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.t15 TSS g10182.t15 8137442 8137442
chr_1 g10182 g10182.t15 isoform g10182.t15 8138263 8139870
chr_1 g10182 g10182.t15 exon g10182.t15.exon1 8138263 8138476
chr_1 g10182 g10182.t15 cds g10182.t15.CDS1 8138422 8138476
chr_1 g10182 g10182.t15 exon g10182.t15.exon2 8138700 8138790
chr_1 g10182 g10182.t15 cds g10182.t15.CDS2 8138700 8138790
chr_1 g10182 g10182.t15 exon g10182.t15.exon3 8138854 8138883
chr_1 g10182 g10182.t15 cds g10182.t15.CDS3 8138854 8138883
chr_1 g10182 g10182.t15 exon g10182.t15.exon4 8139024 8139066
chr_1 g10182 g10182.t15 cds g10182.t15.CDS4 8139024 8139066
chr_1 g10182 g10182.t15 exon g10182.t15.exon5 8139156 8139259
chr_1 g10182 g10182.t15 cds g10182.t15.CDS5 8139156 8139259
chr_1 g10182 g10182.t15 exon g10182.t15.exon6 8139327 8139870
chr_1 g10182 g10182.t15 cds g10182.t15.CDS6 8139327 8139870
chr_1 g10182 g10182.t15 TTS g10182.t15 8140068 8140068

Sequences

>g10182.t15 Gene=g10182 Length=1026
ATGGCGGATGAACAAGGTTTTTTATTAATTTTTTTATTTTTCACAAACGTTTAAAAATGC
CTAACAAATTTTCAATTGCTTTATTATTTATATTATTTAGAATATAGTGGAGGAAAAAAG
AAAAATAATAGTTTACCTATCTATGGAAATCATGAAACGATGAATCTTAATAACTTAATT
TTAACAAATATTCAATCAAGTGTTTATTTCAAAGTGACATTATTTCAGCTGAAAACGTAT
CATGAAGTCATTGATGAAATCTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAAT
TCCCGAAAAACTCAAGGAAATTCAGGAATGTGCGGGAGCGTAAGGGGAGTGGGCTCGGGT
GGAATAGTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACACTGAAATTGACACGA
AAACAGCTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCCGTGCTTTAGGATTC
ATGTATATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGTATGAGGAGTTTCTT
CAAGATGAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTTTGACAATAGGTCAA
ATGTGTAGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCTTTCCACGAATTCCT
GTTCCAATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACAAACAAAATGGAATT
GTAGCTCAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTGAACGCTCTTCAAAA
GAGTATTACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGAAGCGTTCACGATCA
CCAACAGAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGACATTCAAGACGATCA
CATAGCCGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGA
TCTCGTTCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGAGAAGTTCACGTCGT
TATTAA

>g10182.t15 Gene=g10182 Length=288
MNLNNLILTNIQSSVYFKVTLFQLKTYHEVIDEIYYQVKHLEPWELNSRKTQGNSGMCGS
VRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRALGFMYIRYTQPPADLF
GWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIPVPIQKSIEQRLND
YDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRSPTERRYRGDFDDD
ARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10182.t15 MobiDBLite mobidb-lite consensus disorder prediction 196 288 -
6 g10182.t15 MobiDBLite mobidb-lite consensus disorder prediction 200 216 -
5 g10182.t15 MobiDBLite mobidb-lite consensus disorder prediction 223 288 -
2 g10182.t15 PANTHER PTHR23142 UNCHARACTERIZED 1 287 2.3E-97
3 g10182.t15 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 1 287 2.3E-97
1 g10182.t15 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