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.t35 TTS g3384.t35 25009832 25009832
chr_3 g3384 g3384.t35 isoform g3384.t35 25010043 25011604
chr_3 g3384 g3384.t35 exon g3384.t35.exon1 25010043 25010140
chr_3 g3384 g3384.t35 cds g3384.t35.CDS1 25010113 25010140
chr_3 g3384 g3384.t35 exon g3384.t35.exon2 25010223 25011001
chr_3 g3384 g3384.t35 cds g3384.t35.CDS2 25010223 25011001
chr_3 g3384 g3384.t35 exon g3384.t35.exon3 25011280 25011370
chr_3 g3384 g3384.t35 cds g3384.t35.CDS3 25011280 25011330
chr_3 g3384 g3384.t35 exon g3384.t35.exon4 25011567 25011604
chr_3 g3384 g3384.t35 TSS g3384.t35 25011604 25011604

Sequences

>g3384.t35 Gene=g3384 Length=1006
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAACGTT
GGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTGATG
GGCAAGAACACTATGATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCCCTC
GACAGAATTTTACCACACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGATTTG
AATGAAGTTCGCGAAAAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCA
ATTGCTCCTTGTGAAGTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAAACA
AGTTTCTTCCAAGCTCTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATTATC
AATGATGTGCCCATCTTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTGCTC
AACATGTTGAACATCTCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGATTCA
GGAAGCATCTTCTCTCCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTC
CAACAAGGAGTTGCAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCC
TCTGCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACC
GATGTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTT
GCCGCTGCCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGAGTC
AGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA

>g3384.t35 Gene=g3384 Length=285
MVRENKATWKANYFLKVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTMM
RKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCEV
IIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNIS
PFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHSI
ANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAACFCRCTSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3384.t35 CDD cd05795 Ribosomal_P0_L10e 9 181 0
6 g3384.t35 Gene3D G3DSA:3.90.105.20 - 109 181 0
3 g3384.t35 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 277 0
4 g3384.t35 PANTHER PTHR45699:SF3 60S ACIDIC RIBOSOMAL PROTEIN P0 1 277 0
7 g3384.t35 PIRSF PIRSF039087 L10E 1 283 0
2 g3384.t35 Pfam PF00466 Ribosomal protein L10 10 103 0
1 g3384.t35 Pfam PF17777 Insertion domain in 60S ribosomal protein L10P 110 179 0
5 g3384.t35 SUPERFAMILY SSF160369 Ribosomal protein L10-like 18 130 0

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. There were no conditions that were differentially expressed