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.t5 TSS g3473.t5 25773588 25773588
chr_3 g3473 g3473.t5 isoform g3473.t5 25773678 25775406
chr_3 g3473 g3473.t5 exon g3473.t5.exon1 25773678 25774172
chr_3 g3473 g3473.t5 cds g3473.t5.CDS1 25773948 25774172
chr_3 g3473 g3473.t5 exon g3473.t5.exon2 25774230 25775095
chr_3 g3473 g3473.t5 cds g3473.t5.CDS2 25774230 25775095
chr_3 g3473 g3473.t5 exon g3473.t5.exon3 25775151 25775406
chr_3 g3473 g3473.t5 cds g3473.t5.CDS3 25775151 25775406
chr_3 g3473 g3473.t5 TTS g3473.t5 25775455 25775455

Sequences

>g3473.t5 Gene=g3473 Length=1617
ATGAAAAATAAAGACGAAGATATTAAAGAAGATGGTATATATAAAGTTTTATTTATTTTA
AAGTAATTAAATGGAGAATATACATTTTAGAAAAAGTTGATTTAAAAAGGAAACTTGAAG
TAAAAGAAGAAGAAGATGATGATGACGATGAACCAATGATTCCGAATAACAAAATGGTTA
TTAAACAATGTCCATTTTTGGACACAATAAACCGTCATGTTCTGGACTTTGATTTTGAGA
AATTATGCTCAATTTCTTTAACGAGAATTAATGGTGAGTGCATTAGGACATAAATTTGTT
ATTAATTTTAATTTACAAATTCTTTCTTCAGTTTATGCATGTTTGGTTTGCGGAAAATAT
TTCCAAGGAAGAGGGAAGAGTACTCATGCATATACACATTCAGTGGCAGAATCACATCAT
GTTTTTCTCAATCTCTCAAATTTGAGATTTTACTGTTTACCAGATAATTATGAAATCATC
GATTCATCTTTAGATGATATAAAGTATGTTCTTAATCCAACTTTTACAAAAAATGATATA
AAAGTACTTGATGATTCAGAGAAGACTTCAAGAACTCTTGATGGAACTTTATATTTTCCT
GGGATAGTTGGTCTCAATAATATTAAAGCAAATGACTATTGTAATGTTGTTCTTCAAGCA
CTCTCACATGTGACACCAATTAGAGACTATTTTCTATGTGAACAAAATTATTCAAAAATT
AAGCATTCATCGGGCGATTCTGCTTTTGCAATTGTGCAACGCTTCGGTGAATTAATGAGA
AAATTGTGGAATCCAAGAAATTTTAAAGCTCATGTTTCTCCGCATGAAATGCTTCAAGCT
GTTGTTCTTTGGAGCAATAAAAGATTTCAAATTATTGAACAGAGCGATCCAATTGATTTT
CTTACATGGTTTTTGCATGAATTACATCGTCAATTGAGAGGAAATAAAAATCTTAACTCA
AGCATTATCAATAAAACTTTCTTAGGAGAGATGAAAATTTACTCAAGAAAAATTCCACCT
GTTGAATGCGATGATGCCCAAAAAGAATTGTTGCTTGCAACTGAAGAGTATCAAGAAAAA
ATTGAAACAACAAATTTTCTTTATTTAACATGCGATTTACCGCCACCACCTCTATTCATC
GATGAGCACCGTGAGAATATTATTCCTCAAGTCAATTTATATCAATTGCTTGCAAAATTC
AATGGAGTTACAGAAAAAGAATATAAATCATATAAAGACAATTTCTTGAAACGCTTTGAA
ATTGTAAGACTGCCAAAATTTATTATTTTGTTTATCAAACGTTTCACCAAAAATACTTTC
TTTGTGGACAAAAATCCAACAATTGTCAATTTTCCTGTCAAAAATGTTGATTTCGGTGAC
ATCTTGACACCAGAGCATAAGAAAAATCACACTGAGACTCGTTATAATTTGATTGCAAAC
ATAGTTCATGATGGTGAGCCCAATAAAGGTACATATCGTGCACACATCCTTTATAAAGCA
ACAAATCAGTGGTTTGAAATGCAAGATCTTCATGTCACTGATATTCTGCCACAAATGATT
ACTCTTACAGAGGCATATATTCAAATCTATGAACAACAGAGCACAACAACTAAATAG

>g3473.t5 Gene=g3473 Length=448
MVSALGHKFVINFNLQILSSVYACLVCGKYFQGRGKSTHAYTHSVAESHHVFLNLSNLRF
YCLPDNYEIIDSSLDDIKYVLNPTFTKNDIKVLDDSEKTSRTLDGTLYFPGIVGLNNIKA
NDYCNVVLQALSHVTPIRDYFLCEQNYSKIKHSSGDSAFAIVQRFGELMRKLWNPRNFKA
HVSPHEMLQAVVLWSNKRFQIIEQSDPIDFLTWFLHELHRQLRGNKNLNSSIINKTFLGE
MKIYSRKIPPVECDDAQKELLLATEEYQEKIETTNFLYLTCDLPPPPLFIDEHRENIIPQ
VNLYQLLAKFNGVTEKEYKSYKDNFLKRFEIVRLPKFIILFIKRFTKNTFFVDKNPTIVN
FPVKNVDFGDILTPEHKKNHTETRYNLIANIVHDGEPNKGTYRAHILYKATNQWFEMQDL
HVTDILPQMITLTEAYIQIYEQQSTTTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3473.t5 CDD cd02669 Peptidase_C19M 20 441 0.0
9 g3473.t5 Coils Coil Coil 253 273 -
8 g3473.t5 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 14 81 4.9E-25
7 g3473.t5 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 82 444 4.5E-86
3 g3473.t5 PANTHER PTHR21646 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 23 443 1.7E-121
4 g3473.t5 PANTHER PTHR21646:SF16 U4/U6.U5 TRI-SNRNP-ASSOCIATED PROTEIN 2 23 443 1.7E-121
1 g3473.t5 Pfam PF02148 Zn-finger in ubiquitin-hydrolases and other protein 19 73 2.2E-12
2 g3473.t5 Pfam PF00443 Ubiquitin carboxyl-terminal hydrolase 113 440 1.6E-38
12 g3473.t5 ProSiteProfiles PS50271 Zinc finger UBP-type profile. 10 71 15.156
13 g3473.t5 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 113 443 32.979
11 g3473.t5 SMART SM00290 Zf_UBP_1 11 60 6.3E-6
5 g3473.t5 SUPERFAMILY SSF57850 RING/U-box 19 86 9.18E-17
6 g3473.t5 SUPERFAMILY SSF54001 Cysteine proteinases 110 442 1.06E-59

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:0008270 zinc ion binding MF
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