General information for g1642.t9
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.t9 | TSS | g1642.t9 | 12271880 | 12271880 |
| chr_3 | g1642 | g1642.t9 | isoform | g1642.t9 | 12272736 | 12273946 |
| chr_3 | g1642 | g1642.t9 | exon | g1642.t9.exon1 | 12272736 | 12273418 |
| chr_3 | g1642 | g1642.t9 | cds | g1642.t9.CDS1 | 12272829 | 12273065 |
| chr_3 | g1642 | g1642.t9 | exon | g1642.t9.exon2 | 12273479 | 12273892 |
| chr_3 | g1642 | g1642.t9 | exon | g1642.t9.exon3 | 12273944 | 12273946 |
| chr_3 | g1642 | g1642.t9 | TTS | g1642.t9 | NA | NA |
Sequences
>g1642.t9 Gene=g1642 Length=1100
AAAATTCCAGATGACATTTTCGATAGTCTTAGTGAAATCATAAAACATATTTTAAAACGC
AATTATATAGCTGCTAGTGATGCATATTTGACAATGGCAATCGGTAATGCACCTTGGCCC
ATTGGAGTCACTATGGTTGGTATTCATGCTCGTACTGGTCGTGAAAAAATTTTCTCCAAA
AATGTTGCACATGTGTTAAATGATGAGACACAAAGAAAATATATTCAGGGACTTAAAAGA
TTGATGACAAAATGTCAAGAATTTTTTCCAACAGATCCATCAATGAGTGTGGAGTATGTA
AGCAAAAAAGATTTAGCGAGGAACGAATAATGGAATGAAATTTTATTGTCACTTGTATTG
ATGAATAAATATTTTAATGAGATCATATATTAAATTAATTTTCTGACATTTCCTTTGAGC
GCTTTGTTGCAGCTTCAATTGCATTGAATAGTGTATTTCGTATTCCACCTTTTTCAAGTT
CATGTATGGCATGAATTGTTGTACCACCACTGCTTGTTACTTGATCTTTTAATTGACCAA
CGTGAAATGAACTTTCTAAGACTGTTTTTGAGGCACCAAGAAGTGTTTGTGCTGCAAAAC
GAGTGGCAATATCTCTCGGAAGACCTTGTTTAACACCAGCATCACTTAAGGCATCAATTA
TTATGTAGACATAAGCTGGCCCATACCTGAAAGAGCAGTTATAGCATGAAATTTGCTTTC
ATCAAGGACATCCACAAGACCAAGTGAGCAAAAAATAGCTTTTACTGCGTTATAACTATT
TAAAAGATCTAGTGAAGCATTAAAAATAGTTATTGCAGAACATCCGGCTCCTACTTGAAG
CGGAGTGTTAGGCATAACACGTATATATGATCCAAAATTTGGAATTGCTTCTCTAAGAGT
ATTCAATGATGTTCCAGCAAGAATAGAAACAAGTGTCTTATTTAAATTAGACAAATCTAT
TTCATCGGGATTAAGGAAATTCTTTTTGAGAGAAATTGCAACAGCATCCAAATGAGCAGG
CTTGACACACAAAAAAATTATAGCTGCCGCTCTTACAACCTCATTATTGTTTTTTGTTGT
ATTAATTTTTCCTAATGACT
>g1642.t9 Gene=g1642 Length=78
MAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVLNDETQRKYIQGLKRLMTKCQEFFPT
DPSMSVEYVSKKDLARNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g1642.t9 | Gene3D | G3DSA:1.20.940.10 | Functional domain of the splicing factor Prp18 | 1 | 64 | 0 |
| 2 | g1642.t9 | PANTHER | PTHR13007:SF19 | PRE-MRNA-SPLICING FACTOR 18 | 1 | 72 | 0 |
| 3 | g1642.t9 | PANTHER | PTHR13007 | PRE-MRNA SPLICING FACTOR-RELATED | 1 | 72 | 0 |
| 1 | g1642.t9 | Pfam | PF02840 | Prp18 domain | 1 | 60 | 0 |
| 4 | g1642.t9 | SUPERFAMILY | SSF47938 | Functional domain of the splicing factor Prp18 | 1 | 61 | 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 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.
