General information for g17074.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 g17074 is located on chr_4: 12399943..12400896 (+ 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 | g17074 | g17074.t1 | TSS | g17074.t1 | 12399928 | 12399928 |
| chr_4 | g17074 | g17074.t1 | isoform | g17074.t1 | 12399943 | 12400896 |
| chr_4 | g17074 | g17074.t1 | exon | g17074.t1.exon1 | 12399943 | 12400896 |
| chr_4 | g17074 | g17074.t1 | cds | g17074.t1.CDS1 | 12399943 | 12400896 |
| chr_4 | g17074 | g17074.t1 | TTS | g17074.t1 | 12400090 | 12400090 |
Sequences
>g17074.t1 Gene=g17074 Length=954
ATGAGTGAATTTAAAAATTTATATAAAAATCAATCAAATTTAGCTCAACAACAGTCACTT
CGAAGAGCTAAACTTTTAGAAGAACAAAAACAAAGACGAGAAAATCAATTTTCATCTCAA
CGTGATATAAAATCTGAAAATGAGCAGCAAAAGAAGAAAAAAATTTACAAAGATTTCGAT
TATAAAAACAATTTAATGTTGTCAGAATGGATGATGGAAACACCAGAAGATTTAGAAGAT
TTTCTTTTAATTCCATGCCCAAAAGGAATTCGATCAACTTTATCAAATGAAAAGACAAAA
AATAAAAATTGCCGGTTGTATTACAAAAATGGAACTGAAAATTTAAGATTTAAGACAAAT
TTGCCACAACAAACAATTCTCGATTGTATTTTAGATAAAATTTCAAACACTTTATTCATT
CTGGATGTTATAAAATATGATGGACGAGATTTTATGAATTGTGATACATCATTTCGGCAT
TTTTGGATTAAAAATAAATTTATTGAATCAGATCTAAAAATAATTGATGAGGAAAGTGAT
ATGAAAATGCAATTATTAGACGTTTATGATTTAGCAGACTCAAATCAAGGATTTTCATGT
TTTCAAAAATATCCGATGTTCAATGAAGGCACAGAACTTGATGGATTTTTGTTTTATCAT
AAAGAAGCTGATTATACTATTGGTGAGACACCGTTAGTTTTATGGCTTTTTCCTTTCATG
ATTGAAGAAGTTTTATCAATGTTCAAAGTTCATCCAAATTATAATAATCAAAAACCTGAC
AATTATAGAAATTATTTAGATTATATAAAAATCTTCAATGAGACTCTAAAGAAAAAACGA
AGATCAAGAAATAAGAGTGAAAGTAGCATGGAAATTCAAGAAAATCAAGATGAAAATGAA
TTTGATATGCAAAATGAGATTCAAAAAATGATTGACTTAGAACGTTTTGGCTAA
>g17074.t1 Gene=g17074 Length=317
MSEFKNLYKNQSNLAQQQSLRRAKLLEEQKQRRENQFSSQRDIKSENEQQKKKKIYKDFD
YKNNLMLSEWMMETPEDLEDFLLIPCPKGIRSTLSNEKTKNKNCRLYYKNGTENLRFKTN
LPQQTILDCILDKISNTLFILDVIKYDGRDFMNCDTSFRHFWIKNKFIESDLKIIDEESD
MKMQLLDVYDLADSNQGFSCFQKYPMFNEGTELDGFLFYHKEADYTIGETPLVLWLFPFM
IEEVLSMFKVHPNYNNQKPDNYRNYLDYIKIFNETLKKKRRSRNKSESSMEIQENQDENE
FDMQNEIQKMIDLERFG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g17074.t1 | CDD | cd09232 | Snurportin-1_C | 60 | 239 | 4.09658E-57 |
| 6 | g17074.t1 | Coils | Coil | Coil | 16 | 36 | - |
| 5 | g17074.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 2 | 269 | 3.5E-64 |
| 3 | g17074.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 49 | - |
| 4 | g17074.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 280 | 303 | - |
| 1 | g17074.t1 | PANTHER | PTHR13403 | SNURPORTIN1 RNUT1 PROTEIN RNA, U TRANSPORTER 1 | 8 | 299 | 3.3E-45 |
| 2 | g17074.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 57 | 232 | 3.74E-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 transcript has been annotated with K13151 (snurportin-1)
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.
