General information for g5638.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L10, mitochondrial.
Parent gene
- The parent gene g5638 is located on chr_2: 10794160..10795080 (- 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 | g5638 | g5638.t3 | isoform | g5638.t3 | 10790806 | 10795080 |
| chr_2 | g5638 | g5638.t3 | exon | g5638.t3.exon1 | 10790806 | 10790871 |
| chr_2 | g5638 | g5638.t3 | cds | g5638.t3.CDS1 | 10790838 | 10790871 |
| chr_2 | g5638 | g5638.t3 | exon | g5638.t3.exon2 | 10794164 | 10794864 |
| chr_2 | g5638 | g5638.t3 | cds | g5638.t3.CDS2 | 10794164 | 10794672 |
| chr_2 | g5638 | g5638.t3 | exon | g5638.t3.exon3 | 10795059 | 10795080 |
| chr_2 | g5638 | g5638.t3 | TSS | g5638.t3 | 10795148 | 10795148 |
| chr_2 | g5638 | g5638.t3 | TTS | g5638.t3 | NA | NA |
Sequences
>g5638.t3 Gene=g5638 Length=789
ATGGCAAATTTAATAAGAAAATCGTCCAAGAGTCCATCATTTTGAAAGAGCATTAGTTGT
TGAATTGACAAAACCGATATATCCAAAAAAGGAACGACTAAAGCCATGTCCAGTTGATGA
ATCTTTTTTCACTAAGAAAAATAAATCTGAAGAGATTCATCCATATGTGAGAATTATTGC
TAAAGAAGTGAAAAATTGGTTTGATCATTCAAAAATGATTGGAATTGTCCACATTAATCC
AATGAGCTCTAAAGAATTCTTCAAAGCGCGTGTAGCTTTTCATAAAAGTGGAATGCAAGT
AAAAAAGTATGGCAGTGCTATTTTAAAAACAGCTATAGCTGACACAAAATACGATGTAAT
TAAAGAACTCAACAATAACAAATTCTTTTCGACTGGTTTCATCTTTTGCACTGAACACAA
CAAAGTCAATCAAATGCTGAATATTCTTAAGAAAACTCCTCAAATGACACTACTTTGTGG
AATTGTTGAAGATCGGTTATTATCAAGAAATGAGTTAATTGATTACGCTAATATGCCTGA
TATTCAAATTGTTCGATCACAATTTGCAAATGTGCTAAATTTAGCTGGTAGCACTATTGT
GCAGAATCTTGAGAGTCATCAATTAAATTTGGTTAATATTCTCGATGCACACGTACGTGT
AAATCAAAAATCAGATGAAACAAAAGAAGAATTAACAGCAACAACAAATGAAGCTGAAAA
ATCCTCAACGACTGATGTACATCTGAGAGGAAAATAAAAAGTCGAGAGAAGAGGAGCTGA
AAGGAAAAT
>g5638.t3 Gene=g5638 Length=180
MIGIVHINPMSSKEFFKARVAFHKSGMQVKKYGSAILKTAIADTKYDVIKELNNNKFFST
GFIFCTEHNKVNQMLNILKKTPQMTLLCGIVEDRLLSRNELIDYANMPDIQIVRSQFANV
LNLAGSTIVQNLESHQLNLVNILDAHVRVNQKSDETKEELTATTNEAEKSSTTDVHLRGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5638.t3 | Gene3D | G3DSA:3.30.70.1730 | - | 1 | 107 | 8.3E-24 |
| 4 | g5638.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 154 | 180 | - |
| 1 | g5638.t3 | PANTHER | PTHR11560:SF8 | 39S RIBOSOMAL PROTEIN L10, MITOCHONDRIAL | 1 | 159 | 1.7E-21 |
| 2 | g5638.t3 | PANTHER | PTHR11560 | 39S RIBOSOMAL PROTEIN L10, MITOCHONDRIAL | 1 | 159 | 1.7E-21 |
| 3 | g5638.t3 | SUPERFAMILY | SSF160369 | Ribosomal protein L10-like | 1 | 147 | 3.14E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5638/g5638.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5638.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042254 | ribosome biogenesis | BP |
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. There were no conditions that were differentially expressed