Gene loci information

Transcript annotation

  • This transcript has been annotated as U4/U6.U5 tri-snRNP-associated protein 2.

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_3 g3473 g3473.t8 TSS g3473.t8 25773588 25773588
chr_3 g3473 g3473.t8 isoform g3473.t8 25774245 25775406
chr_3 g3473 g3473.t8 exon g3473.t8.exon1 25774245 25775095
chr_3 g3473 g3473.t8 cds g3473.t8.CDS1 25774509 25775095
chr_3 g3473 g3473.t8 exon g3473.t8.exon2 25775151 25775406
chr_3 g3473 g3473.t8 cds g3473.t8.CDS2 25775151 25775406
chr_3 g3473 g3473.t8 TTS g3473.t8 25775455 25775455

Sequences

>g3473.t8 Gene=g3473 Length=1107
CTTAATCCAACTTTTACAAAAAATGATATAAAAGTACTTGATGATTCAGAGAAGACTTCA
AGAACTCTTGATGGAACTTTATATTTTCCTGGGATAGTTGGTCTCAATAATATTAAAGCA
AATGACTATTGTAATGTTGTTCTTCAAGCACTCTCACATGTGACACCAATTAGAGACTAT
TTTCTATGTGAACAAAATTATTCAAAAATTAAGCATTCATCGGGCGATTCTGCTTTTGCA
ATTGTGCAACGCTTCGGTGAATTAATGAGAAAATTGTGGAATCCAAGAAATTTTAAAGCT
CATGTTTCTCCGCATGAAATGCTTCAAGCTGTTGTTCTTTGGAGCAATAAAAGATTTCAA
ATTATTGAACAGAGCGATCCAATTGATTTTCTTACATGGTTTTTGCATGAATTACATCGT
CAATTGAGAGGAAATAAAAATCTTAACTCAAGCATTATCAATAAAACTTTCTTAGGAGAG
ATGAAAATTTACTCAAGAAAAATTCCACCTGTTGAATGCGATGATGCCCAAAAAGAATTG
TTGCTTGCAACTGAAGAGTATCAAGAAAAAATTGAAACAACAAATTTTCTTTATTTAACA
TGCGATTTACCGCCACCACCTCTATTCATCGATGAGCACCGTGAGAATATTATTCCTCAA
GTCAATTTATATCAATTGCTTGCAAAATTCAATGGAGTTACAGAAAAAGAATATAAATCA
TATAAAGACAATTTCTTGAAACGCTTTGAAATTGTAAGACTGCCAAAATTTATTATTTTG
TTTATCAAACGTTTCACCAAAAATACTTTCTTTGTGGACAAAAATCCAACAATTGTCAAT
TTTCCTGTCAAAAATGTTGATTTCGGTGACATCTTGACACCAGAGCATAAGAAAAATCAC
ACTGAGACTCGTTATAATTTGATTGCAAACATAGTTCATGATGGTGAGCCCAATAAAGGT
ACATATCGTGCACACATCCTTTATAAAGCAACAAATCAGTGGTTTGAAATGCAAGATCTT
CATGTCACTGATATTCTGCCACAAATGATTACTCTTACAGAGGCATATATTCAAATCTAT
GAACAACAGAGCACAACAACTAAATAG

>g3473.t8 Gene=g3473 Length=280
MRKLWNPRNFKAHVSPHEMLQAVVLWSNKRFQIIEQSDPIDFLTWFLHELHRQLRGNKNL
NSSIINKTFLGEMKIYSRKIPPVECDDAQKELLLATEEYQEKIETTNFLYLTCDLPPPPL
FIDEHRENIIPQVNLYQLLAKFNGVTEKEYKSYKDNFLKRFEIVRLPKFIILFIKRFTKN
TFFVDKNPTIVNFPVKNVDFGDILTPEHKKNHTETRYNLIANIVHDGEPNKGTYRAHILY
KATNQWFEMQDLHVTDILPQMITLTEAYIQIYEQQSTTTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3473.t8 Coils Coil Coil 85 105 -
5 g3473.t8 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 1 276 3.3E-62
2 g3473.t8 PANTHER PTHR21646 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2 275 3.9E-73
3 g3473.t8 PANTHER PTHR21646:SF16 U4/U6.U5 TRI-SNRNP-ASSOCIATED PROTEIN 2 2 275 3.9E-73
1 g3473.t8 Pfam PF00443 Ubiquitin carboxyl-terminal hydrolase 3 272 1.9E-27
7 g3473.t8 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 1 275 24.124
4 g3473.t8 SUPERFAMILY SSF54001 Cysteine proteinases 2 274 3.34E-44

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:0006397 mRNA processing BP
GO:0004843 thiol-dependent deubiquitinase MF
GO:0016579 protein deubiquitination BP
GO:0000245 spliceosomal complex assembly BP

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.

Raw TPM values