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.t27 TTS g3384.t27 25009832 25009832
chr_3 g3384 g3384.t27 isoform g3384.t27 25010043 25011371
chr_3 g3384 g3384.t27 exon g3384.t27.exon1 25010043 25010140
chr_3 g3384 g3384.t27 cds g3384.t27.CDS1 25010043 25010140
chr_3 g3384 g3384.t27 exon g3384.t27.exon2 25010203 25011032
chr_3 g3384 g3384.t27 cds g3384.t27.CDS2 25010203 25010938
chr_3 g3384 g3384.t27 exon g3384.t27.exon3 25011277 25011371
chr_3 g3384 g3384.t27 TSS g3384.t27 25011604 25011604

Sequences

>g3384.t27 Gene=g3384 Length=1023
GTTCTTTAAATCTGAAATCAGTACCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGG
CCACCTGGAAAGCTAACTACTTCTTAAAAGTCGTGTTAATTATTTGTCTTTTTTTTTTTT
TTTTAGACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAACGTTGGT
TCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTGATGGGC
AAGAACACTATGATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCCCTCGAC
AGAATTTTACCACACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGATTTGAAT
GAAGTTCGCGAAAAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCAATT
GCTCCTTGTGAAGTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAAACAAGT
TTCTTCCAAGCTCTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATTATCAAT
GATGTGCCCATCTTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTGCTCAAC
ATGTTGAACATCTCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGATTCAGGA
AGCATCTTCTCTCCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTCCAA
CAAGGAGTTGCAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCCTCT
GCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGAT
GTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCC
GCTGCTGCTGCTGCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAA
GCCAAGAAAGAAGAGTCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGAT
TAA

>g3384.t27 Gene=g3384 Length=277
MQQIRISLRGLAVVLMGKNTMMRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVR
EKLLQNKVRAPARAGAIAPCEVIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVP
ILKPGDKVGASEATLLNMLNISPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGV
ANVAALSLAMGYPTIASAPHSIANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAA
AASAPAASAAAPAAKAEAKKEESEPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t27 CDD cd05795 Ribosomal_P0_L10e 1 143 8.9591E-84
8 g3384.t27 Gene3D G3DSA:3.90.105.20 - 71 143 3.2E-32
7 g3384.t27 MobiDBLite mobidb-lite consensus disorder prediction 245 277 -
4 g3384.t27 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 277 1.7E-126
5 g3384.t27 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 277 1.7E-126
9 g3384.t27 PIRSF PIRSF039087 L10E 1 277 2.9E-124
2 g3384.t27 Pfam PF00466 Ribosomal protein L10 1 65 5.3E-11
1 g3384.t27 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 72 141 4.4E-22
3 g3384.t27 Pfam PF00428 60s Acidic ribosomal protein 192 276 1.3E-18
6 g3384.t27 SUPERFAMILY SSF160369 Ribosomal protein L10-like 1 92 5.89E-11

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

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. There were no conditions that were differentially expressed