Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-splicing factor 18.

Parent gene

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.t1 TSS g1642.t1 12271880 12271880
chr_3 g1642 g1642.t1 isoform g1642.t1 12271951 12273065
chr_3 g1642 g1642.t1 exon g1642.t1.exon1 12271951 12272013
chr_3 g1642 g1642.t1 cds g1642.t1.CDS1 12271951 12272013
chr_3 g1642 g1642.t1 exon g1642.t1.exon2 12272079 12273065
chr_3 g1642 g1642.t1 cds g1642.t1.CDS2 12272079 12273065
chr_3 g1642 g1642.t1 TTS g1642.t1 12273128 12273128

Sequences

>g1642.t1 Gene=g1642 Length=1050
ATGGATATTCTTAAAGCTGAAATTGCAAGAAAAAGAAAATTATTAGAAGAGAAGAAGTTA
GTTGATAATAACAAAAAGTTTTTTAAAAGAGGAGATCTAATAGAAAAAGAAAAAGAAGAA
TATGCACAAAAATATCTTAGACAAGAGTCAACGAACAGTAATGCATCCACATCATCAGAT
AACAACAATTCAAATTATTTTTCAAAAGATCCTGCTGCAGAGATTGCAAATTTACCAAGA
TCAGAAGTCGTTAGAAAACTGAGAGAAAGAGGTGAGCCGATTTTGTTATTTGGCGAATCT
GAACAAGACTCCTGCTTCCGTCTAAGACAACTCGAAATCTCCGCACCAGAAGTTAATAAA
GGATTTAGAAATGATTTTCAAGAAGCACTTGAAGAAGTCGATCAAGCATATTTACAAGAA
ATTCAAAATGATGTTGTGGACCCAAATAAAGATAAAAATAAGAATGAAGACATTGATATT
GATGAATCAATCACATATGAGTCATTACAAGCAGAAGCCGAGAAAATGGGGAGAGGAAAT
AAAGAACATGACACTTATGTTACACTTACACTCTTGAAATTTTTGTTAAAGAAATGGAAT
GATCAACTGAATTCAGTGTCATCAGATGAGAAAATGAAAACTAAAACAAAAATCGCAAAG
GCTACATTCACACAAACGAGAGTTTATTTAAAACCACTATTAAAAAAACTCAAAAATAAT
AAAATTCCAGATGACATTTTCGATAGTCTTAGTGAAATCATAAAACATATTTTAAAACGC
AATTATATAGCTGCTAGTGATGCATATTTGACAATGGCAATCGGTAATGCACCTTGGCCC
ATTGGAGTCACTATGGTTGGTATTCATGCTCGTACTGGTCGTGAAAAAATTTTCTCCAAA
AATGTTGCACATGTGTTAAATGATGAGACACAAAGAAAATATATTCAGGGACTTAAAAGA
TTGATGACAAAATGTCAAGAATTTTTTCCAACAGATCCATCAATGAGTGTGGAGTATGTA
AGCAAAAAAGATTTAGCGAGGAACGAATAA

>g1642.t1 Gene=g1642 Length=349
MDILKAEIARKRKLLEEKKLVDNNKKFFKRGDLIEKEKEEYAQKYLRQESTNSNASTSSD
NNNSNYFSKDPAAEIANLPRSEVVRKLRERGEPILLFGESEQDSCFRLRQLEISAPEVNK
GFRNDFQEALEEVDQAYLQEIQNDVVDPNKDKNKNEDIDIDESITYESLQAEAEKMGRGN
KEHDTYVTLTLLKFLLKKWNDQLNSVSSDEKMKTKTKIAKATFTQTRVYLKPLLKKLKNN
KIPDDIFDSLSEIIKHILKRNYIAASDAYLTMAIGNAPWPIGVTMVGIHARTGREKIFSK
NVAHVLNDETQRKYIQGLKRLMTKCQEFFPTDPSMSVEYVSKKDLARNE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1642.t1 Gene3D G3DSA:1.10.720.150 - 50 124 0
8 g1642.t1 Gene3D G3DSA:1.20.940.10 Functional domain of the splicing factor Prp18 150 335 0
3 g1642.t1 PANTHER PTHR13007:SF19 PRE-MRNA-SPLICING FACTOR 18 1 343 0
4 g1642.t1 PANTHER PTHR13007 PRE-MRNA SPLICING FACTOR-RELATED 1 343 0
2 g1642.t1 Pfam PF08799 pre-mRNA processing factor 4 (PRP4) like 83 111 0
1 g1642.t1 Pfam PF02840 Prp18 domain 190 331 0
7 g1642.t1 SMART SM00500 pr04_2 78 128 0
6 g1642.t1 SUPERFAMILY SSF158230 PRP4-like 72 120 0
5 g1642.t1 SUPERFAMILY SSF47938 Functional domain of the splicing factor Prp18 177 332 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

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.

Raw TPM values