General information for g2688.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | isoform | g2688.t1 | 19719738 | 19720635 |
| chr_3 | g2688 | g2688.t1 | exon | g2688.t1.exon1 | 19719738 | 19719824 |
| chr_3 | g2688 | g2688.t1 | cds | g2688.t1.CDS1 | 19719738 | 19719824 |
| chr_3 | g2688 | g2688.t1 | exon | g2688.t1.exon2 | 19719887 | 19720216 |
| chr_3 | g2688 | g2688.t1 | cds | g2688.t1.CDS2 | 19719887 | 19720216 |
| chr_3 | g2688 | g2688.t1 | exon | g2688.t1.exon3 | 19720279 | 19720635 |
| chr_3 | g2688 | g2688.t1 | cds | g2688.t1.CDS3 | 19720279 | 19720635 |
| chr_3 | g2688 | g2688.t1 | TTS | g2688.t1 | 19720730 | 19720730 |
| chr_3 | g2688 | g2688.t1 | TSS | g2688.t1 | NA | NA |
Sequences
>g2688.t1 Gene=g2688 Length=774
ATGTTGAGATCAATATTTAAAAGTGGAATTAATTCCATTTCTACGCATTTATTAACATCT
AATAATGCTGTAACACAGCAAGTTAGAACAACTTTTATATTGAGAAGAAAATATCCATTA
GAATTGCATAAAAAGAATCAAAAACCAAGAAAATTAAGAGGAAAACATTTTAATTATGTC
CTTGTTGAAGACACAAATAGAACAGTTAAACCTGACATTGAGGTTGTTTTAAAGCAGTTT
ATTCATGGTGTAGGAAAGAAAGGCGAAATTGTAAAAGTTCGACCAAATTTTGCTTATAAT
GAACTTCTTTTGACTGATAAAGCAGCTTATGCTACACCTGAAAATATAGAGAAATATAAA
TTGAAAGAAGGCGAAGAGAGTCAAGAAGAGAAGTATAGTTCACCATATGCTCAAAGAACA
GTAAATATGCTTCAGAATCGTGTATTTGCTATAGTAATGAATAAGGAACAACCTTGGGTA
ATTGAACCATGGCATGTTCGAGCTTCTTTACGAAAATGCGGCTATCATATCTTATCAGAT
GATGCTATTGAATTACCACAAGAAAAAATTACTGGTCCTGACTTACAAAAACAGAATAAA
GAATTTATTGTTACTGTAACAATCAATAAAATGGAAAAAGCTAAAGTAAGATGTCGAATC
CATCATTGGAGCACAAATCCTAGTGATCGACTTCCATACGTTTATGAACATTGGTTACAA
GATACAGAACCGCTTTTTCCTTCTGAACAAAAATCAAACGAATCATCTTCGTAA
>g2688.t1 Gene=g2688 Length=257
MLRSIFKSGINSISTHLLTSNNAVTQQVRTTFILRRKYPLELHKKNQKPRKLRGKHFNYV
LVEDTNRTVKPDIEVVLKQFIHGVGKKGEIVKVRPNFAYNELLLTDKAAYATPENIEKYK
LKEGEESQEEKYSSPYAQRTVNMLQNRVFAIVMNKEQPWVIEPWHVRASLRKCGYHILSD
DAIELPQEKITGPDLQKQNKEFIVTVTINKMEKAKVRCRIHHWSTNPSDRLPYVYEHWLQ
DTEPLFPSEQKSNESSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2688.t1 | Gene3D | G3DSA:3.40.5.10 | Ribosomal Protein L9 | 73 | 132 | 0 |
| 2 | g2688.t1 | PANTHER | PTHR21368:SF18 | 39S RIBOSOMAL PROTEIN L9, MITOCHONDRIAL | 65 | 222 | 0 |
| 3 | g2688.t1 | PANTHER | PTHR21368 | 50S RIBOSOMAL PROTEIN L9 | 65 | 222 | 0 |
| 1 | g2688.t1 | Pfam | PF01281 | Ribosomal protein L9, N-terminal domain | 74 | 118 | 0 |
| 4 | g2688.t1 | SUPERFAMILY | SSF55658 | L9 N-domain-like | 73 | 126 | 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 K02939 (large subunit ribosomal protein L9)
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.
