General information for g10885.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L23, mitochondrial.
Parent gene
- The parent gene g10885 is located on chr_1: 12445895..12446465 (- 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 | g10885 | g10885.t1 | TTS | g10885.t1 | 12445305 | 12445305 |
| chr_1 | g10885 | g10885.t1 | isoform | g10885.t1 | 12445366 | 12445895 |
| chr_1 | g10885 | g10885.t1 | exon | g10885.t1.exon1 | 12445366 | 12445686 |
| chr_1 | g10885 | g10885.t1 | cds | g10885.t1.CDS1 | 12445366 | 12445686 |
| chr_1 | g10885 | g10885.t1 | exon | g10885.t1.exon2 | 12445752 | 12445895 |
| chr_1 | g10885 | g10885.t1 | cds | g10885.t1.CDS2 | 12445752 | 12445895 |
| chr_1 | g10885 | g10885.t1 | TSS | g10885.t1 | 12445965 | 12445965 |
Sequences
>g10885.t1 Gene=g10885 Length=465
ATGAGTACAAGATGGTATCCACTTTATCAAAAAGGCAATCCACAATTACGTGTCTTCTTG
CCTAATTTTTGGATGAAACTTCTTAAACCAGCTCATCAAACGCAACCGAAGAATGTTGTT
TGCTTTGAAGTTTCTATGCAAATGACAAAAGCCGATATAAAGAATTATTTAGAAAAGATT
TATAAACTTCCAGTAGTTGATGTACGAACGAGAATAAGAATGGGAAGATTTAAGAGAGAA
GAGAGATCAGGCTATATTATTAAAGAAAAAGATCCAAAACTCGCTTATGTCACATTACCT
AAAGAAGTCAGCTTTACTTTTCCAGATTTATTTCCTGAAGATAATGAAACTAAGAAGAAT
CTTAAAGATGATGAAAAAGCATTGGATCAAGCAAAAGAGAAATATAAAGAATTTCTCGAT
AGAAATTCAAAACGACGCGATCTACCTGGATGGTTTTCTATTTAA
>g10885.t1 Gene=g10885 Length=154
MSTRWYPLYQKGNPQLRVFLPNFWMKLLKPAHQTQPKNVVCFEVSMQMTKADIKNYLEKI
YKLPVVDVRTRIRMGRFKREERSGYIIKEKDPKLAYVTLPKEVSFTFPDLFPEDNETKKN
LKDDEKALDQAKEKYKEFLDRNSKRRDLPGWFSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10885.t1 | Coils | Coil | Coil | 114 | 141 | - |
| 4 | g10885.t1 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 154 | 5.9E-50 |
| 2 | g10885.t1 | PANTHER | PTHR12059 | RIBOSOMAL PROTEIN L23-RELATED | 6 | 153 | 6.9E-39 |
| 1 | g10885.t1 | Pfam | PF00276 | Ribosomal protein L23 | 35 | 106 | 3.0E-14 |
| 3 | g10885.t1 | SUPERFAMILY | SSF54189 | Ribosomal proteins S24e, L23 and L15e | 9 | 104 | 9.35E-21 |
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 K02892 (large subunit ribosomal protein L23)
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.
