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.t9 TSS g10182.t9 8137442 8137442
chr_1 g10182 g10182.t9 isoform g10182.t9 8138263 8139870
chr_1 g10182 g10182.t9 exon g10182.t9.exon1 8138263 8138278
chr_1 g10182 g10182.t9 exon g10182.t9.exon2 8138363 8138476
chr_1 g10182 g10182.t9 exon g10182.t9.exon3 8138684 8138790
chr_1 g10182 g10182.t9 exon g10182.t9.exon4 8138854 8138889
chr_1 g10182 g10182.t9 exon g10182.t9.exon5 8139024 8139066
chr_1 g10182 g10182.t9 exon g10182.t9.exon6 8139156 8139259
chr_1 g10182 g10182.t9 cds g10182.t9.CDS1 8139258 8139259
chr_1 g10182 g10182.t9 exon g10182.t9.exon7 8139327 8139870
chr_1 g10182 g10182.t9 cds g10182.t9.CDS2 8139327 8139870
chr_1 g10182 g10182.t9 TTS g10182.t9 8140068 8140068

Sequences

>g10182.t9 Gene=g10182 Length=964
ATGGCGGATGAACAAGAATATAGTGGAGGAAAAAAGAAAAATAATAGTTTACCTATCTAT
GGAAATCATGAAACGATGAATCTTAATAACTTAATTTTAACAAATATTCAATCAAGTGTT
TATTTCAAAGTCTTTCTTCATTTTAGTGACATTATTTCAGCTGAAAACGTATCATGAAGT
CATTGATGAAATCTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGAAA
AACTCAAGGAAATTCAGGAATGTGCGGGTAAGAGAGCGTAAGGGGAGTGGGCTCGGGTGG
AATAGTTAGTAGTGCATTTTGTCTTTTATACAAACTATATACACTGAAATTGACACGAAA
ACAGCTAAATGGTTTAATAAAGCATACAGATTCGCCATATATCCGTGCTTTAGGATTCAT
GTATATTCGCTACACTCAACCTCCTGCTGATTTATTTGGATGGTATGAGGAGTTTCTTCA
AGATGAAGAAGAGATTGATATTAAAGCTGGTGGAGGCCATATTTTGACAATAGGTCAAAT
GTGTAGACAATTCCTTGTAAAGCTCGATTGGTTTAGTACACTCTTTCCACGAATTCCTGT
TCCAATACAAAAAAGTATAGAACAGCGATTAAATGACTATGACAAACAAAATGGAATTGT
AGCTCAACCAATTGTTTCCATCCCACAACAACCAGAACGACGTGAACGCTCTTCAAAAGA
GTATTACAGAAGTGAAAGGAGACGTTCTCGATCACCGATAGCGAAGCGTTCACGATCACC
AACAGAAAGGCGTTATAGAGGTGACTTTGATGATGACGCAAGACATTCAAGACGATCACA
TAGCCGAGAGAAATATTCATCAAGTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGATC
TCGTTCTAGAGAACGTAATGATCGAAGAAGATACGAAGAATCGAGAAGTTCACGTCGTTA
TTAA

>g10182.t9 Gene=g10182 Length=181
MYIRYTQPPADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIP
VPIQKSIEQRLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRS
PTERRYRGDFDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRR
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10182.t9 MobiDBLite mobidb-lite consensus disorder prediction 89 181 -
5 g10182.t9 MobiDBLite mobidb-lite consensus disorder prediction 93 109 -
6 g10182.t9 MobiDBLite mobidb-lite consensus disorder prediction 116 181 -
2 g10182.t9 PANTHER PTHR23142 UNCHARACTERIZED 1 180 3.2E-37
3 g10182.t9 PANTHER PTHR23142:SF2 PRE-MRNA-SPLICING FACTOR 38B 1 180 3.2E-37
1 g10182.t9 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