCAAAATTGG
TTATCATCGCCAACAACACTCCACACTTGAGAAAGTCAGAAATTGAATACTACGCTATGT
TGGCAAAGACTGGTGTTCATCATTACAATGGCAACAACATTGAATTGGGAACAGCTTGCG
GTAAATACTTCCGTGTTTGCACACTCTCAATTACAGATGCTGGCGATTCAGACATTATCA
GAACACTTCCAGAAGCACAAACTGGAAACTAA
>g10884.t4 Gene=g10884 Length=115
MVTQKKQKKALESINSRLALVMKSGKYCLGYKQTLKTLRQGKAKLVIIANNTPHLRKSEI
EYYAMLAKTGVHHYNGNNIELGTACGKYFRVCTLSITDAGDSDIIRTLPEAQTGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10884.t4 | Gene3D | G3DSA:3.30.1330.30 | - | 2 | 108 | 2.4E-54 |
| 4 | g10884.t4 | Hamap | MF_00481 | 50S ribosomal protein L30e [rpl30e]. | 12 | 109 | 21.627201 |
| 2 | g10884.t4 | PANTHER | PTHR11449:SF12 | 60S RIBOSOMAL PROTEIN L30 | 1 | 112 | 4.8E-59 |
| 3 | g10884.t4 | PANTHER | PTHR11449 | RIBOSOMAL PROTEIN L30 | 1 | 112 | 4.8E-59 |
| 1 | g10884.t4 | Pfam | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | 13 | 105 | 2.1E-25 |
| 6 | g10884.t4 | ProSitePatterns | PS00709 | Ribosomal protein L30e signature 1. | 24 | 48 | - |
| 7 | g10884.t4 | ProSitePatterns | PS00993 | Ribosomal protein L30e signature 2. | 80 | 100 | - |
| 5 | g10884.t4 | SUPERFAMILY | SSF55315 | L30e-like | 13 | 106 | 9.43E-36 |
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:0003723 | RNA binding | MF |
| GO:0022625 | cytosolic large ribosomal subunit | CC |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02908 (large subunit ribosomal protein L30e)
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.
