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.t41 TTS g3384.t41 25009832 25009832
chr_3 g3384 g3384.t41 isoform g3384.t41 25010043 25011604
chr_3 g3384 g3384.t41 exon g3384.t41.exon1 25010043 25010140
chr_3 g3384 g3384.t41 cds g3384.t41.CDS1 25010043 25010140
chr_3 g3384 g3384.t41 exon g3384.t41.exon2 25010203 25010974
chr_3 g3384 g3384.t41 cds g3384.t41.CDS2 25010203 25010974
chr_3 g3384 g3384.t41 exon g3384.t41.exon3 25011280 25011370
chr_3 g3384 g3384.t41 cds g3384.t41.CDS3 25011280 25011330
chr_3 g3384 g3384.t41 exon g3384.t41.exon4 25011567 25011604
chr_3 g3384 g3384.t41 TSS g3384.t41 25011604 25011604

Sequences

>g3384.t41 Gene=g3384 Length=999
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATGCAGCAAATTCGT
ATCTCACTTCGTGGACTCGCTGTAGTCTTGATGGGCAAGAACACTATGATGCGTAAAGCC
ATTAAGGGCCATTTGGAAAACAATCAAGCCCTCGACAGAATTTTACCACACATTCGTGGT
AATGTTGGTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAAAAGTTGTTGCAA
AACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAAGTAATTATTCCT
GCTCAAAATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCTCTTTCAATTCCA
ACAAAGATTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATCTTAAAGCCTGGT
GACAAAGTCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATCTCTCCATTCTCA
TATGGTTTGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCTCCAAATATCTTG
GACATCAAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCAAACGTTGCCGCT
CTTTCATTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCAATTGCCAATGGT
TTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAGCAGGCTGAAACT
GTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCTGCATCAGCTCCA
GCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGAGTCAGAACCA
GAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA

>g3384.t41 Gene=g3384 Length=306
MVRENKATWKANYFLKVFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTMMRKAIKGHLE
NNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCEVIIPAQNTGL
GPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNISPFSYGLVIE
QVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHSIANGFKNLLA
IAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKKEESEPESDDDM
GFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t41 CDD cd05795 Ribosomal_P0_L10e 9 172 1.93814E-94
8 g3384.t41 Gene3D G3DSA:3.90.105.20 - 100 172 3.8E-32
7 g3384.t41 MobiDBLite mobidb-lite consensus disorder prediction 274 306 -
4 g3384.t41 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 306 4.3E-139
5 g3384.t41 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 306 4.3E-139
9 g3384.t41 PIRSF PIRSF039087 L10E 3 306 2.6E-133
2 g3384.t41 Pfam PF00466 Ribosomal protein L10 16 94 3.8E-16
1 g3384.t41 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 101 170 5.2E-22
3 g3384.t41 Pfam PF00428 60s Acidic ribosomal protein 221 305 1.6E-18
6 g3384.t41 SUPERFAMILY SSF160369 Ribosomal protein L10-like 15 122 1.96E-14

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