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.t157 TTS g10243.t157 8511949 8511949
chr_1 g10243 g10243.t157 isoform g10243.t157 8512099 8513429
chr_1 g10243 g10243.t157 exon g10243.t157.exon1 8512099 8512167
chr_1 g10243 g10243.t157 cds g10243.t157.CDS1 8512099 8512167
chr_1 g10243 g10243.t157 exon g10243.t157.exon2 8512760 8513197
chr_1 g10243 g10243.t157 cds g10243.t157.CDS2 8512760 8513197
chr_1 g10243 g10243.t157 exon g10243.t157.exon3 8513278 8513429
chr_1 g10243 g10243.t157 cds g10243.t157.CDS3 8513278 8513409
chr_1 g10243 g10243.t157 TSS g10243.t157 8513684 8513684

Sequences

>g10243.t157 Gene=g10243 Length=659
TTATTTCAGAATAGTCAATAATGGCTGCAGAAGTCGCAGAAAATTTTGAAGAAACCGAGC
AATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATATTAAACTTTTTG
GAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATTATATTGCCGTGAAAGAAAAATATG
CTCGTTATTTGCCACATTCGGCCGGTAGATTTGCAGTTAAGCGTTTCCGTAAAGCTCAAT
GTCCAATTGTTGAACGTTTGACATGCTCGCTTATGATGAAAGGTCGCAACAATGGTAAAA
AGTTGATGGCTGTCCGTATTGTGAAACACGCATTTGAAATCATTCACCTTCTTACTGGTG
AAAATCCACTTCAAATCCTTGTATCGGCCATCATCAACTCAGGACCTCGTGAAGATTCAA
CTCGTATCGGTCGCGCTGGTACTGTTCGTCGTCAAGCCGTTGATGTCTCACCATTGAGAC
GTGTCAACCAAGCAATTTGGTTACTCTGCACAGGTGCTCGCGAAGCTGCATTCCGAAACA
TTAAGACAATTGCTGAATGTTTAGCTGATGAGCTTATCAACGCCGCAAAGGGATCATCAA
ACTCCTACGCTATTAAAAAGAAGGACGAATTGGAACGTGTTGCGAAATCTAACCGTTAA

>g10243.t157 Gene=g10243 Length=212
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQVSDYIAVKEKYARYLPHS
AGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGENPLQIL
VSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAEC
LADELINAAKGSSNSYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10243.t157 CDD cd14867 uS7_Eukaryote 31 212 9.01801E-134
7 g10243.t157 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 212 2.5E-99
3 g10243.t157 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 17 45 3.9E-115
5 g10243.t157 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 17 45 3.9E-115
2 g10243.t157 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 44 212 3.9E-115
4 g10243.t157 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 44 212 3.9E-115
8 g10243.t157 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 1 212 1.9E-40
1 g10243.t157 Pfam PF00177 Ribosomal protein S7p/S5e 67 212 3.2E-37
10 g10243.t157 ProSitePatterns PS00052 Ribosomal protein S7 signature. 78 104 -
6 g10243.t157 SUPERFAMILY SSF47973 Ribosomal protein S7 31 212 2.09E-64
11 g10243.t157 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 212 1.6E-87

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