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.t1 TTS g3384.t1 25009832 25009832
chr_3 g3384 g3384.t1 isoform g3384.t1 25010043 25011330
chr_3 g3384 g3384.t1 exon g3384.t1.exon1 25010043 25010140
chr_3 g3384 g3384.t1 cds g3384.t1.CDS1 25010043 25010140
chr_3 g3384 g3384.t1 exon g3384.t1.exon2 25010203 25011001
chr_3 g3384 g3384.t1 cds g3384.t1.CDS2 25010203 25011001
chr_3 g3384 g3384.t1 exon g3384.t1.exon3 25011277 25011330
chr_3 g3384 g3384.t1 cds g3384.t1.CDS3 25011277 25011330
chr_3 g3384 g3384.t1 TSS g3384.t1 25011604 25011604

Sequences

>g3384.t1 Gene=g3384 Length=951
ATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTCTTAAAAGTCGTGACATAT
CTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATG
CAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTGATGGGCAAGAACACTATG
ATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCCCTCGACAGAATTTTACCA
CACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAA
AAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAA
GTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCT
CTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATC
TTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATC
TCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCT
CCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCA
AACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCA
ATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAG
CAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCT
GCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAA
GAGTCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA

>g3384.t1 Gene=g3384 Length=316
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCE
VIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNI
SPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHS
IANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKKE
ESEPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t1 CDD cd05795 Ribosomal_P0_L10e 9 182 3.16915E-101
8 g3384.t1 Gene3D G3DSA:3.90.105.20 - 110 182 4.0E-32
7 g3384.t1 MobiDBLite mobidb-lite consensus disorder prediction 284 316 -
4 g3384.t1 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 316 3.2E-149
5 g3384.t1 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 316 3.2E-149
9 g3384.t1 PIRSF PIRSF039087 L10E 1 316 3.0E-140
2 g3384.t1 Pfam PF00466 Ribosomal protein L10 7 104 1.7E-19
1 g3384.t1 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 111 180 5.5E-22
3 g3384.t1 Pfam PF00428 60s Acidic ribosomal protein 231 315 1.7E-18
6 g3384.t1 SUPERFAMILY SSF160369 Ribosomal protein L10-like 8 132 9.94E-17

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