Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S20.

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_1 g9715 g9715.t18 TSS g9715.t18 4777068 4777068
chr_1 g9715 g9715.t18 isoform g9715.t18 4777159 4779348
chr_1 g9715 g9715.t18 exon g9715.t18.exon1 4777159 4777161
chr_1 g9715 g9715.t18 cds g9715.t18.CDS1 4777159 4777161
chr_1 g9715 g9715.t18 exon g9715.t18.exon2 4777312 4777467
chr_1 g9715 g9715.t18 cds g9715.t18.CDS2 4777312 4777467
chr_1 g9715 g9715.t18 exon g9715.t18.exon3 4777688 4777777
chr_1 g9715 g9715.t18 cds g9715.t18.CDS3 4777688 4777777
chr_1 g9715 g9715.t18 exon g9715.t18.exon4 4778031 4778202
chr_1 g9715 g9715.t18 cds g9715.t18.CDS4 4778031 4778147
chr_1 g9715 g9715.t18 exon g9715.t18.exon5 4779321 4779348
chr_1 g9715 g9715.t18 TTS g9715.t18 NA NA

Sequences

>g9715.t18 Gene=g9715 Length=449
ATGGCGGCCGTTGGTAAAGATATTGAAAAGCAGCAACAAGCTGAAACATCATCAGTTCAT
CGCATTCGCATTGTATTGACTGCATGCAATGTTCGTTCATTGGAAAAAGTTTGCACTGAC
TTGATCTCTGGCGCAAAGAAACAAAAGTTGCGCGTTAAGGGACCAATTCGTATGCCAACA
AATACATTGCGCATCACAACACGTAAAACACCTTGCGGTGAAGGTTCAAAAACCTGGGAT
CGCTTCCAAATGAGAATCCATAAGCGTATCATTGATTTGCACTCACCATCAGAAATTGTG
CGTCAAATCACATCAATTAACATCGAACCAGGTGTACAAGTTGAAGTTACCATTGCCGAC
AATTAAAATGGAAATTTCATCGGAAATTTTAGGAGCACAATTCCTGATTATTAATAAAAT
CTAAATGAATATCAAAGGAAAGAAAAAGT

>g9715.t18 Gene=g9715 Length=121
MAAVGKDIEKQQQAETSSVHRIRIVLTACNVRSLEKVCTDLISGAKKQKLRVKGPIRMPT
NTLRITTRKTPCGEGSKTWDRFQMRIHKRIIDLHSPSEIVRQITSINIEPGVQVEVTIAD
N

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9715.t18 Gene3D G3DSA:3.30.70.600 - 6 120 0.00000
4 g9715.t18 Hamap MF_00508 30S ribosomal protein S10 [rpsJ]. 19 118 18.74581
2 g9715.t18 PANTHER PTHR11700 30S RIBOSOMAL PROTEIN S10 FAMILY MEMBER 9 120 0.00000
3 g9715.t18 PANTHER PTHR11700:SF8 40S RIBOSOMAL PROTEIN S20 9 120 0.00000
6 g9715.t18 PRINTS PR00971 Ribosomal protein S10 family signature 21 34 0.00000
7 g9715.t18 PRINTS PR00971 Ribosomal protein S10 family signature 56 71 0.00000
5 g9715.t18 PRINTS PR00971 Ribosomal protein S10 family signature 78 92 0.00000
1 g9715.t18 Pfam PF00338 Ribosomal protein S10p/S20e 23 117 0.00000
10 g9715.t18 SMART SM01403 Ribosomal_S10_2 23 117 0.00000
8 g9715.t18 SUPERFAMILY SSF54999 Ribosomal protein S10 21 118 0.00000
11 g9715.t18 TIGRFAM TIGR01046 uS10_euk_arch: ribosomal protein uS10 20 118 0.00000

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:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC

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