General information for g14568.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L27.
Parent gene
- The parent gene g14568 is located on chr_4: 1370804..1371456 (- 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_4 | g14568 | g14568.t4 | TTS | g14568.t4 | 1370129 | 1370129 |
| chr_4 | g14568 | g14568.t4 | isoform | g14568.t4 | 1370263 | 1371405 |
| chr_4 | g14568 | g14568.t4 | exon | g14568.t4.exon1 | 1370263 | 1370454 |
| chr_4 | g14568 | g14568.t4 | cds | g14568.t4.CDS1 | 1370263 | 1370454 |
| chr_4 | g14568 | g14568.t4 | exon | g14568.t4.exon2 | 1370803 | 1371041 |
| chr_4 | g14568 | g14568.t4 | cds | g14568.t4.CDS2 | 1370803 | 1371021 |
| chr_4 | g14568 | g14568.t4 | exon | g14568.t4.exon3 | 1371347 | 1371405 |
| chr_4 | g14568 | g14568.t4 | TSS | g14568.t4 | 1371456 | 1371456 |
Sequences
>g14568.t4 Gene=g14568 Length=490
TATTAAAAATCAAAAAATCAGTGGAAAATGTGAAAGAAAATTTATGAAAAGTTAATTAAA
AACATTAAAAAAGCCAAACATGGGGAAGATCATGAAATCCGGTAAAGTTGTGCTCGTGCT
GAGCGGGCGATATGCTGGTCGCAAAGCGATCATTATGAAGACATTTGATGAAGGTACATC
AGAAAAGCTCTTCGGACAAGCGCTCGTAGCAGGCATTGATCGCTATCCAAGACGTGTCAC
AAGAAGAATGAATAAAGCTAAAGTGCACAAAAATTGCAGAATTAAGCCATTCGTTAAGCT
CATTAACTACAATCACCTTATGCCAACACGTTATAGCGTACCAGAAGTGACACTTGATAA
CAAATACAGCGTGAAGGACTTGAAAGATCCAATTAAACGCAAAAAGGCCCGCTTCCAAAT
TAGAATGCGCTTTGAAGATCGCTACAAGAGTGGAAAGAACAAATGGTTCTTCACTAAACT
TCGCTTCTAA
>g14568.t4 Gene=g14568 Length=136
MGKIMKSGKVVLVLSGRYAGRKAIIMKTFDEGTSEKLFGQALVAGIDRYPRRVTRRMNKA
KVHKNCRIKPFVKLINYNHLMPTRYSVPEVTLDNKYSVKDLKDPIKRKKARFQIRMRFED
RYKSGKNKWFFTKLRF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g14568.t4 | CDD | cd06090 | KOW_RPL27 | 6 | 87 | 6.42406E-42 |
| 7 | g14568.t4 | Gene3D | G3DSA:2.30.30.770 | - | 1 | 136 | 1.8E-58 |
| 3 | g14568.t4 | PANTHER | PTHR10497:SF0 | 60S RIBOSOMAL PROTEIN L27 | 1 | 136 | 1.2E-50 |
| 4 | g14568.t4 | PANTHER | PTHR10497 | 60S RIBOSOMAL PROTEIN L27 | 1 | 136 | 1.2E-50 |
| 2 | g14568.t4 | Pfam | PF00467 | KOW motif | 8 | 32 | 3.5E-5 |
| 1 | g14568.t4 | Pfam | PF01777 | Ribosomal L27e protein family | 52 | 136 | 9.4E-32 |
| 6 | g14568.t4 | ProSitePatterns | PS01107 | Ribosomal protein L27e signature. | 125 | 136 | - |
| 5 | g14568.t4 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 3 | 136 | 2.18E-17 |
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 K02901 (large subunit ribosomal protein L27e)
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.
