General information for g2607.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g2607 is located on chr_3: 19030677..19031441 (- 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 | g2607 | g2607.t1 | TTS | g2607.t1 | 19030578 | 19030578 |
| chr_3 | g2607 | g2607.t1 | isoform | g2607.t1 | 19030677 | 19031441 |
| chr_3 | g2607 | g2607.t1 | exon | g2607.t1.exon1 | 19030677 | 19030705 |
| chr_3 | g2607 | g2607.t1 | cds | g2607.t1.CDS1 | 19030677 | 19030705 |
| chr_3 | g2607 | g2607.t1 | exon | g2607.t1.exon2 | 19030776 | 19030995 |
| chr_3 | g2607 | g2607.t1 | cds | g2607.t1.CDS2 | 19030776 | 19030995 |
| chr_3 | g2607 | g2607.t1 | exon | g2607.t1.exon3 | 19031436 | 19031441 |
| chr_3 | g2607 | g2607.t1 | cds | g2607.t1.CDS3 | 19031436 | 19031441 |
| chr_3 | g2607 | g2607.t1 | TSS | g2607.t1 | 19031473 | 19031473 |
Sequences
>g2607.t1 Gene=g2607 Length=255
ATGCCGTTAGCGAAGGATTTATTACATCCGCTTCCAGCTGAAGAGAAGCGTAAGCATAAA
CTAAAGCGACTAGTACAGCACCCTAATAGCTATTTCATGGACGTTAAATGTCCTGGCTGC
TATAAGATCACTACAGTTTTCAGTCATGCTCAAGGAGTTGTTGTATGCACTGGCTGTTCA
ACAATCTTATGCCAACCAACTGGTGGTAGAGCTAAATTGACAGAGGGATGCTCATTCAGA
AAAAAACCATACTAA
>g2607.t1 Gene=g2607 Length=84
MPLAKDLLHPLPAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQGVVVCTGCS
TILCQPTGGRAKLTEGCSFRKKPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2607.t1 | Gene3D | G3DSA:2.20.25.640 | - | 1 | 84 | 9.1E-50 |
| 4 | g2607.t1 | Hamap | MF_00371 | 30S ribosomal protein S27e [rps27e]. | 22 | 82 | 17.07641 |
| 2 | g2607.t1 | PANTHER | PTHR11594:SF4 | 40S RIBOSOMAL PROTEIN S27 | 1 | 82 | 3.5E-48 |
| 3 | g2607.t1 | PANTHER | PTHR11594 | 40S RIBOSOMAL PROTEIN S27 | 1 | 82 | 3.5E-48 |
| 1 | g2607.t1 | Pfam | PF01667 | Ribosomal protein S27 | 28 | 82 | 5.8E-28 |
| 6 | g2607.t1 | ProSitePatterns | PS01168 | Ribosomal protein S27e signature. | 36 | 68 | - |
| 5 | g2607.t1 | SUPERFAMILY | SSF57829 | Zn-binding ribosomal proteins | 28 | 82 | 2.01E-22 |
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 K02978 (small subunit ribosomal protein S27e)
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.
