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.t1 TSS g3473.t1 25773588 25773588
chr_3 g3473 g3473.t1 isoform g3473.t1 25773678 25775406
chr_3 g3473 g3473.t1 exon g3473.t1.exon1 25773678 25773711
chr_3 g3473 g3473.t1 cds g3473.t1.CDS1 25773678 25773711
chr_3 g3473 g3473.t1 exon g3473.t1.exon2 25773768 25773950
chr_3 g3473 g3473.t1 cds g3473.t1.CDS2 25773768 25773950
chr_3 g3473 g3473.t1 exon g3473.t1.exon3 25774009 25774172
chr_3 g3473 g3473.t1 cds g3473.t1.CDS3 25774009 25774172
chr_3 g3473 g3473.t1 exon g3473.t1.exon4 25774230 25775095
chr_3 g3473 g3473.t1 cds g3473.t1.CDS4 25774230 25775095
chr_3 g3473 g3473.t1 exon g3473.t1.exon5 25775151 25775406
chr_3 g3473 g3473.t1 cds g3473.t1.CDS5 25775151 25775406
chr_3 g3473 g3473.t1 TTS g3473.t1 25775455 25775455

Sequences

>g3473.t1 Gene=g3473 Length=1503
ATGAAAAATAAAGACGAAGATATTAAAGAAGATGAAAAAGTTGATTTAAAAAGGAAACTT
GAAGTAAAAGAAGAAGAAGATGATGATGACGATGAACCAATGATTCCGAATAACAAAATG
GTTATTAAACAATGTCCATTTTTGGACACAATAAACCGTCATGTTCTGGACTTTGATTTT
GAGAAATTATGCTCAATTTCTTTAACGAGAATTAATGTTTATGCATGTTTGGTTTGCGGA
AAATATTTCCAAGGAAGAGGGAAGAGTACTCATGCATATACACATTCAGTGGCAGAATCA
CATCATGTTTTTCTCAATCTCTCAAATTTGAGATTTTACTGTTTACCAGATAATTATGAA
ATCATCGATTCATCTTTAGATGATATAAAGTATGTTCTTAATCCAACTTTTACAAAAAAT
GATATAAAAGTACTTGATGATTCAGAGAAGACTTCAAGAACTCTTGATGGAACTTTATAT
TTTCCTGGGATAGTTGGTCTCAATAATATTAAAGCAAATGACTATTGTAATGTTGTTCTT
CAAGCACTCTCACATGTGACACCAATTAGAGACTATTTTCTATGTGAACAAAATTATTCA
AAAATTAAGCATTCATCGGGCGATTCTGCTTTTGCAATTGTGCAACGCTTCGGTGAATTA
ATGAGAAAATTGTGGAATCCAAGAAATTTTAAAGCTCATGTTTCTCCGCATGAAATGCTT
CAAGCTGTTGTTCTTTGGAGCAATAAAAGATTTCAAATTATTGAACAGAGCGATCCAATT
GATTTTCTTACATGGTTTTTGCATGAATTACATCGTCAATTGAGAGGAAATAAAAATCTT
AACTCAAGCATTATCAATAAAACTTTCTTAGGAGAGATGAAAATTTACTCAAGAAAAATT
CCACCTGTTGAATGCGATGATGCCCAAAAAGAATTGTTGCTTGCAACTGAAGAGTATCAA
GAAAAAATTGAAACAACAAATTTTCTTTATTTAACATGCGATTTACCGCCACCACCTCTA
TTCATCGATGAGCACCGTGAGAATATTATTCCTCAAGTCAATTTATATCAATTGCTTGCA
AAATTCAATGGAGTTACAGAAAAAGAATATAAATCATATAAAGACAATTTCTTGAAACGC
TTTGAAATTGTAAGACTGCCAAAATTTATTATTTTGTTTATCAAACGTTTCACCAAAAAT
ACTTTCTTTGTGGACAAAAATCCAACAATTGTCAATTTTCCTGTCAAAAATGTTGATTTC
GGTGACATCTTGACACCAGAGCATAAGAAAAATCACACTGAGACTCGTTATAATTTGATT
GCAAACATAGTTCATGATGGTGAGCCCAATAAAGGTACATATCGTGCACACATCCTTTAT
AAAGCAACAAATCAGTGGTTTGAAATGCAAGATCTTCATGTCACTGATATTCTGCCACAA
ATGATTACTCTTACAGAGGCATATATTCAAATCTATGAACAACAGAGCACAACAACTAAA
TAG

>g3473.t1 Gene=g3473 Length=500
MKNKDEDIKEDEKVDLKRKLEVKEEEDDDDDEPMIPNNKMVIKQCPFLDTINRHVLDFDF
EKLCSISLTRINVYACLVCGKYFQGRGKSTHAYTHSVAESHHVFLNLSNLRFYCLPDNYE
IIDSSLDDIKYVLNPTFTKNDIKVLDDSEKTSRTLDGTLYFPGIVGLNNIKANDYCNVVL
QALSHVTPIRDYFLCEQNYSKIKHSSGDSAFAIVQRFGELMRKLWNPRNFKAHVSPHEML
QAVVLWSNKRFQIIEQSDPIDFLTWFLHELHRQLRGNKNLNSSIINKTFLGEMKIYSRKI
PPVECDDAQKELLLATEEYQEKIETTNFLYLTCDLPPPPLFIDEHRENIIPQVNLYQLLA
KFNGVTEKEYKSYKDNFLKRFEIVRLPKFIILFIKRFTKNTFFVDKNPTIVNFPVKNVDF
GDILTPEHKKNHTETRYNLIANIVHDGEPNKGTYRAHILYKATNQWFEMQDLHVTDILPQ
MITLTEAYIQIYEQQSTTTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g3473.t1 CDD cd02669 Peptidase_C19M 46 493 0.0
10 g3473.t1 Coils Coil Coil 6 26 -
9 g3473.t1 Coils Coil Coil 305 325 -
8 g3473.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 45 133 1.8E-39
7 g3473.t1 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 134 496 6.4E-86
3 g3473.t1 PANTHER PTHR21646 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 30 495 9.4E-126
4 g3473.t1 PANTHER PTHR21646:SF16 U4/U6.U5 TRI-SNRNP-ASSOCIATED PROTEIN 2 30 495 9.4E-126
1 g3473.t1 Pfam PF02148 Zn-finger in ubiquitin-hydrolases and other protein 67 125 7.6E-13
2 g3473.t1 Pfam PF00443 Ubiquitin carboxyl-terminal hydrolase 165 492 2.2E-38
13 g3473.t1 ProSiteProfiles PS50271 Zinc finger UBP-type profile. 62 123 17.651
14 g3473.t1 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 165 495 32.979
12 g3473.t1 SMART SM00290 Zf_UBP_1 63 112 2.1E-12
5 g3473.t1 SUPERFAMILY SSF57850 RING/U-box 43 138 6.0E-23
6 g3473.t1 SUPERFAMILY SSF54001 Cysteine proteinases 162 494 1.49E-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

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