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.t46 isoform g10243.t46 8511947 8513429
chr_1 g10243 g10243.t46 exon g10243.t46.exon1 8511947 8512167
chr_1 g10243 g10243.t46 TTS g10243.t46 8511949 8511949
chr_1 g10243 g10243.t46 cds g10243.t46.CDS1 8512099 8512167
chr_1 g10243 g10243.t46 exon g10243.t46.exon2 8512760 8513197
chr_1 g10243 g10243.t46 cds g10243.t46.CDS2 8512760 8513197
chr_1 g10243 g10243.t46 exon g10243.t46.exon3 8513290 8513429
chr_1 g10243 g10243.t46 cds g10243.t46.CDS3 8513290 8513409
chr_1 g10243 g10243.t46 TSS g10243.t46 8513684 8513684

Sequences

>g10243.t46 Gene=g10243 Length=799
TTATTTCAGAATAGTCAATAATGGCTGCAGAAGTCGCAGAAAATTTTGAAGAAACCGAGC
AATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATATTAAACTTTTTG
GAAGATGGAGTTGTGATGAAGATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGC
CACATTCGGCCGGTAGATTTGCAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTG
AACGTTTGACATGCTCGCTTATGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTG
TCCGTATTGTGAAACACGCATTTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTC
AAATCCTTGTATCGGCCATCATCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTC
GCGCTGGTACTGTTCGTCGTCAAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAG
CAATTTGGTTACTCTGCACAGGTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTG
CTGAATGTTTAGCTGATGAGCTTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTA
TTAAAAAGAAGGACGAATTGGAACGTGTTGCGAAATCTAACCGTTAAGATAATAGAATTG
AGCGTGATGAAACTAAGCATGGAGCAATTGAAAATTCTAAACATCATCTTCATCGTCTTA
AGAATTATGTAAAACAGCAAAAGTCTCCATCAGAAATATTTGATAATATTAATAAAACAA
CACAAGGATTAAAAGATAA

>g10243.t46 Gene=g10243 Length=208
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEDYIAVKEKYARYLPHSAGRF
AVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGENPLQILVSAI
INSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADE
LINAAKGSSNSYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t46 CDD cd14867 uS7_Eukaryote 31 208 1.3625E-130
5 g10243.t46 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 208 8.3E-96
2 g10243.t46 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 40 208 3.6E-113
3 g10243.t46 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 40 208 3.6E-113
6 g10243.t46 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 2 208 4.8E-39
1 g10243.t46 Pfam PF00177 Ribosomal protein S7p/S5e 63 208 3.0E-37
8 g10243.t46 ProSitePatterns PS00052 Ribosomal protein S7 signature. 74 100 -
4 g10243.t46 SUPERFAMILY SSF47973 Ribosomal protein S7 32 208 3.14E-63
9 g10243.t46 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 30 208 1.9E-83

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