General information for g11608.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11608 is located on chr_1: 17432157..17433996 (+ 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 | g11608 | g11608.t3 | TSS | g11608.t3 | 17430574 | 17430574 |
| chr_1 | g11608 | g11608.t3 | isoform | g11608.t3 | 17430584 | 17432674 |
| chr_1 | g11608 | g11608.t3 | exon | g11608.t3.exon1 | 17430584 | 17430604 |
| chr_1 | g11608 | g11608.t3 | exon | g11608.t3.exon2 | 17432163 | 17432674 |
| chr_1 | g11608 | g11608.t3 | cds | g11608.t3.CDS1 | 17432550 | 17432615 |
| chr_1 | g11608 | g11608.t3 | TTS | g11608.t3 | 17432683 | 17432683 |
Sequences
>g11608.t3 Gene=g11608 Length=533
GACTGGTGTTTTTTACGAAAGATCTTCGTCAAAACACTAACAGGCAAGACCATTACACTT
GAGGTCGAGCCATCTGATACAATCGAAAATGTCAAAGCTAAAATTCAAGACAAAGAAGGC
ATTCCTCCAGATCAACAGCGTTTAATCTTTGCTGGTAAACAATTGGAGGATGGACGAACA
TTGAGTGATTACAACATTCAAAAAGAATCAACATTGCATTTGGTCCTTCGTCTCCGCGGT
GGTGCCAAAAAACGCAAGAAGAAGAATTACTCAACACCGAAGAAGATCAAGCATAAGCGC
AAGAAGGTTAAACTTGCTGTTTTGAAGTACTACAAAGTTGATGAGAACGGCAAAATCCAT
CGATTGAGACGTGAATGCCCGGCAGAAACATGCGGTGCTGGAGTCTTCATGGCAGCACAT
GAAAATCGCGCTTACTGTGGCAAATGTACACTCACATTCGTCGATAAGGAATAAATTTAT
CAACTGTGTATATTTCCATAAGTAAAACACAAGAAATAAATGAATCCATTTAT
>g11608.t3 Gene=g11608 Length=21
MAAHENRAYCGKCTLTFVDKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g11608.t3 | Gene3D | G3DSA:2.20.25.660 | - | 1 | 20 | 1.0e-06 |
| 1 | g11608.t3 | Pfam | PF01599 | Ribosomal protein S27a | 1 | 16 | 1.5e-06 |
| 2 | g11608.t3 | SUPERFAMILY | SSF57829 | Zn-binding ribosomal proteins | 1 | 20 | 5.9e-06 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
