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.t72 isoform g10243.t72 8511947 8513667
chr_1 g10243 g10243.t72 exon g10243.t72.exon1 8511947 8512167
chr_1 g10243 g10243.t72 TTS g10243.t72 8511949 8511949
chr_1 g10243 g10243.t72 cds g10243.t72.CDS1 8512099 8512167
chr_1 g10243 g10243.t72 exon g10243.t72.exon2 8512760 8512836
chr_1 g10243 g10243.t72 cds g10243.t72.CDS2 8512760 8512836
chr_1 g10243 g10243.t72 exon g10243.t72.exon3 8512912 8513197
chr_1 g10243 g10243.t72 cds g10243.t72.CDS3 8512912 8513197
chr_1 g10243 g10243.t72 exon g10243.t72.exon4 8513263 8513420
chr_1 g10243 g10243.t72 cds g10243.t72.CDS4 8513263 8513409
chr_1 g10243 g10243.t72 exon g10243.t72.exon5 8513626 8513667
chr_1 g10243 g10243.t72 TSS g10243.t72 8513684 8513684

Sequences

>g10243.t72 Gene=g10243 Length=784
CGTGTGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGAATAGTCAATAATGGCTG
CAGAAGTCGCAGAAAATTTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTG
TAAATGCTGAACTTCCAGATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAG
TTTCGGATATGTCTTTACAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGC
CACATTCGGCCGGTAGATTTGCAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTG
AACGTTTGACATGCTCGCTTATGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTG
TCCGTATTGTGAAACACGCATTTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTC
AAATCCTTGTATCGGCCATCATCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTC
GCGCTGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTG
ATGAGCTTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGACG
AATTGGAACGTGTTGCGAAATCTAACCGTTAAGATAATAGAATTGAGCGTGATGAAACTA
AGCATGGAGCAATTGAAAATTCTAAACATCATCTTCATCGTCTTAAGAATTATGTAAAAC
AGCAAAAGTCTCCATCAGAAATATTTGATAATATTAATAAAACAACACAAGGATTAAAAG
ATAA

>g10243.t72 Gene=g10243 Length=192
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKK
KDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10243.t72 CDD cd14867 uS7_Eukaryote 31 192 6.0152E-113
10 g10243.t72 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 146 1.4E-63
9 g10243.t72 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 147 192 7.2E-20
4 g10243.t72 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 146 1.2E-90
6 g10243.t72 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 146 1.2E-90
3 g10243.t72 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 145 192 1.2E-90
5 g10243.t72 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 145 192 1.2E-90
11 g10243.t72 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 148 1.7E-22
12 g10243.t72 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 143 192 1.2E-8
1 g10243.t72 Pfam PF00177 Ribosomal protein S7p/S5e 73 147 4.6E-14
2 g10243.t72 Pfam PF00177 Ribosomal protein S7p/S5e 148 192 1.4E-10
8 g10243.t72 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
7 g10243.t72 SUPERFAMILY SSF47973 Ribosomal protein S7 30 192 5.49E-55

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:0003723 RNA binding MF
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