General information for g12442.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable ribosome biogenesis protein RLP24.
Parent gene
- The parent gene g12442 is located on chr_1: 23670383..23670998 (- 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_1 | g12442 | g12442.t1 | TTS | g12442.t1 | 23670306 | 23670306 |
| chr_1 | g12442 | g12442.t1 | isoform | g12442.t1 | 23670383 | 23670998 |
| chr_1 | g12442 | g12442.t1 | exon | g12442.t1.exon1 | 23670383 | 23670856 |
| chr_1 | g12442 | g12442.t1 | cds | g12442.t1.CDS1 | 23670383 | 23670856 |
| chr_1 | g12442 | g12442.t1 | exon | g12442.t1.exon2 | 23670918 | 23670998 |
| chr_1 | g12442 | g12442.t1 | cds | g12442.t1.CDS2 | 23670918 | 23670998 |
| chr_1 | g12442 | g12442.t1 | TSS | g12442.t1 | 23671109 | 23671109 |
Sequences
>g12442.t1 Gene=g12442 Length=555
ATGAGAATAGAAACGTGTTATTTTTGTTCAAGTAAAATTTATCCAGGACATGGAATGCTT
TTCGTTAGAAATGATTGCAAACAATTCAGATTTTGTCGTAAAAAGTGTAGGAAAGCGTTT
CAAAGAAAGAAGAATCCAAGAAAGGCAAAATGGACAAAGGCATATCGTAAATTGGCTGGA
AAAGAGCTCACAATTGATCCATGTTTTGAATTTGAGAAACGAAGAAATGTTCCAGTCAAA
TATGATCGTGAGTTGTGGACAAAAACAATTGATGCAATCAAAAAGATCAATGAAATCAAA
GAAAGACGTGAAAGACACTTTGTTATGGAGAGATTGCGTAAAGGAACACAACGTGAAATT
CACAATGATATTCGTGATGTACAAAAGAATCTATCATTGATTAGAGCACCAGAAGGAATT
CGAAAGAAGGATACAGAAGACGAAATGAAAATGGAAGAAGATGAAGAAGAAATCGAGTAC
ATGCCTGCACTTGAAATGGAAAAGAAATTATCTGCTGGTATTATGGATATCGATACTGTG
AAAATGAAGAATTAA
>g12442.t1 Gene=g12442 Length=184
MRIETCYFCSSKIYPGHGMLFVRNDCKQFRFCRKKCRKAFQRKKNPRKAKWTKAYRKLAG
KELTIDPCFEFEKRRNVPVKYDRELWTKTIDAIKKINEIKERRERHFVMERLRKGTQREI
HNDIRDVQKNLSLIRAPEGIRKKDTEDEMKMEEDEEEIEYMPALEMEKKLSAGIMDIDTV
KMKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12442.t1 | CDD | cd00472 | Ribosomal_L24e_L24 | 1 | 54 | 1.84652E-26 |
| 7 | g12442.t1 | Gene3D | G3DSA:2.30.170.20 | - | 1 | 67 | 4.1E-30 |
| 2 | g12442.t1 | PANTHER | PTHR10792:SF26 | RIBOSOME BIOGENESIS PROTEIN RLP24-RELATED | 1 | 150 | 1.9E-58 |
| 3 | g12442.t1 | PANTHER | PTHR10792 | 60S RIBOSOMAL PROTEIN L24 | 1 | 150 | 1.9E-58 |
| 1 | g12442.t1 | Pfam | PF01246 | Ribosomal protein L24e | 1 | 64 | 1.3E-31 |
| 6 | g12442.t1 | ProSitePatterns | PS01073 | Ribosomal protein L24e signature. | 8 | 25 | - |
| 5 | g12442.t1 | SMART | SM00746 | 4TRASH | 6 | 44 | 8.5E-9 |
| 4 | g12442.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 4 | 56 | 4.99E-20 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K02896 (large subunit ribosomal protein L24e)
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.
