General information for g1161.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1161 is located on chr_3: 8439760..8440243 (- 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_3 | g1161 | g1161.t1 | TTS | g1161.t1 | 8439732 | 8439732 |
| chr_3 | g1161 | g1161.t1 | isoform | g1161.t1 | 8439760 | 8440243 |
| chr_3 | g1161 | g1161.t1 | exon | g1161.t1.exon1 | 8439760 | 8440060 |
| chr_3 | g1161 | g1161.t1 | cds | g1161.t1.CDS1 | 8439760 | 8440060 |
| chr_3 | g1161 | g1161.t1 | exon | g1161.t1.exon2 | 8440122 | 8440243 |
| chr_3 | g1161 | g1161.t1 | cds | g1161.t1.CDS2 | 8440122 | 8440243 |
| chr_3 | g1161 | g1161.t1 | TSS | g1161.t1 | 8440267 | 8440267 |
Sequences
>g1161.t1 Gene=g1161 Length=423
ATGAATTTCCTAAATAATTTTAAGAATTTGCTTCAATCTTCAAATGTATGTACAAATATC
GTCAGAAATGCAAGTAAGAAAACAAGTGGCAGTACACGAAATCCAAAGAATCCACACGGA
AGACCAAAACATCGTGGATGGAAGAGACAAGAGGGACATTATGTCACAAGCGGAACAATT
CTGGCAACTCAATTAAAACCTCGATTTTTCCCTGGATTAAATGTTGGATATGGCAGAAAT
ACACTTTTTGCAATGACAAATGGTCGTGTTTATGTTTCATGTGAAAAAGTTGATTTAAAT
TGGGATCATAGTCTTGTACAAAAACATTTTGCTGGTAGGCACGATCAAACAATATATAAG
AAATATTTTAATGTAGTTCCTGAACCACAACATCAAAGGTTTCGATTAGTCGATGAAAAT
TAA
>g1161.t1 Gene=g1161 Length=140
MNFLNNFKNLLQSSNVCTNIVRNASKKTSGSTRNPKNPHGRPKHRGWKRQEGHYVTSGTI
LATQLKPRFFPGLNVGYGRNTLFAMTNGRVYVSCEKVDLNWDHSLVQKHFAGRHDQTIYK
KYFNVVPEPQHQRFRLVDEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1161.t1 | Gene3D | G3DSA:2.40.50.1030 | - | 28 | 139 | 3.9E-37 |
| 5 | g1161.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 47 | - |
| 2 | g1161.t1 | PANTHER | PTHR15893 | RIBOSOMAL PROTEIN L27 | 12 | 131 | 3.3E-19 |
| 3 | g1161.t1 | PANTHER | PTHR15893:SF0 | 39S RIBOSOMAL PROTEIN L27, MITOCHONDRIAL | 12 | 131 | 3.3E-19 |
| 1 | g1161.t1 | Pfam | PF01016 | Ribosomal L27 protein | 24 | 93 | 1.5E-16 |
| 4 | g1161.t1 | SUPERFAMILY | SSF110324 | Ribosomal L27 protein-like | 24 | 105 | 1.53E-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:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02899 (large subunit ribosomal protein L27)
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.
