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.t104 isoform g10243.t104 8511947 8513667
chr_1 g10243 g10243.t104 exon g10243.t104.exon1 8511947 8512167
chr_1 g10243 g10243.t104 TTS g10243.t104 8511949 8511949
chr_1 g10243 g10243.t104 cds g10243.t104.CDS1 8512014 8512167
chr_1 g10243 g10243.t104 exon g10243.t104.exon2 8512767 8513197
chr_1 g10243 g10243.t104 cds g10243.t104.CDS2 8512767 8513197
chr_1 g10243 g10243.t104 exon g10243.t104.exon3 8513263 8513420
chr_1 g10243 g10243.t104 cds g10243.t104.CDS3 8513263 8513409
chr_1 g10243 g10243.t104 exon g10243.t104.exon4 8513622 8513667
chr_1 g10243 g10243.t104 TSS g10243.t104 8513684 8513684

Sequences

>g10243.t104 Gene=g10243 Length=856
CGTGTGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGGTGTAATAGTCAATAATG
GCTGCAGAAGTCGCAGAAAATTTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCA
GTTGTAAATGCTGAACTTCCAGATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTG
CAAGTTTCGGATATGTCTTTACAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTAT
TTGCCACATTCGGCCGGTAGATTTGCAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATT
GTTGAACGTTTGACATGCTCGCTTATGATGAAAGGTCGCAACAATGGTAAAAAGTTGATG
GCTGTCCGTATTGTGAAACACGCATTTGAAATCATTCACCTTCTTACTGGTGAAAATCCA
CTTCAAATCCTTGTATCGGCCATCATCAACTCAGGACCTCGTGAAGATTCAACTCGTATC
GGTCGCGCTGGTACTGTTCGTCGTCAAGCCGTTGATGTCTCACCATTGAGACGTGTCAAC
CAAGCAATTTGGTTACTCTGCACAGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACA
ATTGCTGAATGTTTAGCTGATGAGCTTATCAACGCGGATCATCAAACTCCTACGCTATTA
AAAAGAAGGACGAATTGGAACGTGTTGCGAAATCTAACCGTTAAGATAATAGAATTGAGC
GTGATGAAACTAAGCATGGAGCAATTGAAAATTCTAAACATCATCTTCATCGTCTTAAGA
ATTATGTAAAACAGCAAAAGTCTCCATCAGAAATATTTGATAATATTAATAAAACAACAC
AAGGATTAAAAGATAA

>g10243.t104 Gene=g10243 Length=243
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK
TIAECLADELINADHQTPTLLKRRTNWNVLRNLTVKIIELSVMKLSMEQLKILNIIFIVL
RIM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10243.t104 CDD cd14867 uS7_Eukaryote 31 193 6.77874E-119
6 g10243.t104 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 208 2.1E-90
2 g10243.t104 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 195 1.2E-102
3 g10243.t104 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 195 1.2E-102
1 g10243.t104 Pfam PF00177 Ribosomal protein S7p/S5e 73 205 6.1E-29
5 g10243.t104 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t104 SUPERFAMILY SSF47973 Ribosomal protein S7 30 206 1.15E-56
7 g10243.t104 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 197 7.2E-80

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