Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S5a.

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 g10243 g10243.t95 isoform g10243.t95 8511947 8513667
chr_1 g10243 g10243.t95 exon g10243.t95.exon1 8511947 8512167
chr_1 g10243 g10243.t95 TTS g10243.t95 8511949 8511949
chr_1 g10243 g10243.t95 cds g10243.t95.CDS1 8512099 8512167
chr_1 g10243 g10243.t95 exon g10243.t95.exon2 8512760 8513067
chr_1 g10243 g10243.t95 cds g10243.t95.CDS2 8512760 8513067
chr_1 g10243 g10243.t95 exon g10243.t95.exon3 8513146 8513197
chr_1 g10243 g10243.t95 cds g10243.t95.CDS3 8513146 8513197
chr_1 g10243 g10243.t95 exon g10243.t95.exon4 8513263 8513420
chr_1 g10243 g10243.t95 cds g10243.t95.CDS4 8513263 8513409
chr_1 g10243 g10243.t95 exon g10243.t95.exon5 8513626 8513667
chr_1 g10243 g10243.t95 TSS g10243.t95 8513684 8513684

Sequences

>g10243.t95 Gene=g10243 Length=781
CGTGTGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGAATAGTCAATAATGGCTG
CAGAAGTCGCAGAAAATTTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTG
TAAATGCTGAACTTCCAGATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAG
TTTCGGATATGTCTTTACAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGC
CACATTCGGCCGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACACG
CATTTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATCGGCCA
TCATCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTC
GTCAAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTCTGCA
CAGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTGATG
AGCTTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGACGAAT
TGGAACGTGTTGCGAAATCTAACCGTTAAGATAATAGAATTGAGCGTGATGAAACTAAGC
ATGGAGCAATTGAAAATTCTAAACATCATCTTCATCGTCTTAAGAATTATGTAAAACAGC
AAAAGTCTCCATCAGAAATATTTGATAATATTAATAAAACAACACAAGGATTAAAAGATA
A

>g10243.t95 Gene=g10243 Length=191
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRNNGKKLMAVRIVKHAFEIIHLLTGENPLQILVSAIINSGPREDSTRIGRAGT
VRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKK
DELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10243.t95 CDD cd14867 uS7_Eukaryote 31 191 0.00
8 g10243.t95 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 68 0.00
7 g10243.t95 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 69 191 0.00
3 g10243.t95 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 68 0.00
5 g10243.t95 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 68 0.00
2 g10243.t95 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 67 191 0.00
4 g10243.t95 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 67 191 0.00
11 g10243.t95 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 67 0.55
10 g10243.t95 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 69 191 0.00
1 g10243.t95 Pfam PF00177 Ribosomal protein S7p/S5e 70 191 0.00
6 g10243.t95 SUPERFAMILY SSF47973 Ribosomal protein S7 30 191 0.00
9 g10243.t95 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 66 191 0.00

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

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