General information for g10243.t171
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S5a.
Parent gene
- The parent gene g10243 is located on chr_1: 8512977..8516967 (- strand)
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.t171 | TTS | g10243.t171 | 8511949 | 8511949 |
| chr_1 | g10243 | g10243.t171 | isoform | g10243.t171 | 8512099 | 8513663 |
| chr_1 | g10243 | g10243.t171 | exon | g10243.t171.exon1 | 8512099 | 8512167 |
| chr_1 | g10243 | g10243.t171 | cds | g10243.t171.CDS1 | 8512099 | 8512167 |
| chr_1 | g10243 | g10243.t171 | exon | g10243.t171.exon2 | 8512760 | 8513197 |
| chr_1 | g10243 | g10243.t171 | cds | g10243.t171.CDS2 | 8512760 | 8513197 |
| chr_1 | g10243 | g10243.t171 | exon | g10243.t171.exon3 | 8513263 | 8513399 |
| chr_1 | g10243 | g10243.t171 | cds | g10243.t171.CDS3 | 8513263 | 8513274 |
| chr_1 | g10243 | g10243.t171 | exon | g10243.t171.exon4 | 8513622 | 8513663 |
| chr_1 | g10243 | g10243.t171 | TSS | g10243.t171 | 8513684 | 8513684 |
Sequences
>g10243.t171 Gene=g10243 Length=686
TGCAGAAGAGTATTCTTGTGAAATTTAATTATTTACAGGTGTAAGTCGCAGAAAATTTTG
AAGAAACCGAGCAATTTGTAGAGACAGTTGCTCCAGTTGTAAATGCTGAACTTCCAGATA
TTAAACTTTTTGGAAGATGGAGTTGTGATGAAGTGCAAGTTTCGGATATGTCTTTACAAG
ATTATATTGCCGTGAAAGAAAAATATGCTCGTTATTTGCCACATTCGGCCGGTAGATTTG
CAGTTAAGCGTTTCCGTAAAGCTCAATGTCCAATTGTTGAACGTTTGACATGCTCGCTTA
TGATGAAAGGTCGCAACAATGGTAAAAAGTTGATGGCTGTCCGTATTGTGAAACACGCAT
TTGAAATCATTCACCTTCTTACTGGTGAAAATCCACTTCAAATCCTTGTATCGGCCATCA
TCAACTCAGGACCTCGTGAAGATTCAACTCGTATCGGTCGCGCTGGTACTGTTCGTCGTC
AAGCCGTTGATGTCTCACCATTGAGACGTGTCAACCAAGCAATTTGGTTACTCTGCACAG
GTGCTCGCGAAGCTGCATTCCGAAACATTAAGACAATTGCTGAATGTTTAGCTGATGAGC
TTATCAACGCCGCAAAGGGATCATCAAACTCCTACGCTATTAAAAAGAAGGACGAATTGG
AACGTGTTGCGAAATCTAACCGTTAA
>g10243.t171 Gene=g10243 Length=172
MSLQDYIAVKEKYARYLPHSAGRFAVKRFRKAQCPIVERLTCSLMMKGRNNGKKLMAVRI
VKHAFEIIHLLTGENPLQILVSAIINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIW
LLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDELERVAKSNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10243.t171 | CDD | cd14867 | uS7_Eukaryote | 1 | 172 | 1.83641E-126 |
| 5 | g10243.t171 | Gene3D | G3DSA:1.10.455.10 | Ribosomal Protein S7; | 1 | 172 | 1.6E-92 |
| 2 | g10243.t171 | PANTHER | PTHR11205:SF34 | 40S RIBOSOMAL PROTEIN S5 | 3 | 172 | 1.4E-108 |
| 3 | g10243.t171 | PANTHER | PTHR11205 | RIBOSOMAL PROTEIN S7 | 3 | 172 | 1.4E-108 |
| 6 | g10243.t171 | PIRSF | PIRSF002122 | RPS7p_RPS7a_RPS5e_RPS7o | 1 | 172 | 9.8E-39 |
| 1 | g10243.t171 | Pfam | PF00177 | Ribosomal protein S7p/S5e | 27 | 172 | 1.5E-37 |
| 8 | g10243.t171 | ProSitePatterns | PS00052 | Ribosomal protein S7 signature. | 38 | 64 | - |
| 4 | g10243.t171 | SUPERFAMILY | SSF47973 | Ribosomal protein S7 | 2 | 172 | 1.19E-63 |
| 9 | g10243.t171 | TIGRFAM | TIGR01028 | uS7_euk_arch: ribosomal protein uS7 | 1 | 172 | 2.3E-84 |
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.
