Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t12 TSS g10182.t12 8137442 8137442
chr_1 g10182 g10182.t12 isoform g10182.t12 8138263 8139870
chr_1 g10182 g10182.t12 exon g10182.t12.exon1 8138263 8138278
chr_1 g10182 g10182.t12 exon g10182.t12.exon2 8138363 8138488
chr_1 g10182 g10182.t12 exon g10182.t12.exon3 8138700 8138790
chr_1 g10182 g10182.t12 exon g10182.t12.exon4 8138854 8138889
chr_1 g10182 g10182.t12 exon g10182.t12.exon5 8139024 8139066
chr_1 g10182 g10182.t12 exon g10182.t12.exon6 8139156 8139259
chr_1 g10182 g10182.t12 cds g10182.t12.CDS1 8139258 8139259
chr_1 g10182 g10182.t12 exon g10182.t12.exon7 8139327 8139870
chr_1 g10182 g10182.t12 cds g10182.t12.CDS2 8139327 8139870
chr_1 g10182 g10182.t12 TTS g10182.t12 8140068 8140068

Sequences

>g10182.t12 Gene=g10182 Length=960
ATGGCGGATGAACAAGAATATAGTGGAGGAAAAAAGAAAAATAATAGTTTACCTATCTAT
GGAAATCATGAAACGATGAATCTTAATAACTTAATTTTAACAAATATTCAATCAAGTGTT
TATTTCAAAGGTAAGCTTCTATTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATT
GATGAAATCTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGAAAAACT
CAAGGAAATTCAGGAATGTGCGGGTAAGAGAGCGTAAGGGGAGTGGGCTCGGGTGGAATA
GTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACACTGAAATTGACACGAAAACAG
CTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCCGTGCTTTAGGATTCATGTAT
ATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGTATGAGGAGTTTCTTCAAGAT
GAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTTTGACAATAGGTCAAATGTGT
AGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCTTTCCACGAATTCCTGTTCCA
ATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACAAACAAAATGGAATTGTAGCT
CAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTGAACGCTCTTCAAAAGAGTAT
TACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGAAGCGTTCACGATCACCAACA
GAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGACATTCAAGACGATCACATAGC
CGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGATCTCGT
TCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGAGAAGTTCACGTCGTTATTAA

>g10182.t12 Gene=g10182 Length=181
MYIRYTQPPADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIP
VPIQKSIEQRLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRS
PTERRYRGDFDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRR
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10182.t12 MobiDBLite mobidb-lite consensus disorder prediction 89 181 -
5 g10182.t12 MobiDBLite mobidb-lite consensus disorder prediction 93 109 -
6 g10182.t12 MobiDBLite mobidb-lite consensus disorder prediction 116 181 -
2 g10182.t12 PANTHER PTHR23142 UNCHARACTERIZED 1 180 3.2E-37
3 g10182.t12 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 1 180 3.2E-37
1 g10182.t12 Pfam PF03371 PRP38 family 1 67 3.2E-13

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

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. There were no conditions that were differentially expressed