Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t9 isoform g3384.t9 25009825 25011604
chr_3 g3384 g3384.t9 exon g3384.t9.exon1 25009825 25010140
chr_3 g3384 g3384.t9 TTS g3384.t9 25009832 25009832
chr_3 g3384 g3384.t9 cds g3384.t9.CDS1 25010043 25010140
chr_3 g3384 g3384.t9 exon g3384.t9.exon2 25010203 25010400
chr_3 g3384 g3384.t9 cds g3384.t9.CDS2 25010203 25010400
chr_3 g3384 g3384.t9 exon g3384.t9.exon3 25010751 25011001
chr_3 g3384 g3384.t9 cds g3384.t9.CDS3 25010751 25010769
chr_3 g3384 g3384.t9 exon g3384.t9.exon4 25011280 25011370
chr_3 g3384 g3384.t9 exon g3384.t9.exon5 25011567 25011604
chr_3 g3384 g3384.t9 TSS g3384.t9 25011604 25011604

Sequences

>g3384.t9 Gene=g3384 Length=894
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAACGTT
GGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTGATG
GGCAAGAACACTATGATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCCCTC
GACAGAATTTTACCACACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGATTTG
AATGAAGTTCGCGAAAAGTTTTGCAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCC
AACAATTGCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGC
AGCTGTTACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCC
ATCTAAGTTTGCCGCTGCTGCTGCTGCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGC
TGCTAAAGCTGAAGCCAAGAAAGAAGAGTCAGAACCAGAGTCTGATGACGACATGGGATT
CGGACTTTTTGATTAAACATTGCAACATCATCAAATGGTCATTACAATTTGAATCAACGT
TAATTTTCTTCTGCAATAAATTTGCAAATACTTGCCCATCAATGGCAACTTGCAATTTTT
ATTGCAAAATAAAGAATTGATTCTTTTCACACCATTACATCATTTAAATTGTGTTTTTGC
CTGAAGACCGGCAATTTAATGCTGAAATAAAATTGACCAAAAAAAAACAAAATA

>g3384.t9 Gene=g3384 Length=104
MKFAKSFANVAALSLAMGYPTIASAPHSIANGFKNLLAIAAVTDVEFKQAETVKEFLKDP
SKFAAAAAASAPAASAAAPAAKAEAKKEESEPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3384.t9 MobiDBLite mobidb-lite consensus disorder prediction 72 104 -
3 g3384.t9 PANTHER PTHR45699 60S ACIDIC RIBOSOMAL PROTEIN P0 2 104 7.0E-28
4 g3384.t9 PANTHER PTHR45699:SF13 60S ACIDIC RIBOSOMAL PROTEIN P0-LIKE 2 104 7.0E-28
2 g3384.t9 Pfam PF00428 60s Acidic ribosomal protein 19 103 1.0E-19
9 g3384.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 23 -
10 g3384.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 9 -
11 g3384.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 10 18 -
12 g3384.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 23 -
8 g3384.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 24 104 -
1 g3384.t9 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 25 -
7 g3384.t9 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 25 -
5 g3384.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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