General information for g4250.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L24.
Parent gene
- The parent gene g4250 is located on chr_2: 643419..643856 (+ 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 | g4250 | g4250.t2 | isoform | g4250.t2 | 642967 | 643856 |
| chr_2 | g4250 | g4250.t2 | exon | g4250.t2.exon1 | 642967 | 642977 |
| chr_2 | g4250 | g4250.t2 | exon | g4250.t2.exon2 | 643187 | 643217 |
| chr_2 | g4250 | g4250.t2 | cds | g4250.t2.CDS1 | 643213 | 643217 |
| chr_2 | g4250 | g4250.t2 | exon | g4250.t2.exon3 | 643279 | 643354 |
| chr_2 | g4250 | g4250.t2 | cds | g4250.t2.CDS2 | 643279 | 643354 |
| chr_2 | g4250 | g4250.t2 | exon | g4250.t2.exon4 | 643419 | 643666 |
| chr_2 | g4250 | g4250.t2 | cds | g4250.t2.CDS3 | 643419 | 643666 |
| chr_2 | g4250 | g4250.t2 | exon | g4250.t2.exon5 | 643730 | 643856 |
| chr_2 | g4250 | g4250.t2 | cds | g4250.t2.CDS4 | 643730 | 643856 |
| chr_2 | g4250 | g4250.t2 | TTS | g4250.t2 | 643979 | 643979 |
| chr_2 | g4250 | g4250.t2 | TSS | g4250.t2 | NA | NA |
Sequences
>g4250.t2 Gene=g4250 Length=493
TCATTTCTTAGGAATTTGAAACCTAAAAGAAATCAAAATGAAGATTGGCCTTTGCGTCTT
CAGTGGATATAAAATTTACCCAGGAATGGGAAAAACTCTTGTCAAGAGTGATGGAAAAAC
CTTCACATTCATCAACAAAAAATGTGAGCGTTCGTTTTTGATGAAGCGCAACCCTCGTAA
AGTTAAATGGACTGTACTTTATCGTCGCAAGCATAAGAAAGGTATTGAAGAGGAAGCTGC
AAGAAAGAGAACACGCCGTACAGTGAAACATGCCAGAGCTATTGTTGGAGCTACAATGGC
TGACATTATGGCCAAGCGTAACATGAAGCCAGAAGTTCGCAAAGCTCAACGTGAACAAGC
TATTAAAGCTGCAAAGGAGCAGAAAAAGGCAAAAACCGATGCAAAGAAAGCCAAAACTGC
ACCAACCAAACAAAAAGCAAAACCAGCTCAGAAACAACAAAAATCTGCTCCTCGCGTTGG
TGGAAAACGATAA
>g4250.t2 Gene=g4250 Length=151
MKIGLCVFSGYKIYPGMGKTLVKSDGKTFTFINKKCERSFLMKRNPRKVKWTVLYRRKHK
KGIEEEAARKRTRRTVKHARAIVGATMADIMAKRNMKPEVRKAQREQAIKAAKEQKKAKT
DAKKAKTAPTKQKAKPAQKQQKSAPRVGGKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4250.t2 | CDD | cd00472 | Ribosomal_L24e_L24 | 1 | 54 | 3.42796E-24 |
| 9 | g4250.t2 | Gene3D | G3DSA:2.30.170.20 | - | 1 | 68 | 1.3E-31 |
| 8 | g4250.t2 | Gene3D | G3DSA:3.30.160.440 | - | 69 | 98 | 1.3E-10 |
| 6 | g4250.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 93 | 151 | - |
| 7 | g4250.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 94 | 128 | - |
| 2 | g4250.t2 | PANTHER | PTHR10792 | 60S RIBOSOMAL PROTEIN L24 | 1 | 144 | 4.4E-56 |
| 3 | g4250.t2 | PANTHER | PTHR10792:SF27 | 60S RIBOSOMAL PROTEIN L24 | 1 | 144 | 4.4E-56 |
| 1 | g4250.t2 | Pfam | PF01246 | Ribosomal protein L24e | 1 | 66 | 7.2E-31 |
| 5 | g4250.t2 | SMART | SM00746 | 4TRASH | 6 | 44 | 2.4E-5 |
| 4 | g4250.t2 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 5 | 56 | 1.57E-19 |
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.
