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.t33 TTS g3384.t33 25009832 25009832
chr_3 g3384 g3384.t33 isoform g3384.t33 25010043 25011604
chr_3 g3384 g3384.t33 exon g3384.t33.exon1 25010043 25010119
chr_3 g3384 g3384.t33 cds g3384.t33.CDS1 25010043 25010119
chr_3 g3384 g3384.t33 exon g3384.t33.exon2 25010203 25011001
chr_3 g3384 g3384.t33 cds g3384.t33.CDS2 25010203 25011001
chr_3 g3384 g3384.t33 exon g3384.t33.exon3 25011277 25011370
chr_3 g3384 g3384.t33 cds g3384.t33.CDS3 25011277 25011330
chr_3 g3384 g3384.t33 exon g3384.t33.exon4 25011567 25011604
chr_3 g3384 g3384.t33 TSS g3384.t33 25011604 25011604

Sequences

>g3384.t33 Gene=g3384 Length=1008
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCGTGACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAAC
GTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTG
ATGGGCAAGAACACTATGATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCC
CTCGACAGAATTTTACCACACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGAT
TTGAATGAAGTTCGCGAAAAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGC
GCAATTGCTCCTTGTGAAGTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAA
ACAAGTTTCTTCCAAGCTCTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATT
ATCAATGATGTGCCCATCTTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTG
CTCAACATGTTGAACATCTCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGAT
TCAGGAAGCATCTTCTCTCCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAA
TTCCAACAAGGAGTTGCAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATT
GCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTT
ACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAG
TTTGCCGCTGCTGCTGCTGCATCAGCTCCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGAG
TCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA

>g3384.t33 Gene=g3384 Length=309
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCE
VIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNI
SPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHS
IANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAAKAEAKKEESEPESD
DDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3384.t33 CDD cd05795 Ribosomal_P0_L10e 9 182 2.60384E-101
8 g3384.t33 Gene3D G3DSA:3.90.105.20 - 110 182 3.9E-32
7 g3384.t33 MobiDBLite mobidb-lite consensus disorder prediction 284 309 -
4 g3384.t33 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 309 7.2E-147
5 g3384.t33 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 309 7.2E-147
9 g3384.t33 PIRSF PIRSF039087 L10E 1 309 4.4E-138
2 g3384.t33 Pfam PF00466 Ribosomal protein L10 7 104 1.6E-19
1 g3384.t33 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 111 180 5.3E-22
3 g3384.t33 Pfam PF00428 60s Acidic ribosomal protein 231 308 6.7E-15
6 g3384.t33 SUPERFAMILY SSF160369 Ribosomal protein L10-like 8 132 9.42E-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