General information for g7976.t71
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S15a.
Parent gene
- The parent gene g7976 is located on chr_2: 27435452..27440035 (+ 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_2 | g7976 | g7976.t71 | isoform | g7976.t71 | 27434743 | 27435915 |
| chr_2 | g7976 | g7976.t71 | exon | g7976.t71.exon1 | 27434743 | 27435087 |
| chr_2 | g7976 | g7976.t71 | cds | g7976.t71.CDS1 | 27435087 | 27435087 |
| chr_2 | g7976 | g7976.t71 | exon | g7976.t71.exon2 | 27435453 | 27435915 |
| chr_2 | g7976 | g7976.t71 | cds | g7976.t71.CDS2 | 27435453 | 27435775 |
| chr_2 | g7976 | g7976.t71 | TTS | g7976.t71 | 27435968 | 27435968 |
| chr_2 | g7976 | g7976.t71 | TSS | g7976.t71 | NA | NA |
Sequences
>g7976.t71 Gene=g7976 Length=808
ATGCTGTGTGATTTTATTCATTCTCTTCTTGTCTTTGTACGTATTGAGTCAGACTCTTCT
TTTTATTGCATTTATAATTTAATAATGCCCATAAAATTCTTATAATATTAAAATAGCTAT
AATCAATCAAATAAAATTAAATCATATGTTATTCAAAAAGTCTTTTGGCAAATTAAAAAA
TTATGATATCTTCAATATTGAAGTGCAAATTTTTTCTTGCTCAGTTATAACAGTAAAGTT
CAAAATTTGAAATTAAGCAAATTGTTATTCAAAAAAGAGCTACAAAATTTTGATTCTTTC
TTTTTCTTTCTTGTTCATCAACGAGATACGTGAATTCCATAAAAATGGTTCGTGTAAGCG
TATTGGCTGATGCCCTCAAATGCATTAATAATGCAGAAAAACGTGGAAAGCGCCAAGTTT
TAATTCGCCCAAATTCCAAAGTTGTCATTAAATTCCTGACCGTTATGATGAAACATGGAT
ATATCGGAGAATTCGAGATCGTCGATGACCATCGCGCTGGAAAAGTAGTTGTTAATCTTA
CTGGTCGCCTCAATAAAGCTGGTATCATTTCACCCAGATTTGACGTTCCAATTCTCGATA
TTGAAAAGTGGACAAATACACTCCTTCCTTCACGACAGTTTGGGTTAGTTAATAACAAAA
TACTCTAATGAAATATCAGTGATTTAAATGTATATTATTAAATATATTTTGTAGATATGT
TGTTTTAACGACAAGTGGTGGAATCATGGACCATGAAGAGGCCCGTAGAAAACATTTGGG
AGGAAAGATTTTGGGATACTTCTTCTAA
>g7976.t71 Gene=g7976 Length=107
MVRVSVLADALKCINNAEKRGKRQVLIRPNSKVVIKFLTVMMKHGYIGEFEIVDDHRAGK
VVVNLTGRLNKAGIISPRFDVPILDIEKWTNTLLPSRQFGLVNNKIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7976.t71 | Gene3D | G3DSA:3.30.1370.30 | - | 1 | 69 | 0 |
| 5 | g7976.t71 | Gene3D | G3DSA:3.30.1490.10 | - | 70 | 103 | 0 |
| 2 | g7976.t71 | PANTHER | PTHR11758 | 40S RIBOSOMAL PROTEIN S15A | 1 | 98 | 0 |
| 3 | g7976.t71 | PANTHER | PTHR11758:SF13 | 40S RIBOSOMAL PROTEIN S15A | 1 | 98 | 0 |
| 1 | g7976.t71 | Pfam | PF00410 | Ribosomal protein S8 | 7 | 76 | 0 |
| 4 | g7976.t71 | SUPERFAMILY | SSF56047 | Ribosomal protein S8 | 4 | 101 | 0 |
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:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
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.
