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.t66 TTS g3384.t66 25009832 25009832
chr_3 g3384 g3384.t66 isoform g3384.t66 25010043 25011604
chr_3 g3384 g3384.t66 exon g3384.t66.exon1 25010043 25010140
chr_3 g3384 g3384.t66 cds g3384.t66.CDS1 25010045 25010140
chr_3 g3384 g3384.t66 exon g3384.t66.exon2 25010203 25010449
chr_3 g3384 g3384.t66 cds g3384.t66.CDS2 25010203 25010449
chr_3 g3384 g3384.t66 exon g3384.t66.exon3 25010646 25011001
chr_3 g3384 g3384.t66 cds g3384.t66.CDS3 25010646 25011001
chr_3 g3384 g3384.t66 exon g3384.t66.exon4 25011277 25011370
chr_3 g3384 g3384.t66 cds g3384.t66.CDS4 25011277 25011330
chr_3 g3384 g3384.t66 exon g3384.t66.exon5 25011567 25011604
chr_3 g3384 g3384.t66 TSS g3384.t66 25011604 25011604

Sequences

>g3384.t66 Gene=g3384 Length=833
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCGTGACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAAC
GTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTG
ATGGGCAAGAACACTATGATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCC
CTCGACAGAATTTTACCACACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGAT
TTGAATGAAGTTCGCGAAAAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGC
GCAATTGCTCCTTGTGAAGTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAA
ACAAGTTTATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTG
CAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATT
CAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCA
AGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTG
CTGCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAG
AAGAGTCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA

>g3384.t66 Gene=g3384 Length=251
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCE
VIIPAQNTGLGPEKTSLSWTSNQKICVLNSNKELQTLPLFHWLWAIQQLPLLHIQLPMVS
RTCSLSQLLPMSNSSRLKLLKNSLRIHLSLPLLLLHQLQLLLPLHQLLKLKPRKKSQNQS
LMTTWDSDFLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3384.t66 CDD cd05795 Ribosomal_P0_L10e 9 136 2.75609E-70
5 g3384.t66 Gene3D G3DSA:3.30.70.1730 - 4 147 2.1E-51
2 g3384.t66 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 1 137 5.7E-73
3 g3384.t66 PANTHER PTHR45699:SF1 60S ACIDIC RIBOSOMAL PROTEIN P0-RELATED 1 137 5.7E-73
1 g3384.t66 Pfam PF00466 Ribosomal protein L10 7 104 1.0E-19
7 g3384.t66 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 207 -
8 g3384.t66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 228 -
6 g3384.t66 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 229 251 -
4 g3384.t66 SUPERFAMILY SSF160369 Ribosomal protein L10-like 8 132 4.71E-17

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

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.

Raw TPM values