General information for g17115.t1
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.t1 | TSS | g17115.t1 | 12520527 | 12520527 |
| chr_4 | g17115 | g17115.t1 | isoform | g17115.t1 | 12520921 | 12522713 |
| chr_4 | g17115 | g17115.t1 | exon | g17115.t1.exon1 | 12520921 | 12521227 |
| chr_4 | g17115 | g17115.t1 | cds | g17115.t1.CDS1 | 12520921 | 12521227 |
| chr_4 | g17115 | g17115.t1 | exon | g17115.t1.exon2 | 12521571 | 12521733 |
| chr_4 | g17115 | g17115.t1 | cds | g17115.t1.CDS2 | 12521571 | 12521733 |
| chr_4 | g17115 | g17115.t1 | exon | g17115.t1.exon3 | 12521894 | 12522150 |
| chr_4 | g17115 | g17115.t1 | cds | g17115.t1.CDS3 | 12521894 | 12522150 |
| chr_4 | g17115 | g17115.t1 | exon | g17115.t1.exon4 | 12522268 | 12522713 |
| chr_4 | g17115 | g17115.t1 | cds | g17115.t1.CDS4 | 12522268 | 12522713 |
| chr_4 | g17115 | g17115.t1 | TTS | g17115.t1 | 12522787 | 12522787 |
Sequences
>g17115.t1 Gene=g17115 Length=1173
ATGGATTATTCATCAAATGATTTTCAAATCCCAGACTCTCAACAAATAGTTCAATTGAAA
GAATTAAGAATATGTCAAAAGCAATATTTGGAAGAATTAAAAAGAAAAGAAAAAGAAGAA
CAAGAAGCATATAGAGAAGATTTGAAGGGTATTATGAGTGATTTTGATCCTGATAAATAC
AAAAGTGGACAAGATCAAAAAGAGCTCGTTCATAATCCAATGTTTAAAAATATCTTAATG
GGATCTAAATGGATGATGGAAGAACCTAAAGATCTTGATAATTATTTATTGATTCCTTGT
CCTAAAGGCGTAAGAGTTTCAATAACACGACAAGAGGAAAAACTTTCAGAAGTTTTTTCA
CGTGATGGACACAAACTTATGGATTTGATGTTAAATATTCCCAAAAATACACAAATTGAT
GGAATTTTATGCAAAAAGAATAAAACCATTTACATTTTGGATGTTTTATGGTATGACGAC
AATGACATGAGAGTTTCAGAAACTTCATTTCGTCGTTATTGGATAAGAAGTAAATTTTAT
GAGCGTAGATTGGGAGTAATTGATCAAAATAGTGGCTACAAAATGAGCTTCATTGAAAGT
TATGACTTTACAAGACCTGATCAGATAAATTATTGTTTTCAAAAATTCCCAATATTTGAA
GGAGTCGATCTTGATGGATTTTTATTTTATCATAAAGATTTGCTTTATGAAAAGGGAGAA
AATAACAGAGTTTTATGGCTTTTTCCTTACATGGTTGATGAAGTTTTTGCAATGTTTCGT
GTTCACAAAGATTACAGTCTATATAAGCCAATAAATTACACAAATTATCTTGAATACATC
GAAAAATTCAATGAAAAGCAGAAAAAGAAACAAAAAATGAAAAACAAAAGAAAATCAAAA
GAAACAACAGAAACAAAAGTTGATTATCAAAGCAGTAATTTATACAGTTTTGATGATATT
AAAGATCCAAAAAAGAGAAATGCAGATTTTGAGAAATTTTGTCAATTTGATGATGATTGG
TTTAAAGCAGGACCGAGTAATAACAAGAGACAACAAGATTTTAGTCAAGATGAAATGTTC
AGCTATGGAAGACCAGAAAATAGAAGAAAAAATAAAATTCAACAACTTTTCGATGAACGA
GAAAGAGCGTGGAGAATTTATTTTGATTCTTAA
>g17115.t1 Gene=g17115 Length=390
MDYSSNDFQIPDSQQIVQLKELRICQKQYLEELKRKEKEEQEAYREDLKGIMSDFDPDKY
KSGQDQKELVHNPMFKNILMGSKWMMEEPKDLDNYLLIPCPKGVRVSITRQEEKLSEVFS
RDGHKLMDLMLNIPKNTQIDGILCKKNKTIYILDVLWYDDNDMRVSETSFRRYWIRSKFY
ERRLGVIDQNSGYKMSFIESYDFTRPDQINYCFQKFPIFEGVDLDGFLFYHKDLLYEKGE
NNRVLWLFPYMVDEVFAMFRVHKDYSLYKPINYTNYLEYIEKFNEKQKKKQKMKNKRKSK
ETTETKVDYQSSNLYSFDDIKDPKKRNADFEKFCQFDDDWFKAGPSNNKRQQDFSQDEMF
SYGRPENRRKNKIQQLFDERERAWRIYFDS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17115.t1 | Coils | Coil | Coil | 19 | 47 | - |
| 4 | g17115.t1 | Coils | Coil | Coil | 276 | 306 | - |
| 3 | g17115.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 12 | 270 | 5.1E-42 |
| 1 | g17115.t1 | PANTHER | PTHR13403 | SNURPORTIN1 RNUT1 PROTEIN RNA, U TRANSPORTER 1 | 35 | 316 | 4.0E-29 |
| 2 | g17115.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 73 | 243 | 3.17E-13 |
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.
