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.t169 TTS g10243.t169 8511949 8511949
chr_1 g10243 g10243.t169 isoform g10243.t169 8512099 8513654
chr_1 g10243 g10243.t169 exon g10243.t169.exon1 8512099 8512154
chr_1 g10243 g10243.t169 cds g10243.t169.CDS1 8512099 8512154
chr_1 g10243 g10243.t169 exon g10243.t169.exon2 8512756 8513197
chr_1 g10243 g10243.t169 cds g10243.t169.CDS2 8512756 8513197
chr_1 g10243 g10243.t169 exon g10243.t169.exon3 8513263 8513420
chr_1 g10243 g10243.t169 cds g10243.t169.CDS3 8513263 8513409
chr_1 g10243 g10243.t169 exon g10243.t169.exon4 8513626 8513654
chr_1 g10243 g10243.t169 TSS g10243.t169 8513684 8513684

Sequences

>g10243.t169 Gene=g10243 Length=685
GTATTCTTGTGAAATTTAATTATTTACAGAATAGTCAATAATGGCTGCAGAAGTCGCAGA
AAATTTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACT
TCCAGATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATATGTC
TTTACAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGG
TAGATTTGCAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATG
CTCGCTTATGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAA
ACACGCATTTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATC
GGCCATCATCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGT
TCGTCGTCAAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACT
CTGCACAGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGC
TGATGAGCTTATCAACGCCGCAAAGGTTCCCTACGCTATTAAAAAGAAGGACGAATTGGA
ACGTGTTGCGAAATCTAACCGTTAA

>g10243.t169 Gene=g10243 Length=214
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK
TIAECLADELINAAKVPYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t169 CDD cd14867 uS7_Eukaryote 31 214 2.25181E-132
5 g10243.t169 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 214 2.1E-100
2 g10243.t169 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 214 7.0E-111
3 g10243.t169 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 214 7.0E-111
6 g10243.t169 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 214 7.7E-41
1 g10243.t169 Pfam PF00177 Ribosomal protein S7p/S5e 72 214 1.2E-34
8 g10243.t169 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t169 SUPERFAMILY SSF47973 Ribosomal protein S7 30 214 3.01E-63
9 g10243.t169 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 214 1.1E-88

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

Pathway

  • This transcript belongs to the following pathways

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