Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-splicing factor 38B.

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_1 g10182 g10182.t16 TSS g10182.t16 8137442 8137442
chr_1 g10182 g10182.t16 isoform g10182.t16 8138263 8139870
chr_1 g10182 g10182.t16 exon g10182.t16.exon1 8138263 8138488
chr_1 g10182 g10182.t16 cds g10182.t16.CDS1 8138422 8138488
chr_1 g10182 g10182.t16 exon g10182.t16.exon2 8138700 8138790
chr_1 g10182 g10182.t16 cds g10182.t16.CDS2 8138700 8138790
chr_1 g10182 g10182.t16 exon g10182.t16.exon3 8138854 8138883
chr_1 g10182 g10182.t16 cds g10182.t16.CDS3 8138854 8138883
chr_1 g10182 g10182.t16 exon g10182.t16.exon4 8139024 8139066
chr_1 g10182 g10182.t16 cds g10182.t16.CDS4 8139024 8139066
chr_1 g10182 g10182.t16 exon g10182.t16.exon5 8139156 8139259
chr_1 g10182 g10182.t16 cds g10182.t16.CDS5 8139156 8139259
chr_1 g10182 g10182.t16 exon g10182.t16.exon6 8139327 8139870
chr_1 g10182 g10182.t16 cds g10182.t16.CDS6 8139327 8139870
chr_1 g10182 g10182.t16 TTS g10182.t16 8140068 8140068

Sequences

>g10182.t16 Gene=g10182 Length=1038
ATGGCGGATGAACAAGGTTTTTTATTAATTTTTTTATTTTTCACAAACGTTTAAAAATGC
CTAACAAATTTTCAATTGCTTTATTATTTATATTATTTAGAATATAGTGGAGGAAAAAAG
AAAAATAATAGTTTACCTATCTATGGAAATCATGAAACGATGAATCTTAATAACTTAATT
TTAACAAATATTCAATCAAGTGTTTATTTCAAAGGTAAGCTTCTATTGACATTATTTCAG
CTGAAAACGTATCATGAAGTCATTGATGAAATCTACTATCAAGTAAAACATCTTGAGCCT
TGGGAACTTAATTCCCGAAAAACTCAAGGAAATTCAGGAATGTGCGGGAGCGTAAGGGGA
GTGGGCTCGGGTGGAATAGTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACACTG
AAATTGACACGAAAACAGCTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCCGT
GCTTTAGGATTCATGTATATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGTAT
GAGGAGTTTCTTCAAGATGAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTTTG
ACAATAGGTCAAATGTGTAGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCTTT
CCACGAATTCCTGTTCCAATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACAAA
CAAAATGGAATTGTAGCTCAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTGAA
CGCTCTTCAAAAGAGTATTACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGAAG
CGTTCACGATCACCAACAGAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGACAT
TCAAGACGATCACATAGCCGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATAGA
GATCGTTCAAGATCTCGTTCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGAGA
AGTTCACGTCGTTATTAA

>g10182.t16 Gene=g10182 Length=292
MNLNNLILTNIQSSVYFKGKLLLTLFQLKTYHEVIDEIYYQVKHLEPWELNSRKTQGNSG
MCGSVRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRALGFMYIRYTQPP
ADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIPVPIQKSIEQ
RLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRSPTERRYRGD
FDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g10182.t16 MobiDBLite mobidb-lite consensus disorder prediction 200 292 -
4 g10182.t16 MobiDBLite mobidb-lite consensus disorder prediction 204 220 -
6 g10182.t16 MobiDBLite mobidb-lite consensus disorder prediction 227 292 -
2 g10182.t16 PANTHER PTHR23142 UNCHARACTERIZED 1 291 1.7E-94
3 g10182.t16 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 1 291 1.7E-94
1 g10182.t16 Pfam PF03371 PRP38 family 1 178 1.1E-46

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed