General information for g6993.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S19a.
Parent gene
- The parent gene g6993 is located on chr_2: 20405134..20412963 (+ 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 | g6993 | g6993.t5 | TSS | g6993.t5 | 20404581 | 20404581 |
| chr_2 | g6993 | g6993.t5 | isoform | g6993.t5 | 20404606 | 20405505 |
| chr_2 | g6993 | g6993.t5 | exon | g6993.t5.exon1 | 20404606 | 20404620 |
| chr_2 | g6993 | g6993.t5 | exon | g6993.t5.exon2 | 20405022 | 20405505 |
| chr_2 | g6993 | g6993.t5 | cds | g6993.t5.CDS1 | 20405035 | 20405505 |
| chr_2 | g6993 | g6993.t5 | TTS | g6993.t5 | 20405616 | 20405616 |
Sequences
>g6993.t5 Gene=g6993 Length=499
TATAAACGTGTGAAAGTGATTAATCAAAATGCCTGGCTCAACAGTCAAGGATGTCGATCA
AGACAAAATCGTGCAAGGAGTTGCACTTTTCCTTAAAAAATCGGGCAAATTGAAGGTCCC
TGATAATATGGATATCGTAAAGACCTCAAAAGCAAAGGATTTAGGTCCAGTAAATTCAGA
TTGGTTCTATGTTCGTTGCGCTTCAATCTTGCGTCGTATGTATCATCGTGGTCCAATTGG
TGTTGGTGGTGTAAAGAAAATTTTTGGTAGCAGAAAGCGTAATGGAGTCTGTCCATCACA
TTATTGTCGCGCTGATGGAGCCGTTTCACGTCGTGCATTACAAGCTCTTGAACACATTAA
GCTCATCGAGAAACATTCAGATGGTGGCCGTAAATTAACGCCCCAAGGTCAACGTGATTT
AGACCGTATTGCTTCACAAATTGTTGCCACCAGTCGATTGGTAGCAAAGAAGGAAGTTCT
TTCAATTGGTGATGAATAA
>g6993.t5 Gene=g6993 Length=156
MPGSTVKDVDQDKIVQGVALFLKKSGKLKVPDNMDIVKTSKAKDLGPVNSDWFYVRCASI
LRRMYHRGPIGVGGVKKIFGSRKRNGVCPSHYCRADGAVSRRALQALEHIKLIEKHSDGG
RKLTPQGQRDLDRIASQIVATSRLVAKKEVLSIGDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6993.t5 | Gene3D | G3DSA:1.10.10.2700 | - | 2 | 144 | 0 |
| 2 | g6993.t5 | PANTHER | PTHR11710 | 40S RIBOSOMAL PROTEIN S19 | 1 | 143 | 0 |
| 3 | g6993.t5 | PANTHER | PTHR11710:SF17 | 40S RIBOSOMAL PROTEIN S19 | 1 | 143 | 0 |
| 1 | g6993.t5 | Pfam | PF01090 | Ribosomal protein S19e | 5 | 139 | 0 |
| 5 | g6993.t5 | SMART | SM01413 | Ribosomal_S19e_2 | 5 | 141 | 0 |
| 4 | g6993.t5 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 5 | 140 | 0 |
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 K02966 (small subunit ribosomal protein S19e)
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.
