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.t6 TSS g10182.t6 8137442 8137442
chr_1 g10182 g10182.t6 isoform g10182.t6 8138166 8139870
chr_1 g10182 g10182.t6 exon g10182.t6.exon1 8138166 8138212
chr_1 g10182 g10182.t6 exon g10182.t6.exon2 8138356 8138476
chr_1 g10182 g10182.t6 cds g10182.t6.CDS1 8138422 8138476
chr_1 g10182 g10182.t6 exon g10182.t6.exon3 8138700 8138790
chr_1 g10182 g10182.t6 cds g10182.t6.CDS2 8138700 8138790
chr_1 g10182 g10182.t6 exon g10182.t6.exon4 8138854 8138883
chr_1 g10182 g10182.t6 cds g10182.t6.CDS3 8138854 8138883
chr_1 g10182 g10182.t6 exon g10182.t6.exon5 8139024 8139066
chr_1 g10182 g10182.t6 cds g10182.t6.CDS4 8139024 8139066
chr_1 g10182 g10182.t6 exon g10182.t6.exon6 8139156 8139259
chr_1 g10182 g10182.t6 cds g10182.t6.CDS5 8139156 8139259
chr_1 g10182 g10182.t6 exon g10182.t6.exon7 8139327 8139870
chr_1 g10182 g10182.t6 cds g10182.t6.CDS6 8139327 8139870
chr_1 g10182 g10182.t6 TTS g10182.t6 8140068 8140068

Sequences

>g10182.t6 Gene=g10182 Length=980
TTTTAATCAAGTTCTTGCTGTAATCACACCAATTTTATTCTCAAGTTTATTTAGAATATA
GTGGAGGAAAAAAGAAAAATAATAGTTTACCTATCTATGGAAATCATGAAACGATGAATC
TTAATAACTTAATTTTAACAAATATTCAATCAAGTGTTTATTTCAAAGTGACATTATTTC
AGCTGAAAACGTATCATGAAGTCATTGATGAAATCTACTATCAAGTAAAACATCTTGAGC
CTTGGGAACTTAATTCCCGAAAAACTCAAGGAAATTCAGGAATGTGCGGGAGCGTAAGGG
GAGTGGGCTCGGGTGGAATAGTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACAC
TGAAATTGACACGAAAACAGCTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCC
GTGCTTTAGGATTCATGTATATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGT
ATGAGGAGTTTCTTCAAGATGAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTT
TGACAATAGGTCAAATGTGTAGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCT
TTCCACGAATTCCTGTTCCAATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACA
AACAAAATGGAATTGTAGCTCAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTG
AACGCTCTTCAAAAGAGTATTACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGA
AGCGTTCACGATCACCAACAGAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGAC
ATTCAAGACGATCACATAGCCGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATA
GAGATCGTTCAAGATCTCGTTCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGA
GAAGTTCACGTCGTTATTAA

>g10182.t6 Gene=g10182 Length=288
MNLNNLILTNIQSSVYFKVTLFQLKTYHEVIDEIYYQVKHLEPWELNSRKTQGNSGMCGS
VRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRALGFMYIRYTQPPADLF
GWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIPVPIQKSIEQRLND
YDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRSPTERRYRGDFDDD
ARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10182.t6 MobiDBLite mobidb-lite consensus disorder prediction 196 288 -
6 g10182.t6 MobiDBLite mobidb-lite consensus disorder prediction 200 216 -
5 g10182.t6 MobiDBLite mobidb-lite consensus disorder prediction 223 288 -
2 g10182.t6 PANTHER PTHR23142 UNCHARACTERIZED 1 287 2.3E-97
3 g10182.t6 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 1 287 2.3E-97
1 g10182.t6 Pfam PF03371 PRP38 family 1 174 7.7E-50

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