General information for g6215.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L28.
Parent gene
- The parent gene g6215 is located on chr_2: 15292124..15292626 (- 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 | g6215 | g6215.t20 | TTS | g6215.t20 | 15291317 | 15291317 |
| chr_2 | g6215 | g6215.t20 | isoform | g6215.t20 | 15291398 | 15292626 |
| chr_2 | g6215 | g6215.t20 | exon | g6215.t20.exon1 | 15291398 | 15291598 |
| chr_2 | g6215 | g6215.t20 | cds | g6215.t20.CDS1 | 15291398 | 15291598 |
| chr_2 | g6215 | g6215.t20 | exon | g6215.t20.exon2 | 15291781 | 15291909 |
| chr_2 | g6215 | g6215.t20 | cds | g6215.t20.CDS2 | 15291781 | 15291909 |
| chr_2 | g6215 | g6215.t20 | exon | g6215.t20.exon3 | 15292095 | 15292192 |
| chr_2 | g6215 | g6215.t20 | cds | g6215.t20.CDS3 | 15292095 | 15292184 |
| chr_2 | g6215 | g6215.t20 | exon | g6215.t20.exon4 | 15292291 | 15292626 |
| chr_2 | g6215 | g6215.t20 | TSS | g6215.t20 | 15292596 | 15292596 |
Sequences
>g6215.t20 Gene=g6215 Length=764
ATGATGCAGAGAAAAAATGATGCGAACTTTCTTTTCGTTCCATCTGTCAAAATGTAAGTA
ATCACTAAACCTTTATTTCTAAATTTGTGCTTGCAAATAATGGAAATTAAGTAACAAAAA
GTGGTTTATTAATATATTTGAATGTATCTTTATCGTATAATTATCGAGTTTGCATGAAAT
AATTGTGTTTGTAGTGTATAAATGGAAAATTAATTTTTCCACACGCGGTTTACAAAACAA
AAAATTCAAAATGACTGCTTTTTTGTGTTTGCAAGTAAAACAACTTATTAATTATATTAA
AAGCATGATTAAAAATGAGTGCCATACTAAACTAACAGAGAAAAATGGCCTCGTCGCATC
TCAATTGGCTGATTGTTCGCGATAACAACGCTTTTATTTTAAAGCAACGTAATATCCGCA
AGCCATTCAGCAAGGAACCAAACAATTTGATGAATGTCAGCACATTCCGCTATAGTGGAT
TAGTTCATCCACACGCGATTGGTATCACACCATCAGTTGACAAGAAGGGAATCATCTTTT
CATACAAAAAACCCAAAAAATTGTATAAACCAGCTGAAAGCATTGGAAGAATCACCTTCA
AATCGGGCCAGAAGCGTACATTGAAGAAAGTTAAGAACGTCATTCAATCAAAGAAATACC
GTCGTGATTTACAACAGGCTGCTTTGAGACGTGTCAGTGCTATCTATCGCTCACAGAAAA
CAAAGCCCGCTAAAAAGAAGGGCGGCGCAAAGAAAGCCGAATAA
>g6215.t20 Gene=g6215 Length=139
MASSHLNWLIVRDNNAFILKQRNIRKPFSKEPNNLMNVSTFRYSGLVHPHAIGITPSVDK
KGIIFSYKKPKKLYKPAESIGRITFKSGQKRTLKKVKNVIQSKKYRRDLQQAALRRVSAI
YRSQKTKPAKKKGGAKKAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6215.t20 | Gene3D | G3DSA:3.30.390.110 | - | 3 | 128 | 4.8E-44 |
| 5 | g6215.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 139 | - |
| 4 | g6215.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 139 | - |
| 2 | g6215.t20 | PANTHER | PTHR10544:SF0 | 60S RIBOSOMAL PROTEIN L28 | 1 | 132 | 2.8E-38 |
| 3 | g6215.t20 | PANTHER | PTHR10544 | 60S RIBOSOMAL PROTEIN L28 | 1 | 132 | 2.8E-38 |
| 1 | g6215.t20 | Pfam | PF01778 | Ribosomal L28e protein family | 6 | 123 | 1.1E-31 |
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 K02903 (large subunit ribosomal protein L28e)
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.
