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.t18 isoform g10243.t18 8511083 8513634
chr_1 g10243 g10243.t18 exon g10243.t18.exon1 8511083 8511085
chr_1 g10243 g10243.t18 exon g10243.t18.exon2 8511942 8512167
chr_1 g10243 g10243.t18 cds g10243.t18.CDS1 8512099 8512167
chr_1 g10243 g10243.t18 exon g10243.t18.exon3 8512760 8513197
chr_1 g10243 g10243.t18 cds g10243.t18.CDS2 8512760 8513197
chr_1 g10243 g10243.t18 exon g10243.t18.exon4 8513263 8513420
chr_1 g10243 g10243.t18 cds g10243.t18.CDS3 8513263 8513409
chr_1 g10243 g10243.t18 exon g10243.t18.exon5 8513626 8513634
chr_1 g10243 g10243.t18 TSS g10243.t18 8513684 8513684
chr_1 g10243 g10243.t18 TTS g10243.t18 NA NA

Sequences

>g10243.t18 Gene=g10243 Length=834
TATTTACAGAATAGTCAATAATGGCTGCAGAAGTCGCAGAAAATTTTGAAGAAACCGAGC
AATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATATTAAACTTTTTG
GAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATATGTCTTTACAAGATTATATTGCCG
TGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGGTAGATTTGCAGTTAAGCGTT
TCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATGCTCGCTTATGATGAAAGGTC
GCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACACGCATTTGAAATCATTC
ACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATCGGCCATCATCAACTCAGGAC
CTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTCGTCAAGCCGTTGATG
TCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTCTGCACAGGTGCTCGCGAAG
CTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTGATGAGCTTATCAACGCCG
CAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGACGAATTGGAACGTGTTGCGA
AATCTAACCGTTAAGATAATAGAATTGAGCGTGATGAAACTAAGCATGGAGCAATTGAAA
ATTCTAAACATCATCTTCATCGTCTTAAGAATTATGTAAAACAGCAAAAGTCTCCATCAG
AAATATTTGATAATATTAATAAAACAACACAAGGATTAAAAGATAATGGTCTGG

>g10243.t18 Gene=g10243 Length=217
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK
TIAECLADELINAAKGSSNSYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t18 CDD cd14867 uS7_Eukaryote 31 217 1.83359E-139
5 g10243.t18 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 217 2.7E-105
2 g10243.t18 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 217 8.0E-118
3 g10243.t18 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 217 8.0E-118
6 g10243.t18 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 217 6.8E-43
1 g10243.t18 Pfam PF00177 Ribosomal protein S7p/S5e 73 217 3.6E-37
8 g10243.t18 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t18 SUPERFAMILY SSF47973 Ribosomal protein S7 30 217 1.96E-68
9 g10243.t18 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 217 1.6E-93

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.

Raw TPM values