General information for g2688.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L9, mitochondrial.
Parent gene
- The parent gene g2688 is located on chr_3: 19719738..19721021 (+ 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 | g2688 | g2688.t3 | isoform | g2688.t3 | 19719738 | 19720635 |
| chr_3 | g2688 | g2688.t3 | exon | g2688.t3.exon1 | 19719738 | 19719824 |
| chr_3 | g2688 | g2688.t3 | cds | g2688.t3.CDS1 | 19719738 | 19719824 |
| chr_3 | g2688 | g2688.t3 | exon | g2688.t3.exon2 | 19719887 | 19720216 |
| chr_3 | g2688 | g2688.t3 | cds | g2688.t3.CDS2 | 19719887 | 19720216 |
| chr_3 | g2688 | g2688.t3 | exon | g2688.t3.exon3 | 19720283 | 19720635 |
| chr_3 | g2688 | g2688.t3 | cds | g2688.t3.CDS3 | 19720283 | 19720285 |
| chr_3 | g2688 | g2688.t3 | TTS | g2688.t3 | 19720730 | 19720730 |
| chr_3 | g2688 | g2688.t3 | TSS | g2688.t3 | NA | NA |
Sequences
>g2688.t3 Gene=g2688 Length=770
ATGTTGAGATCAATATTTAAAAGTGGAATTAATTCCATTTCTACGCATTTATTAACATCT
AATAATGCTGTAACACAGCAAGTTAGAACAACTTTTATATTGAGAAGAAAATATCCATTA
GAATTGCATAAAAAGAATCAAAAACCAAGAAAATTAAGAGGAAAACATTTTAATTATGTC
CTTGTTGAAGACACAAATAGAACAGTTAAACCTGACATTGAGGTTGTTTTAAAGCAGTTT
ATTCATGGTGTAGGAAAGAAAGGCGAAATTGTAAAAGTTCGACCAAATTTTGCTTATAAT
GAACTTCTTTTGACTGATAAAGCAGCTTATGCTACACCTGAAAATATAGAGAAATATAAA
TTGAAAGAAGGCGAAGAGAGTCAAGAAGAGAAGTATAGTTCACCATATGCTCAAAGATAA
ATATGCTTCAGAATCGTGTATTTGCTATAGTAATGAATAAGGAACAACCTTGGGTAATTG
AACCATGGCATGTTCGAGCTTCTTTACGAAAATGCGGCTATCATATCTTATCAGATGATG
CTATTGAATTACCACAAGAAAAAATTACTGGTCCTGACTTACAAAAACAGAATAAAGAAT
TTATTGTTACTGTAACAATCAATAAAATGGAAAAAGCTAAAGTAAGATGTCGAATCCATC
ATTGGAGCACAAATCCTAGTGATCGACTTCCATACGTTTATGAACATTGGTTACAAGATA
CAGAACCGCTTTTTCCTTCTGAACAAAAATCAAACGAATCATCTTCGTAA
>g2688.t3 Gene=g2688 Length=139
MLRSIFKSGINSISTHLLTSNNAVTQQVRTTFILRRKYPLELHKKNQKPRKLRGKHFNYV
LVEDTNRTVKPDIEVVLKQFIHGVGKKGEIVKVRPNFAYNELLLTDKAAYATPENIEKYK
LKEGEESQEEKYSSPYAQR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2688.t3 | Gene3D | G3DSA:3.40.5.10 | Ribosomal Protein L9 | 73 | 132 | 7.0E-11 |
| 3 | g2688.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 139 | - |
| 4 | g2688.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 132 | - |
| 1 | g2688.t3 | Pfam | PF01281 | Ribosomal protein L9, N-terminal domain | 74 | 118 | 2.2E-15 |
| 2 | g2688.t3 | SUPERFAMILY | SSF55658 | L9 N-domain-like | 73 | 126 | 2.79E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
