General information for g5638.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g5638.t1 | 10794098 | 10794098 |
| chr_2 | g5638 | g5638.t1 | isoform | g5638.t1 | 10794160 | 10795080 |
| chr_2 | g5638 | g5638.t1 | exon | g5638.t1.exon1 | 10794160 | 10794864 |
| chr_2 | g5638 | g5638.t1 | cds | g5638.t1.CDS1 | 10794160 | 10794864 |
| chr_2 | g5638 | g5638.t1 | exon | g5638.t1.exon2 | 10794929 | 10794993 |
| chr_2 | g5638 | g5638.t1 | cds | g5638.t1.CDS2 | 10794929 | 10794993 |
| chr_2 | g5638 | g5638.t1 | exon | g5638.t1.exon3 | 10795059 | 10795080 |
| chr_2 | g5638 | g5638.t1 | cds | g5638.t1.CDS3 | 10795059 | 10795080 |
| chr_2 | g5638 | g5638.t1 | TSS | g5638.t1 | 10795148 | 10795148 |
Sequences
>g5638.t1 Gene=g5638 Length=792
ATGGCAAATTTAATAAGAAAATCTTTTCTATCGCCACAGCTACCAAATTTAGCATTTAAG
CGCTTTCGAGGAAAAATTAACATTCAACGTCCAAGAGTCCATCATTTTGAAAGAGCATTA
GTTGTTGAATTGACAAAACCGATATATCCAAAAAAGGAACGACTAAAGCCATGTCCAGTT
GATGAATCTTTTTTCACTAAGAAAAATAAATCTGAAGAGATTCATCCATATGTGAGAATT
ATTGCTAAAGAAGTGAAAAATTGGTTTGATCATTCAAAAATGATTGGAATTGTCCACATT
AATCCAATGAGCTCTAAAGAATTCTTCAAAGCGCGTGTAGCTTTTCATAAAAGTGGAATG
CAAGTAAAAAAGTATGGCAGTGCTATTTTAAAAACAGCTATAGCTGACACAAAATACGAT
GTAATTAAAGAACTCAACAATAACAAATTCTTTTCGACTGGTTTCATCTTTTGCACTGAA
CACAACAAAGTCAATCAAATGCTGAATATTCTTAAGAAAACTCCTCAAATGACACTACTT
TGTGGAATTGTTGAAGATCGGTTATTATCAAGAAATGAGTTAATTGATTACGCTAATATG
CCTGATATTCAAATTGTTCGATCACAATTTGCAAATGTGCTAAATTTAGCTGGTAGCACT
ATTGTGCAGAATCTTGAGAGTCATCAATTAAATTTGGTTAATATTCTCGATGCACACGTA
CGTGTAAATCAAAAATCAGATGAAACAAAAGAAGAATTAACAGCAACAACAAATGAAGCT
GAAAAATCGTAA
>g5638.t1 Gene=g5638 Length=263
MANLIRKSFLSPQLPNLAFKRFRGKINIQRPRVHHFERALVVELTKPIYPKKERLKPCPV
DESFFTKKNKSEEIHPYVRIIAKEVKNWFDHSKMIGIVHINPMSSKEFFKARVAFHKSGM
QVKKYGSAILKTAIADTKYDVIKELNNNKFFSTGFIFCTEHNKVNQMLNILKKTPQMTLL
CGIVEDRLLSRNELIDYANMPDIQIVRSQFANVLNLAGSTIVQNLESHQLNLVNILDAHV
RVNQKSDETKEELTATTNEAEKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5638.t1 | Coils | Coil | Coil | 246 | 263 | - |
| 4 | g5638.t1 | Gene3D | G3DSA:3.30.70.1730 | - | 24 | 200 | 8.6E-43 |
| 1 | g5638.t1 | PANTHER | PTHR11560:SF8 | 39S RIBOSOMAL PROTEIN L10, MITOCHONDRIAL | 15 | 252 | 9.5E-33 |
| 2 | g5638.t1 | PANTHER | PTHR11560 | 39S RIBOSOMAL PROTEIN L10, MITOCHONDRIAL | 15 | 252 | 9.5E-33 |
| 3 | g5638.t1 | SUPERFAMILY | SSF160369 | Ribosomal protein L10-like | 80 | 240 | 1.7E-25 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5638/g5638.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5638.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042254 | ribosome biogenesis | BP |
KEGG
Orthology
- This transcript has been annotated with K02864 (large subunit ribosomal protein L10)
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.
