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.t109 isoform g10243.t109 8511947 8513667
chr_1 g10243 g10243.t109 exon g10243.t109.exon1 8511947 8512137
chr_1 g10243 g10243.t109 TTS g10243.t109 8511949 8511949
chr_1 g10243 g10243.t109 cds g10243.t109.CDS1 8512106 8512137
chr_1 g10243 g10243.t109 exon g10243.t109.exon2 8512756 8513197
chr_1 g10243 g10243.t109 cds g10243.t109.CDS2 8512756 8513197
chr_1 g10243 g10243.t109 exon g10243.t109.exon3 8513263 8513420
chr_1 g10243 g10243.t109 cds g10243.t109.CDS3 8513263 8513409
chr_1 g10243 g10243.t109 exon g10243.t109.exon4 8513647 8513667
chr_1 g10243 g10243.t109 TSS g10243.t109 8513684 8513684

Sequences

>g10243.t109 Gene=g10243 Length=812
CGTGTGCAGAAGAGTATTCTTAATAGTCAATAATGGCTGCAGAAGTCGCAGAAAATTTTG
AAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATA
TTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATATGTCTTTACAAG
ATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGGTAGATTTG
CAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATGCTCGCTTA
TGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACACGCAT
TTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATCGGCCATCA
TCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTCGTC
AAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTCTGCACAG
GTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTGATGAGC
TTATCAACGCCGCAAAGGTTCAAGGACGAATTGGAACGTGTTGCGAAATCTAACCGTTAA
GATAATAGAATTGAGCGTGATGAAACTAAGCATGGAGCAATTGAAAATTCTAAACATCAT
CTTCATCGTCTTAAGAATTATGTAAAACAGCAAAAGTCTCCATCAGAAATATTTGATAAT
ATTAATAAAACAACACAAGGATTAAAAGATAA

>g10243.t109 Gene=g10243 Length=206
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDMSLQDYIAVKEKYAR
YLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGEN
PLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIK
TIAECLADELINAAKVQGRIGTCCEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t109 CDD cd14867 uS7_Eukaryote 31 195 7.55979E-122
5 g10243.t109 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 202 1.3E-91
2 g10243.t109 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 196 7.2E-104
3 g10243.t109 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 196 7.2E-104
6 g10243.t109 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 200 6.2E-38
1 g10243.t109 Pfam PF00177 Ribosomal protein S7p/S5e 72 199 2.8E-29
8 g10243.t109 ProSitePatterns PS00052 Ribosomal protein S7 signature. 83 109 -
4 g10243.t109 SUPERFAMILY SSF47973 Ribosomal protein S7 30 199 9.16E-57
9 g10243.t109 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 197 4.7E-81

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