General information for g8270.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L27.
Parent gene
- The parent gene g8270 is located on chr_2: 29417641..29418466 (- 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_2 | g8270 | g8270.t1 | TTS | g8270.t1 | 29417547 | 29417547 |
| chr_2 | g8270 | g8270.t1 | isoform | g8270.t1 | 29417641 | 29418110 |
| chr_2 | g8270 | g8270.t1 | exon | g8270.t1.exon1 | 29417641 | 29418018 |
| chr_2 | g8270 | g8270.t1 | cds | g8270.t1.CDS1 | 29417641 | 29418018 |
| chr_2 | g8270 | g8270.t1 | exon | g8270.t1.exon2 | 29418084 | 29418110 |
| chr_2 | g8270 | g8270.t1 | cds | g8270.t1.CDS2 | 29418084 | 29418110 |
| chr_2 | g8270 | g8270.t1 | TSS | g8270.t1 | 29418301 | 29418301 |
Sequences
>g8270.t1 Gene=g8270 Length=405
ATGGGAAAAATTATGAAGGCAGGAAAGGTCGTTATCGTCCTCGGAGGCAGATTTGCTGGA
CGAAAAGCAGTCATCTTGAAATCTTTAGATGATGGTACAACAGAATTTGCGCAAGCCCTT
ATAGCTGGAATTGCACGATACCCAAGACGTGTTGTACGAAGAATGAAAAAGGATCGAATT
AAGAAAAATATTCGTATCAAACCATTTATCAAATGTATCAATTATAATCATTTGATGCCA
ACACGTTATAGCGTCTCTGATATAACACTTGATCAGAAATATGGCTTAAAAGATCTTCGT
GATCCAGTTAAGCGTAAAAAAGCTGCATTTCAAATTCGTATGAAACTTGAAGATCGCTAT
AAGCAAGGAAAGAACAAATGGTTCTTTCAAAAGTTGCGTTTCTAA
>g8270.t1 Gene=g8270 Length=134
MGKIMKAGKVVIVLGGRFAGRKAVILKSLDDGTTEFAQALIAGIARYPRRVVRRMKKDRI
KKNIRIKPFIKCINYNHLMPTRYSVSDITLDQKYGLKDLRDPVKRKKAAFQIRMKLEDRY
KQGKNKWFFQKLRF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8270.t1 | CDD | cd06090 | KOW_RPL27 | 6 | 85 | 6.66457E-37 |
| 8 | g8270.t1 | Gene3D | G3DSA:2.30.30.770 | - | 1 | 134 | 1.9E-53 |
| 3 | g8270.t1 | PANTHER | PTHR10497:SF0 | 60S RIBOSOMAL PROTEIN L27 | 1 | 134 | 4.8E-45 |
| 4 | g8270.t1 | PANTHER | PTHR10497 | 60S RIBOSOMAL PROTEIN L27 | 1 | 134 | 4.8E-45 |
| 2 | g8270.t1 | Pfam | PF00467 | KOW motif | 8 | 31 | 4.9E-5 |
| 1 | g8270.t1 | Pfam | PF01777 | Ribosomal L27e protein family | 50 | 134 | 1.8E-30 |
| 7 | g8270.t1 | ProSitePatterns | PS01107 | Ribosomal protein L27e signature. | 123 | 134 | - |
| 6 | g8270.t1 | SMART | SM00739 | kow_9 | 4 | 31 | 0.007 |
| 5 | g8270.t1 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 3 | 134 | 2.71E-17 |
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 K02901 (large subunit ribosomal protein L27e)
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.
