General information for g17115.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Snurportin-1.
Parent gene
- The parent gene g17115 is located on chr_4: 12520921..12522713 (+ 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_4 | g17115 | g17115.t5 | TSS | g17115.t5 | 12520527 | 12520527 |
| chr_4 | g17115 | g17115.t5 | isoform | g17115.t5 | 12520921 | 12522137 |
| chr_4 | g17115 | g17115.t5 | exon | g17115.t5.exon1 | 12520921 | 12521227 |
| chr_4 | g17115 | g17115.t5 | cds | g17115.t5.CDS1 | 12520921 | 12521227 |
| chr_4 | g17115 | g17115.t5 | exon | g17115.t5.exon2 | 12521571 | 12521733 |
| chr_4 | g17115 | g17115.t5 | cds | g17115.t5.CDS2 | 12521571 | 12521733 |
| chr_4 | g17115 | g17115.t5 | exon | g17115.t5.exon3 | 12521894 | 12522137 |
| chr_4 | g17115 | g17115.t5 | cds | g17115.t5.CDS3 | 12521894 | 12522137 |
| chr_4 | g17115 | g17115.t5 | TTS | g17115.t5 | 12522787 | 12522787 |
Sequences
>g17115.t5 Gene=g17115 Length=714
ATGGATTATTCATCAAATGATTTTCAAATCCCAGACTCTCAACAAATAGTTCAATTGAAA
GAATTAAGAATATGTCAAAAGCAATATTTGGAAGAATTAAAAAGAAAAGAAAAAGAAGAA
CAAGAAGCATATAGAGAAGATTTGAAGGGTATTATGAGTGATTTTGATCCTGATAAATAC
AAAAGTGGACAAGATCAAAAAGAGCTCGTTCATAATCCAATGTTTAAAAATATCTTAATG
GGATCTAAATGGATGATGGAAGAACCTAAAGATCTTGATAATTATTTATTGATTCCTTGT
CCTAAAGGCGTAAGAGTTTCAATAACACGACAAGAGGAAAAACTTTCAGAAGTTTTTTCA
CGTGATGGACACAAACTTATGGATTTGATGTTAAATATTCCCAAAAATACACAAATTGAT
GGAATTTTATGCAAAAAGAATAAAACCATTTACATTTTGGATGTTTTATGGTATGACGAC
AATGACATGAGAGTTTCAGAAACTTCATTTCGTCGTTATTGGATAAGAAGTAAATTTTAT
GAGCGTAGATTGGGAGTAATTGATCAAAATAGTGGCTACAAAATGAGCTTCATTGAAAGT
TATGACTTTACAAGACCTGATCAGATAAATTATTGTTTTCAAAAATTCCCAATATTTGAA
GGAGTCGATCTTGATGGATTTTTATTTTATCATAAAGATTTGCTTTATGAAAAG
>g17115.t5 Gene=g17115 Length=238
MDYSSNDFQIPDSQQIVQLKELRICQKQYLEELKRKEKEEQEAYREDLKGIMSDFDPDKY
KSGQDQKELVHNPMFKNILMGSKWMMEEPKDLDNYLLIPCPKGVRVSITRQEEKLSEVFS
RDGHKLMDLMLNIPKNTQIDGILCKKNKTIYILDVLWYDDNDMRVSETSFRRYWIRSKFY
ERRLGVIDQNSGYKMSFIESYDFTRPDQINYCFQKFPIFEGVDLDGFLFYHKDLLYEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g17115.t5 | Coils | Coil | Coil | 19 | 47 | - |
| 3 | g17115.t5 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 8 | 238 | 5.8E-34 |
| 1 | g17115.t5 | PANTHER | PTHR13403 | SNURPORTIN1 RNUT1 PROTEIN RNA, U TRANSPORTER 1 | 35 | 237 | 2.0E-22 |
| 2 | g17115.t5 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 73 | 237 | 1.18E-12 |
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:0005634 | nucleus | CC |
| GO:0061015 | snRNA import into nucleus | BP |
| GO:0005737 | cytoplasm | 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.
