General information for g1642.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor 18.
Parent gene
- The parent gene g1642 is located on chr_3: 12273065..12274118 (+ 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_3 | g1642 | g1642.t8 | TSS | g1642.t8 | 12271880 | 12271880 |
| chr_3 | g1642 | g1642.t8 | isoform | g1642.t8 | 12272088 | 12273130 |
| chr_3 | g1642 | g1642.t8 | exon | g1642.t8.exon1 | 12272088 | 12273130 |
| chr_3 | g1642 | g1642.t8 | cds | g1642.t8.CDS1 | 12272541 | 12273065 |
| chr_3 | g1642 | g1642.t8 | TTS | g1642.t8 | 12273128 | 12273128 |
Sequences
>g1642.t8 Gene=g1642 Length=1043
AAAAAGTTTTTTAAAAGAGGAGATCTAATAGAAAAAGAAAAAGAAGAATATGCACAAAAA
TATCTTAGACAAGAGTCAACGAACAGTAATGCATCCACATCATCAGATAACAACAATTCA
AATTATTTTTCAAAAGATCCTGCTGCAGAGATTGCAAATTTACCAAGATCAGAAGTCGTT
AGAAAACTGAGAGAAAGAGGTGAGCCGATTTTGTTATTTGGCGAATCTGAACAAGACTCC
TGCTTCCGTCTAAGACAACTCGAAATCTCCGCACCAGAAGTTAATAAAGGATTTAGAAAT
GATTTTCAAGAAGCACTTGAAGAAGTCGATCAAGCATATTTACAAGAAATTCAAAATGAT
GTTGTGGACCCAAATAAAGATAAAAATAAGAATGAAGACATTGATATTGATGAATCAATC
ACATATGAGTCATTACAAGCAGAAGCCGAGAAAATGGGGAGAGGAAATAAAGAACATGAC
ACTTATGTTACACTTACACTCTTGAAATTTTTGTTAAAGAAATGGAATGATCAACTGAAT
TCAGTGTCATCAGATGAGAAAATGAAAACTAAAACAAAAATCGCAAAGGCTACATTCACA
CAAACGAGAGTTTATTTAAAACCACTATTAAAAAAACTCAAAAATAATAAAATTCCAGAT
GACATTTTCGATAGTCTTAGTGAAATCATAAAACATATTTTAAAACGCAATTATATAGCT
GCTAGTGATGCATATTTGACAATGGCAATCGGTAATGCACCTTGGCCCATTGGAGTCACT
ATGGTTGGTATTCATGCTCGTACTGGTCGTGAAAAAATTTTCTCCAAAAATGTTGCACAT
GTGTTAAATGATGAGACACAAAGAAAATATATTCAGGGACTTAAAAGATTGATGACAAAA
TGTCAAGAATTTTTTCCAACAGATCCATCAATGAGTGTGGAGTATGTAAGCAAAAAAGAT
TTAGCGAGGAACGAATAATGGAATGAAATTTTATTGTCACTTGTATTGATGAATAAATAT
TTTAATGAGATCATATATTAAAT
>g1642.t8 Gene=g1642 Length=174
MGRGNKEHDTYVTLTLLKFLLKKWNDQLNSVSSDEKMKTKTKIAKATFTQTRVYLKPLLK
KLKNNKIPDDIFDSLSEIIKHILKRNYIAASDAYLTMAIGNAPWPIGVTMVGIHARTGRE
KIFSKNVAHVLNDETQRKYIQGLKRLMTKCQEFFPTDPSMSVEYVSKKDLARNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g1642.t8 | Gene3D | G3DSA:1.20.940.10 | Functional domain of the splicing factor Prp18 | 3 | 160 | 0 |
| 2 | g1642.t8 | PANTHER | PTHR13007:SF19 | PRE-MRNA-SPLICING FACTOR 18 | 8 | 168 | 0 |
| 3 | g1642.t8 | PANTHER | PTHR13007 | PRE-MRNA SPLICING FACTOR-RELATED | 8 | 168 | 0 |
| 1 | g1642.t8 | Pfam | PF02840 | Prp18 domain | 15 | 156 | 0 |
| 4 | g1642.t8 | SUPERFAMILY | SSF47938 | Functional domain of the splicing factor Prp18 | 5 | 157 | 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:0005681 | spliceosomal complex | CC |
| GO:0008380 | RNA splicing | BP |
KEGG
Orthology
- This transcript has been annotated with K12817 (pre-mRNA-splicing factor 18)
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.
