Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein.

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 g10571 g10571.t7 isoform g10571.t7 10488870 10489830
chr_1 g10571 g10571.t7 exon g10571.t7.exon1 10488870 10488924
chr_1 g10571 g10571.t7 cds g10571.t7.CDS1 10488870 10488924
chr_1 g10571 g10571.t7 exon g10571.t7.exon2 10488980 10489210
chr_1 g10571 g10571.t7 cds g10571.t7.CDS2 10488980 10489210
chr_1 g10571 g10571.t7 exon g10571.t7.exon3 10489383 10489632
chr_1 g10571 g10571.t7 cds g10571.t7.CDS3 10489383 10489603
chr_1 g10571 g10571.t7 exon g10571.t7.exon4 10489741 10489830
chr_1 g10571 g10571.t7 TSS g10571.t7 NA NA
chr_1 g10571 g10571.t7 TTS g10571.t7 NA NA

Sequences

>g10571.t7 Gene=g10571 Length=626
TACGTTTTTTCTCGATAGAGTTTTGTTTTGTAAATATTTTATTTGATGGTTTTCGGTGAA
TTGTGAGTGCAAAACGTGCCTAAAATGTGATTTTCTCAAATAATAGAATTTTCATAATCA
TGGGACGATCTAGAAGCAGAAGCAGATCACTGTCACCAGTTCGGCGTAAGCGTGCTAAAG
AACGTGATAGATCAAAGAGGAAGCATAGAAATCGTTCAAAATCACGTGAAAAGAGACGAC
GCAGTCGTTCACGCTCAGAAGAATATAGTAGAACTGGAGTAGGCAGCAGTACAGGAAGCT
CATTAATGAGACATAGACGATCTAGTAGATCTCGTTCTAGATCAAGATCTTATGAAAGAA
GGCATCGTTCACGTTCACCATACGCTCCATCAACATCAAAATCCAAAATTTCTTCAGTTA
ATGTTTCGGAAGCTGATTTAGTGGGCAAATCGCCTGATGAAATTGAAATGATGAAAGTGA
TGGGATTCTGTGGCTTTGATACAACAAAGGGCAAAAAAGTTGAAGGAAATAATGTAGGAG
AAGTTCATGTTATTTTAAAAAGAAAATATAGACAATATATGAATCGCAAAGGCGGCTTTA
ATCGACCATTGGACTTTGTTGCATAA

>g10571.t7 Gene=g10571 Length=168
MGRSRSRSRSLSPVRRKRAKERDRSKRKHRNRSKSREKRRRSRSRSEEYSRTGVGSSTGS
SLMRHRRSSRSRSRSRSYERRHRSRSPYAPSTSKSKISSVNVSEADLVGKSPDEIEMMKV
MGFCGFDTTKGKKVEGNNVGEVHVILKRKYRQYMNRKGGFNRPLDFVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10571.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 109 -
7 g10571.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 40 -
5 g10571.t7 MobiDBLite mobidb-lite consensus disorder prediction 49 64 -
6 g10571.t7 MobiDBLite mobidb-lite consensus disorder prediction 65 81 -
3 g10571.t7 MobiDBLite mobidb-lite consensus disorder prediction 88 105 -
2 g10571.t7 PANTHER PTHR31077 U4/U6.U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 27 KDA PROTEIN 1 167 6.8E-37
1 g10571.t7 Pfam PF08648 U4/U6.U5 small nuclear ribonucleoproteins 113 166 1.0E-29
9 g10571.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 71 -
10 g10571.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 51 -
11 g10571.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 52 63 -
12 g10571.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 64 71 -
8 g10571.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 72 168 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008380 RNA splicing BP

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.

Raw TPM values