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.t98 isoform g10243.t98 8511947 8513667
chr_1 g10243 g10243.t98 exon g10243.t98.exon1 8511947 8512167
chr_1 g10243 g10243.t98 TTS g10243.t98 8511949 8511949
chr_1 g10243 g10243.t98 cds g10243.t98.CDS1 8512099 8512167
chr_1 g10243 g10243.t98 exon g10243.t98.exon2 8512760 8513197
chr_1 g10243 g10243.t98 cds g10243.t98.CDS2 8512760 8513197
chr_1 g10243 g10243.t98 exon g10243.t98.exon3 8513284 8513420
chr_1 g10243 g10243.t98 cds g10243.t98.CDS3 8513284 8513409
chr_1 g10243 g10243.t98 exon g10243.t98.exon4 8513626 8513667
chr_1 g10243 g10243.t98 TSS g10243.t98 8513684 8513684

Sequences

>g10243.t98 Gene=g10243 Length=838
CGTGTGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGAATAGTCAATAATGGCTG
CAGAAGTCGCAGAAAATTTTGAAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTG
TAAATGCTGAACTTCCAGATATTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAG
ATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGGTAGATTTG
CAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATGCTCGCTTA
TGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACACGCAT
TTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATCGGCCATCA
TCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTCGTC
AAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTCTGCACAG
GTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTGATGAGC
TTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGACGAATTGG
AACGTGTTGCGAAATCTAACCGTTAAGATAATAGAATTGAGCGTGATGAAACTAAGCATG
GAGCAATTGAAAATTCTAAACATCATCTTCATCGTCTTAAGAATTATGTAAAACAGCAAA
AGTCTCCATCAGAAATATTTGATAATATTAATAAAACAACACAAGGATTAAAAGATAA

>g10243.t98 Gene=g10243 Length=210
MAAEVAENFEETEQFVETVAPVVNAELPDIKLFGRWSCDEVQDYIAVKEKYARYLPHSAG
RFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRIVKHAFEIIHLLTGENPLQILVS
AIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLA
DELINAAKGSSNSYAIKKKDELERVAKSNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10243.t98 CDD cd14867 uS7_Eukaryote 31 210 4.36537E-132
5 g10243.t98 Gene3D G3DSA:1.10.455.10 Ribosomal Protein S7; 15 210 2.2E-97
2 g10243.t98 PANTHER PTHR11205:SF34 40S RIBOSOMAL PROTEIN S5 42 210 2.8E-114
3 g10243.t98 PANTHER PTHR11205 RIBOSOMAL PROTEIN S7 42 210 2.8E-114
6 g10243.t98 PIRSF PIRSF002122 RPS7p_RPS7a_RPS5e_RPS7o 2 210 2.8E-39
1 g10243.t98 Pfam PF00177 Ribosomal protein S7p/S5e 65 210 3.1E-37
8 g10243.t98 ProSitePatterns PS00052 Ribosomal protein S7 signature. 76 102 -
4 g10243.t98 SUPERFAMILY SSF47973 Ribosomal protein S7 31 210 1.16E-63
9 g10243.t98 TIGRFAM TIGR01028 uS7_euk_arch: ribosomal protein uS7 29 210 2.0E-85

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