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.t167 TTS g10243.t167 8511949 8511949
chr_1 g10243 g10243.t167 isoform g10243.t167 8512099 8513650
chr_1 g10243 g10243.t167 exon g10243.t167.exon1 8512099 8512167
chr_1 g10243 g10243.t167 cds g10243.t167.CDS1 8512099 8512167
chr_1 g10243 g10243.t167 exon g10243.t167.exon2 8512760 8512935
chr_1 g10243 g10243.t167 cds g10243.t167.CDS2 8512760 8512935
chr_1 g10243 g10243.t167 exon g10243.t167.exon3 8512993 8513197
chr_1 g10243 g10243.t167 cds g10243.t167.CDS3 8512993 8513197
chr_1 g10243 g10243.t167 exon g10243.t167.exon4 8513263 8513420
chr_1 g10243 g10243.t167 cds g10243.t167.CDS4 8513263 8513409
chr_1 g10243 g10243.t167 exon g10243.t167.exon5 8513626 8513650
chr_1 g10243 g10243.t167 TSS g10243.t167 8513684 8513684

Sequences

>g10243.t167 Gene=g10243 Length=633
TCTTGTGAAATTTAATTATTTACAGAATAGTCAATAATGGCTGCAGAAGTCGCAGAAAAT
TTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCA
GATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATATGTCTTTA
CAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGGTAGA
TTTGCAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATGCTCG
CTTATGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACAC
GCATTTGAAATCATTCACCTTCTTACTGATTCAACTCGTATCGGTCGCGCTGGTACTGTT
CGTCGTCAAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTC
TGCACAGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCT
GATGAGCTTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGAC
GAATTGGAACGTGTTGCGAAATCTAACCGTTAA

>g10243.t167 Gene=g10243 Length=198
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTDST
RIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSN
SYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10243.t167 CDD cd14867 uS7_Eukaryote 31 198 3.39145E-119
6 g10243.t167 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 117 1.0E-46
7 g10243.t167 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 118 198 2.2E-38
2 g10243.t167 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 198 2.6E-97
3 g10243.t167 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 198 2.6E-97
9 g10243.t167 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 120 4.4E-13
8 g10243.t167 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 116 198 2.8E-16
1 g10243.t167 Pfam PF00177 Ribosomal protein S7p/S5e 73 198 4.7E-21
5 g10243.t167 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t167 SUPERFAMILY SSF47973 Ribosomal protein S7 30 198 1.14E-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. There were no conditions that were differentially expressed