General information for g6548.t15
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L37a.
Parent gene
- The parent gene g6548 is located on chr_2: 17606925..17607974 (+ 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 | g6548 | g6548.t15 | isoform | g6548.t15 | 17606637 | 17607265 |
| chr_2 | g6548 | g6548.t15 | exon | g6548.t15.exon1 | 17606637 | 17606676 |
| chr_2 | g6548 | g6548.t15 | exon | g6548.t15.exon2 | 17606996 | 17607265 |
| chr_2 | g6548 | g6548.t15 | cds | g6548.t15.CDS1 | 17607065 | 17607265 |
| chr_2 | g6548 | g6548.t15 | TTS | g6548.t15 | 17607339 | 17607339 |
| chr_2 | g6548 | g6548.t15 | TSS | g6548.t15 | NA | NA |
Sequences
>g6548.t15 Gene=g6548 Length=310
CAATCGTCGAGGTTTGTGTTCATTAATTTTTATTAAAATAGCAAAGCGTACAAAGAAGGT
CGGAATTGTTGGTAAATATGGTACTCGTTATGGTGCATCGCTGAGAAAGATGGTCAAGAA
AATTGAAATCTCACAGCACGGCAAATATACATGCAGTTTCTGTGGTAAAGATGCAATGAA
ACGCACTTGTGTTGGTATCTGGAGTTGCAAACGATGCAAGCGAGTAGTTGCTGGAGGAGC
ATGGGTTTTTTCCACAACAGCAGCAGCCACCGTACGCTCAGCAGTCAGACGTTTGAGAGA
ATTGAACTAA
>g6548.t15 Gene=g6548 Length=66
MVKKIEISQHGKYTCSFCGKDAMKRTCVGIWSCKRCKRVVAGGAWVFSTTAAATVRSAVR
RLRELN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6548.t15 | Coils | Coil | Coil | 55 | 66 | - |
| 4 | g6548.t15 | Gene3D | G3DSA:2.20.25.30 | - | 1 | 66 | 8.9E-31 |
| 2 | g6548.t15 | PANTHER | PTHR48188 | 60S RIBOSOMAL PROTEIN L43 | 1 | 65 | 3.1E-28 |
| 1 | g6548.t15 | Pfam | PF01780 | Ribosomal L37ae protein family | 1 | 64 | 3.5E-28 |
| 3 | g6548.t15 | SUPERFAMILY | SSF57829 | Zn-binding ribosomal proteins | 1 | 57 | 4.64E-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:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02921 (large subunit ribosomal protein L37Ae)
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.
