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.t20 TTS g3384.t20 25009832 25009832
chr_3 g3384 g3384.t20 isoform g3384.t20 25010043 25011371
chr_3 g3384 g3384.t20 exon g3384.t20.exon1 25010043 25010140
chr_3 g3384 g3384.t20 cds g3384.t20.CDS1 25010043 25010140
chr_3 g3384 g3384.t20 exon g3384.t20.exon2 25010203 25011001
chr_3 g3384 g3384.t20 cds g3384.t20.CDS2 25010203 25011001
chr_3 g3384 g3384.t20 exon g3384.t20.exon3 25011283 25011371
chr_3 g3384 g3384.t20 cds g3384.t20.CDS3 25011283 25011330
chr_3 g3384 g3384.t20 TSS g3384.t20 25011604 25011604

Sequences

>g3384.t20 Gene=g3384 Length=986
GTTCTTTAAATCTGAAATCAGTACCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGG
CCACCTGGAAAGCTAACTACTTCTTAAAAACATATCTCGACGAATATCCAAAATGTTTCA
TCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTG
GACTCGCTGTAGTCTTGATGGGCAAGAACACTATGATGCGTAAAGCCATTAAGGGCCATT
TGGAAAACAATCAAGCCCTCGACAGAATTTTACCACACATTCGTGGTAATGTTGGTTTCG
TTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAAAAGTTGTTGCAAAACAAAGTTCGTG
CTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAAGTAATTATTCCTGCTCAAAATACTG
GTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCTCTTTCAATTCCAACAAAGATTTCAA
AGGGTACTATTGAAATTATCAATGATGTGCCCATCTTAAAGCCTGGTGACAAAGTCGGTG
CTTCTGAAGCTACTTTGCTCAACATGTTGAACATCTCTCCATTCTCATATGGTTTGGTAA
TTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCTCCAAATATCTTGGACATCAAACCAG
AAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCAAACGTTGCCGCTCTTTCATTGGCTA
TGGGCTATCCAACAATTGCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGC
TCGCTATCGCAGCTGTTACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCC
TTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCTGCATCAGCTCCAGCTGCTTCTGCCG
CTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGAGTCAGAACCAGAGTCTGATGACG
ACATGGGATTCGGACTTTTTGATTAA

>g3384.t20 Gene=g3384 Length=314
MVRENKATWKANYFLKTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTMMR
KAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCEVI
IPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNISP
FSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHSIA
NGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKKEES
EPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t20 CDD cd05795 Ribosomal_P0_L10e 9 180 4.24388E-100
8 g3384.t20 Gene3D G3DSA:3.90.105.20 - 108 180 4.0E-32
7 g3384.t20 MobiDBLite mobidb-lite consensus disorder prediction 282 314 -
4 g3384.t20 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 314 1.6E-146
5 g3384.t20 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 314 1.6E-146
9 g3384.t20 PIRSF PIRSF039087 L10E 1 314 5.8E-138
2 g3384.t20 Pfam PF00466 Ribosomal protein L10 15 102 3.7E-18
1 g3384.t20 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 109 178 5.5E-22
3 g3384.t20 Pfam PF00428 60s Acidic ribosomal protein 229 313 1.6E-18
6 g3384.t20 SUPERFAMILY SSF160369 Ribosomal protein L10-like 15 129 4.84E-16

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