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.t187 TTS g10243.t187 8511949 8511949
chr_1 g10243 g10243.t187 isoform g10243.t187 8512099 8513680
chr_1 g10243 g10243.t187 exon g10243.t187.exon1 8512099 8512167
chr_1 g10243 g10243.t187 cds g10243.t187.CDS1 8512142 8512167
chr_1 g10243 g10243.t187 exon g10243.t187.exon2 8512768 8513197
chr_1 g10243 g10243.t187 cds g10243.t187.CDS2 8512768 8513197
chr_1 g10243 g10243.t187 exon g10243.t187.exon3 8513263 8513420
chr_1 g10243 g10243.t187 cds g10243.t187.CDS3 8513263 8513409
chr_1 g10243 g10243.t187 exon g10243.t187.exon4 8513622 8513680
chr_1 g10243 g10243.t187 TSS g10243.t187 8513684 8513684

Sequences

>g10243.t187 Gene=g10243 Length=716
TTCCTCTGGCCCTCGTGTGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGGTGTA
ATAGTCAATAATGGCTGCAGAAGTCGCAGAAAATTTTGAAGAAACCGAGCAATTTGTAGA
GACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATATTAAACTTTTTGGAAGATGGAG
TTGTGATGAAGTGCAAGTTTCGGATATGTCTTTACAAGATTATATTGCCGTGAAAGAAAA
ATATGCTCGTTATTTGCCACATTCGGCCGGTAGATTTGCAGTTAAGCGTTTCCGTAAAGC
TCAATGTCCAATTGTTGAACGTTTGACATGCTCGCTTATGATGAAAGGTCGCAACAATGG
TAAAAAGTTGATGGCTGTCCGTATTGTGAAACACGCATTTGAAATCATTCACCTTCTTAC
TGGTGAAAATCCACTTCAAATCCTTGTATCGGCCATCATCAACTCAGGACCTCGTGAAGA
TTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTCGTCAAGCCGTTGATGTCTCACCATT
GAGACGTGTCAACCAAGCAATTTGGTTACTCTGCACAGGTGCTCGCGAAGCTGCATTCCG
AAACATTAAGACAATTGCTGAATGTTTAGCTGATGAGCTTATCAACGGGATCATCAAACT
CCTACGCTATTAAAAAGAAGGACGAATTGGAACGTGTTGCGAAATCTAACCGTTAA

>g10243.t187 Gene=g10243 Length=200
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK
TIAECLADELINGIIKLLRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t187 CDD cd14867 uS7_Eukaryote 31 192 5.21937E-119
5 g10243.t187 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 196 2.6E-89
2 g10243.t187 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 193 3.3E-102
3 g10243.t187 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 193 3.3E-102
6 g10243.t187 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 196 1.1E-35
1 g10243.t187 Pfam PF00177 Ribosomal protein S7p/S5e 72 192 5.0E-27
8 g10243.t187 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t187 SUPERFAMILY SSF47973 Ribosomal protein S7 30 192 1.02E-54
9 g10243.t187 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 192 5.7E-79

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