General information for g3799.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L2, mitochondrial.
Parent gene
- The parent gene g3799 is located on chr_3: 27993965..27995082 (- 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 | g3799 | g3799.t3 | TTS | g3799.t3 | 27992846 | 27992846 |
| chr_3 | g3799 | g3799.t3 | isoform | g3799.t3 | 27992901 | 27993965 |
| chr_3 | g3799 | g3799.t3 | exon | g3799.t3.exon1 | 27992901 | 27993561 |
| chr_3 | g3799 | g3799.t3 | cds | g3799.t3.CDS1 | 27992901 | 27993407 |
| chr_3 | g3799 | g3799.t3 | exon | g3799.t3.exon2 | 27993620 | 27993965 |
| chr_3 | g3799 | g3799.t3 | TSS | g3799.t3 | 27993978 | 27993978 |
Sequences
>g3799.t3 Gene=g3799 Length=1007
ATGAGTTTCAAAATTTTAAGACACTCATTAAATTTATTTTCTAAACAATTACCAGCTCTG
CCAGTCATTTCAAATCACATTAATCTTCAACTTGTACGTGCTCTTCCTCATTTCGTTGAT
AAACCAACACCGGGTAATTTGAATTATATTGTATACGATCAAATTAATTTTAAAGGCTAT
TTATTTATCCTACAGGAAAAGATCATAAACAATATAGAAGAACTGTTCATTTCCCCGAAG
ATGGAAATTATACCATAAAACCACTTGATAACACACATTTAGCTGGTCGAGATCCAGTAA
CAGGAAGAGTTGTTGCAAAAGGTATTGGCGGAGGAATAAAATTCAAATATCATTGGATTA
AATATAATAGAGATGGACCAGAAGAAGGACCTCCACAAGAAGAAAGAGTGTTACAAATTC
TCAAATGCGGTTGCAGAACAGCAGACGTTGCTCTTGTCGGTGTTGGAAAGGAACTCAAAT
ACATTTTAGCAACTGAGAATATGAAGGCTGGCGATATTATTAAAACGTCAAAATTCATTC
CGAGAATTCCTGTTAGAGCAAATGAAGGCGATGCATATCCTCTTGGTGCTCTACCAGTAG
GCACAATCGTTCACAACATTGAAAAATATCCTGGCTGTAATAAACATTTTGTGCATGCTG
CTGGTGTATTTGCTACTATTCTGAGAAAATTTGATGATCGAGTAGTTATATTGATGCCAA
ACAAAAGAGAATATGCTTTGCTAGAGAAATGTATGGCAACTGTAGGTCGATTATCAAATG
TTGAACACTCGAGAACACCAATTCCCTCAGTACACAGATGGCGTGAACTTGGAAACCGAC
CAAGATCGGGACTTTGGCAAAGAAAGAGCGGTAGACATGGTAGAAAAATTAAGAAACCAC
CACCAATGAAACTACATGGACCTCCAAAGCAGCCAGAAAAGCCACCATTAAAGCTCACAA
TCAATCGTGTTTCAAAAGGAGGAGGAACATATATTAATCCACTCTAA
>g3799.t3 Gene=g3799 Length=168
MKAGDIIKTSKFIPRIPVRANEGDAYPLGALPVGTIVHNIEKYPGCNKHFVHAAGVFATI
LRKFDDRVVILMPNKREYALLEKCMATVGRLSNVEHSRTPIPSVHRWRELGNRPRSGLWQ
RKSGRHGRKIKKPPPMKLHGPPKQPEKPPLKLTINRVSKGGGTYINPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3799.t3 | Gene3D | G3DSA:2.30.30.30 | - | 17 | 93 | 7.0E-22 |
| 7 | g3799.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 149 | - |
| 6 | g3799.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 136 | - |
| 2 | g3799.t3 | PANTHER | PTHR13691:SF5 | 39S RIBOSOMAL PROTEIN L2, MITOCHONDRIAL | 2 | 143 | 4.4E-23 |
| 3 | g3799.t3 | PANTHER | PTHR13691 | RIBOSOMAL PROTEIN L2 | 2 | 143 | 4.4E-23 |
| 1 | g3799.t3 | Pfam | PF03947 | Ribosomal Proteins L2, C-terminal domain | 22 | 115 | 8.8E-20 |
| 5 | g3799.t3 | SMART | SM01382 | Ribosomal_L2_C_2 | 20 | 142 | 4.3E-14 |
| 4 | g3799.t3 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 23 | 144 | 1.02E-30 |
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 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.
