Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L24.

Parent gene

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.t9 TSS g4250.t9 643186 643186
chr_2 g4250 g4250.t9 isoform g4250.t9 643267 643856
chr_2 g4250 g4250.t9 exon g4250.t9.exon1 643267 643354
chr_2 g4250 g4250.t9 cds g4250.t9.CDS1 643322 643354
chr_2 g4250 g4250.t9 exon g4250.t9.exon2 643419 643666
chr_2 g4250 g4250.t9 cds g4250.t9.CDS2 643419 643666
chr_2 g4250 g4250.t9 exon g4250.t9.exon3 643730 643856
chr_2 g4250 g4250.t9 cds g4250.t9.CDS3 643730 643856
chr_2 g4250 g4250.t9 TTS g4250.t9 643979 643979

Sequences

>g4250.t9 Gene=g4250 Length=463
AAATCATTTTAGGATTGGCCTTTGCGTCTTCAGTGGATATAAAATTTACCCAGGAATGGG
AAAAACTCTTGTCAAGAGTGATGGAAAAACCTTCACATTCATCAACAAAAAATGTGAGCG
TTCGTTTTTGATGAAGCGCAACCCTCGTAAAGTTAAATGGACTGTACTTTATCGTCGCAA
GCATAAGAAAGGTATTGAAGAGGAAGCTGCAAGAAAGAGAACACGCCGTACAGTGAAACA
TGCCAGAGCTATTGTTGGAGCTACAATGGCTGACATTATGGCCAAGCGTAACATGAAGCC
AGAAGTTCGCAAAGCTCAACGTGAACAAGCTATTAAAGCTGCAAAGGAGCAGAAAAAGGC
AAAAACCGATGCAAAGAAAGCCAAAACTGCACCAACCAAACAAAAAGCAAAACCAGCTCA
GAAACAACAAAAATCTGCTCCTCGCGTTGGTGGAAAACGATAA

>g4250.t9 Gene=g4250 Length=135
MGKTLVKSDGKTFTFINKKCERSFLMKRNPRKVKWTVLYRRKHKKGIEEEAARKRTRRTV
KHARAIVGATMADIMAKRNMKPEVRKAQREQAIKAAKEQKKAKTDAKKAKTAPTKQKAKP
AQKQQKSAPRVGGKR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4250.t9 Gene3D G3DSA:2.30.170.20 - 1 52 1.2E-20
7 g4250.t9 Gene3D G3DSA:3.30.160.440 - 53 82 1.1E-10
5 g4250.t9 MobiDBLite mobidb-lite consensus disorder prediction 77 135 -
6 g4250.t9 MobiDBLite mobidb-lite consensus disorder prediction 78 112 -
2 g4250.t9 PANTHER PTHR10792 60S RIBOSOMAL PROTEIN L24 2 128 5.9E-44
3 g4250.t9 PANTHER PTHR10792:SF27 60S RIBOSOMAL PROTEIN L24 2 128 5.9E-44
1 g4250.t9 Pfam PF01246 Ribosomal protein L24e 2 50 4.0E-20
4 g4250.t9 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 2 40 5.13E-11

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values