General information for g7488.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L19.
Parent gene
- The parent gene g7488 is located on chr_2: 23982272..23988070 (+ 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 | g7488 | g7488.t23 | TSS | g7488.t23 | 23981889 | 23981889 |
| chr_2 | g7488 | g7488.t23 | isoform | g7488.t23 | 23982272 | 23984887 |
| chr_2 | g7488 | g7488.t23 | exon | g7488.t23.exon1 | 23982272 | 23982881 |
| chr_2 | g7488 | g7488.t23 | cds | g7488.t23.CDS1 | 23982390 | 23982725 |
| chr_2 | g7488 | g7488.t23 | TTS | g7488.t23 | 23982841 | 23982841 |
| chr_2 | g7488 | g7488.t23 | exon | g7488.t23.exon2 | 23984857 | 23984887 |
Sequences
>g7488.t23 Gene=g7488 Length=641
CATCATCAAGAAGCCAGTCGTCGTCCACAGTAGATTCCGCGTTCGCAAAAATACCATTGC
TCGTCGTAAGGGACGTCACTGTGGTTATGGAAAGCGTAAAGGTACAGCTAATGCGAGAAT
GCCTCAAAAATTCCTATGGATGACTCGCATGCGTGTCCTTCGTCGTCTCTTGAAAAAATA
CCGTGAAGCAAAGAAAATCGATCGTCATCTGTATCACGATTTGTACATGAAATCAAAAGG
TAATGTTTTCAAAAATAAGCGCGTTCTTATGGAGCACATTCACAAGCGTAAAGCAGAAAA
GGCTCGTACAAAGATGTTGAACGATCAAGCTGAAGCACGCAGAAACAGAGTCCGTGAAGC
AAGAAAACGTCGCGAACAGAGAATCGCAAATAAGAAGCAAGAATTATTGCAGACTTATGC
AAAGGAGGAAGAAACTCCAGCCGCTAAGAAATAAATTATGCGATATTTTAAGAACCTAAC
GCAAATTTCATAATGAAAAAATTTCCATCTGATGTGTGAAAGTAATAAAAGAATTTTTCA
AATAAAATTTACTGAAAAATATCTAAAATCAACTTCAGATATTTAGTTTTTATTGTTCTG
CTCTGTAAAATTTACGTGCTGATGAAAAGGCATGATCTGTT
>g7488.t23 Gene=g7488 Length=111
MPQKFLWMTRMRVLRRLLKKYREAKKIDRHLYHDLYMKSKGNVFKNKRVLMEHIHKRKAE
KARTKMLNDQAEARRNRVREARKRREQRIANKKQELLQTYAKEEETPAAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7488.t23 | Coils | Coil | Coil | 68 | 95 | - |
| 7 | g7488.t23 | Gene3D | G3DSA:1.10.1200.240 | - | 1 | 108 | 5.6E-47 |
| 6 | g7488.t23 | MobiDBLite | mobidb-lite | consensus disorder prediction | 60 | 87 | - |
| 2 | g7488.t23 | PANTHER | PTHR10722:SF30 | RIBOSOMAL PROTEIN L19 | 1 | 106 | 5.4E-42 |
| 3 | g7488.t23 | PANTHER | PTHR10722 | 60S RIBOSOMAL PROTEIN L19 | 1 | 106 | 5.4E-42 |
| 1 | g7488.t23 | Pfam | PF01280 | Ribosomal protein L19e | 1 | 58 | 1.5E-21 |
| 5 | g7488.t23 | SMART | SM01416 | Ribosomal_L19e_2 | 1 | 58 | 3.7E-9 |
| 4 | g7488.t23 | SUPERFAMILY | SSF48140 | Ribosomal protein L19 (L19e) | 1 | 56 | 4.18E-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:0003723 | RNA binding | MF |
| GO:0022625 | cytosolic large ribosomal subunit | 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.
