General information for g6834.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 g6834 is located on chr_2: 18991000..18993560 (+ 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 | g6834 | g6834.t1 | TSS | g6834.t1 | 18990008 | 18990008 |
| chr_2 | g6834 | g6834.t1 | isoform | g6834.t1 | 18990053 | 18991000 |
| chr_2 | g6834 | g6834.t1 | exon | g6834.t1.exon1 | 18990053 | 18991000 |
| chr_2 | g6834 | g6834.t1 | cds | g6834.t1.CDS1 | 18990053 | 18991000 |
| chr_2 | g6834 | g6834.t1 | TTS | g6834.t1 | 18991245 | 18991245 |
Sequences
>g6834.t1 Gene=g6834 Length=948
ATGGGTGAATTTCGAATATTATACAAGAATCTAGCTAATTTATCAAACCAGCAATCACTT
CGAAGAGCTAAACTTTTAGAGGAACAAAGATTGAGACGAGAAAATCAATTTTCGTGCCAA
CGAGACATTAAATCTGAAAATGTTAAGAGAAAAAGAATTTACAAAGATTTCAATTATAAA
AATAATTTAATGTTATCAGAATGGATGTTTGAAGCACCAACAGATTTAGAAGATTTTATT
TTGATTCCTTGTCCAAAAGGAATTCGAGTGACATTATCAAATGAAAAGGCAAAGAATACA
AATTGTCGTTTGTATTACAAAAATGGCACAGAAAATTTAAGTTTTAAAACAAACTTACCG
AAACAAACAATACTGGATTGCATTTTAAATAAAATTTCAAATACTCTATTCATTCTGGAT
GTTATAAAATATGATGGAAGAGATTTTACAAACTGCGATACATCATTAAGACGCTTTTGG
ATTAAAAATAAATTTATTGAAAATGACCTGAAAGTAATTGATGAGAGAAGCGATATTAAA
ATGCAATTATTGGAATCTTTTGATTTAACAGACATGGATCAAATATATTCCTGCTTTCAA
AAATTCCCAATTTTCAATGAAGGAACAGAGCTTGATGGTTTTTTATTTTATCATAAGGAA
GCTGATTACGCTATAGGTGAGACTACACCTTTAGTCTTATGGCTTTTTCCTTTTATGATT
GAAGAAGTTTTGCCAATGTTTCAAGTTCATCCATACTACAAACAAAAACCTGACAATTAC
ACAAATTATCACGACTATATTCGAATGTTTAATGAAAATATAAAGAACAAACGCAAAATA
AGAAGCAAAGATGACCACAAAATGGATGTTCAAGAGAATCAAGAAAAGAATGAATTTGAT
TTACAAAATGAAATTCAGAAAATGATTGATTTGGAACGTTATGGATAA
>g6834.t1 Gene=g6834 Length=315
MGEFRILYKNLANLSNQQSLRRAKLLEEQRLRRENQFSCQRDIKSENVKRKRIYKDFNYK
NNLMLSEWMFEAPTDLEDFILIPCPKGIRVTLSNEKAKNTNCRLYYKNGTENLSFKTNLP
KQTILDCILNKISNTLFILDVIKYDGRDFTNCDTSLRRFWIKNKFIENDLKVIDERSDIK
MQLLESFDLTDMDQIYSCFQKFPIFNEGTELDGFLFYHKEADYAIGETTPLVLWLFPFMI
EEVLPMFQVHPYYKQKPDNYTNYHDYIRMFNENIKNKRKIRSKDDHKMDVQENQEKNEFD
LQNEIQKMIDLERYG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6834.t1 | CDD | cd09232 | Snurportin-1_C | 59 | 238 | 0 |
| 3 | g6834.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 5 | 271 | 0 |
| 1 | g6834.t1 | PANTHER | PTHR13403 | SNURPORTIN1 RNUT1 PROTEIN RNA, U TRANSPORTER 1 | 24 | 297 | 0 |
| 2 | g6834.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 50 | 230 | 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: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.
