Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S acidic ribosomal protein P0.

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_3 g3384 g3384.t7 isoform g3384.t7 25009825 25011330
chr_3 g3384 g3384.t7 exon g3384.t7.exon1 25009825 25010140
chr_3 g3384 g3384.t7 TTS g3384.t7 25009832 25009832
chr_3 g3384 g3384.t7 cds g3384.t7.CDS1 25010043 25010140
chr_3 g3384 g3384.t7 exon g3384.t7.exon2 25010203 25011001
chr_3 g3384 g3384.t7 cds g3384.t7.CDS2 25010203 25011001
chr_3 g3384 g3384.t7 exon g3384.t7.exon3 25011295 25011330
chr_3 g3384 g3384.t7 cds g3384.t7.CDS3 25011295 25011330
chr_3 g3384 g3384.t7 TSS g3384.t7 25011604 25011604

Sequences

>g3384.t7 Gene=g3384 Length=1151
ATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACACATATCTCGACGAATATCCAAAA
TGTTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCA
CTTCGTGGACTCGCTGTAGTCTTGATGGGCAAGAACACTATGATGCGTAAAGCCATTAAG
GGCCATTTGGAAAACAATCAAGCCCTCGACAGAATTTTACCACACATTCGTGGTAATGTT
GGTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAAAAGTTGTTGCAAAACAAA
GTTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAAGTAATTATTCCTGCTCAA
AATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCTCTTTCAATTCCAACAAAG
ATTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATCTTAAAGCCTGGTGACAAA
GTCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATCTCTCCATTCTCATATGGT
TTGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCTCCAAATATCTTGGACATC
AAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCAAACGTTGCCGCTCTTTCA
TTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAG
AACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAA
GAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCTGCATCAGCTCCAGCTGCT
TCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGAGTCAGAACCAGAGTCT
GATGACGACATGGGATTCGGACTTTTTGATTAAACATTGCAACATCATCAAATGGTCATT
ACAATTTGAATCAACGTTAATTTTCTTCTGCAATAAATTTGCAAATACTTGCCCATCAAT
GGCAACTTGCAATTTTTATTGCAAAATAAAGAATTGATTCTTTTCACACCATTACATCAT
TTAAATTGTGTTTTTGCCTGAAGACCGGCAATTTAATGCTGAAATAAAATTGACCAAAAA
AAAACAAAATA

>g3384.t7 Gene=g3384 Length=310
MVRENKATWKANTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTMMRKAIK
GHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCEVIIPAQ
NTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNISPFSYG
LVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHSIANGFK
NLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKKEESEPES
DDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t7 CDD cd05795 Ribosomal_P0_L10e 4 176 1.15234E-97
8 g3384.t7 Gene3D G3DSA:3.90.105.20 - 104 176 3.9E-32
7 g3384.t7 MobiDBLite mobidb-lite consensus disorder prediction 278 310 -
4 g3384.t7 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 310 2.8E-143
5 g3384.t7 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 310 2.8E-143
9 g3384.t7 PIRSF PIRSF039087 L10E 2 310 1.2E-136
2 g3384.t7 Pfam PF00466 Ribosomal protein L10 12 98 1.0E-17
1 g3384.t7 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 105 174 5.3E-22
3 g3384.t7 Pfam PF00428 60s Acidic ribosomal protein 225 309 1.6E-18
6 g3384.t7 SUPERFAMILY SSF160369 Ribosomal protein L10-like 11 126 1.44E-15

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:0042254 ribosome biogenesis BP

KEGG

Orthology

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.

Raw TPM values