Gene loci information

Transcript annotation

  • This transcript has been annotated as Pre-mRNA-processing factor 19.

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_2 g8149 g8149.t5 TTS g8149.t5 28794672 28794672
chr_2 g8149 g8149.t5 isoform g8149.t5 28794782 28796549
chr_2 g8149 g8149.t5 exon g8149.t5.exon1 28794782 28796198
chr_2 g8149 g8149.t5 cds g8149.t5.CDS1 28794982 28796198
chr_2 g8149 g8149.t5 exon g8149.t5.exon2 28796265 28796414
chr_2 g8149 g8149.t5 cds g8149.t5.CDS2 28796265 28796414
chr_2 g8149 g8149.t5 exon g8149.t5.exon3 28796531 28796549
chr_2 g8149 g8149.t5 cds g8149.t5.CDS3 28796531 28796549
chr_2 g8149 g8149.t5 TSS g8149.t5 28796650 28796650

Sequences

>g8149.t5 Gene=g8149 Length=1586
ATGTCTCTTATTTGTGCGATTTCAAACGAAGTTCCAGATGTTCCAGTCATTTCACCAAAT
TCGGGAGCTATATTTGAAAGAAGATTGATAGAGAAATACATTCAGGAGAATGGTGTTGAT
CCAATTTCAGGAAAAGATATGACGATTGAGGAGCTTATTGAAATAAAAACTCCACCCGTT
TTAAAACCAAAACCGCCCAGTGCTACAAGTATTCCAGCAATCTTAAAAATGATGCAAGAT
GAATGGGATGCACTTATGCTTCATTCTTTCACTCAGCGTCAACAACTTCAAACAGCAAGA
CAAGAATTATCTCATGCACTTTACCAACATGATGCTGCTTGTCGTGTAATTGCTCGTTTA
AATAAAGAAGTGACAGCGGCTCGTGAAGCTTTAGCAACTTTGAAACCGCAAGCTGGAATT
AGCACCACTATTCAGCAAACTGTTATTCAACAACCTGTTACTGCAAATGAAGCTCCTGGA
ATTGCTGCTGCTCTACCAGTTGAACAAGCTGGTATGAGTGATGAAATAATTCAGAAATTA
CAAGATAAAGCTACGGTACTCACACAAGAGAGAAAGAAAAAGGGAAAGACTGTTCCCGAA
GAGCTGGTTAGTGCGGAAAAGATCAGAAGCTTTCTCAATTTGGCATCACATCCAGGATTG
CATAGTGCAAGTGTACCTGGTATTTTAGCATTGGACATTAGTAATAGCGATAACAGCAAA
ATTTTAACAGGAGGAAATGACAAAAATGCTACAATTTTCAATAAAGATACAGAACAAGTC
GTAACGATCTTGAAAGGACATTCGAAAAAAGTTACAAAAGTTATATATCATCCAGATGAG
TCTACTGTTATCACCGCCTCTCCAGACACTACAATTCGTGTTTGGAATGTGCCAACATCT
CAAACTACTCTTTTGCTGCGTTGTCACGAAGGACCAGTTACTGGTTTATCATTGCATCCG
ACTGGTGACTATATTCTTTCAACATCTCAAGATAAAAATTGGGCATTCTCTGATATAAGA
ACTGGACGTTTATTAACAATGAAAATTGATTCTGCTGATTGTGGCTTGACAGCTGCACAA
TTTCATCCTGATGGACTTATTTTCGGAACAGGAACTGAAGATGCTCAAGTTCGTATTTGG
GATTTGAAGGAACAAAGCAATGTTGCAAACTTTCCAGGACATATTGGAGAAATTAGTGCC
ATTTCATTTTCTGAAAATGGTTACTATCTTGCTACTGCTGCTTCCGATTCATGCGTAAAA
TTGTGGGATTTAAGAAAATTGAAGAATTTCAAAACAATTCAACTTGAAGATGGCTATGAA
GTCAAAGACTTGTGTTTTGATCAAAGTGGAACATATCTGGCAATTGCAGGCACTGATATT
AGGTAAAACTATTTCTTTAATTTAAATGAAATTTTATATTAAATTCATTTTATCCTTTTA
GAGTTTATTTGTGTAAACAATGGACAGAATTAAAAGTTTTTAATGATCATACTGCGACAT
CAACTGGTGTACGTTTTGGAAGGCATGCTCAATGGCTCGCATCAACTAGTATGGATCGAA
CACTTAAACTCTATGGTATTGAATGA

>g8149.t5 Gene=g8149 Length=461
MSLICAISNEVPDVPVISPNSGAIFERRLIEKYIQENGVDPISGKDMTIEELIEIKTPPV
LKPKPPSATSIPAILKMMQDEWDALMLHSFTQRQQLQTARQELSHALYQHDAACRVIARL
NKEVTAAREALATLKPQAGISTTIQQTVIQQPVTANEAPGIAAALPVEQAGMSDEIIQKL
QDKATVLTQERKKKGKTVPEELVSAEKIRSFLNLASHPGLHSASVPGILALDISNSDNSK
ILTGGNDKNATIFNKDTEQVVTILKGHSKKVTKVIYHPDESTVITASPDTTIRVWNVPTS
QTTLLLRCHEGPVTGLSLHPTGDYILSTSQDKNWAFSDIRTGRLLTMKIDSADCGLTAAQ
FHPDGLIFGTGTEDAQVRIWDLKEQSNVANFPGHIGEISAISFSENGYYLATAASDSCVK
LWDLRKLKNFKTIQLEDGYEVKDLCFDQSGTYLAIAGTDIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g8149.t5 CDD cd16656 RING-Ubox_PRP19 4 56 2.67916E-29
14 g8149.t5 CDD cd00200 WD40 221 459 2.90742E-52
13 g8149.t5 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 2 58 8.0E-20
12 g8149.t5 Gene3D G3DSA:2.130.10.10 - 199 461 1.1E-96
5 g8149.t5 PANTHER PTHR43995:SF1 PRE-MRNA-PROCESSING FACTOR 19 1 461 0.0
6 g8149.t5 PANTHER PTHR43995 PRE-MRNA-PROCESSING FACTOR 19 1 461 0.0
9 g8149.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 283 297 3.3E-6
8 g8149.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 368 382 3.3E-6
7 g8149.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 410 424 3.3E-6
1 g8149.t5 Pfam PF08606 Prp19/Pso4-like 68 133 3.6E-30
4 g8149.t5 Pfam PF00400 WD domain, G-beta repeat 259 296 8.3E-6
3 g8149.t5 Pfam PF00400 WD domain, G-beta repeat 305 332 0.062
2 g8149.t5 Pfam PF00400 WD domain, G-beta repeat 387 423 1.2E-5
17 g8149.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 283 297 -
16 g8149.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 410 424 -
24 g8149.t5 ProSiteProfiles PS51698 U-box domain profile. 1 72 15.172
25 g8149.t5 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 221 461 42.58
28 g8149.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 264 305 15.989
27 g8149.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 349 390 11.812
26 g8149.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 391 432 15.621
18 g8149.t5 SMART SM00504 Ubox_2 2 68 4.3E-23
21 g8149.t5 SMART SM00320 WD40_4 204 254 6.0
23 g8149.t5 SMART SM00320 WD40_4 257 296 3.8E-9
22 g8149.t5 SMART SM00320 WD40_4 299 338 0.0022
20 g8149.t5 SMART SM00320 WD40_4 342 381 0.04
19 g8149.t5 SMART SM00320 WD40_4 384 423 4.3E-8
10 g8149.t5 SUPERFAMILY SSF57850 RING/U-box 3 55 8.83E-12
11 g8149.t5 SUPERFAMILY SSF50978 WD40 repeat-like 227 459 9.66E-57

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:0061630 ubiquitin protein ligase activity MF
GO:0006281 DNA repair BP
GO:0005515 protein binding MF
GO:0000398 mRNA splicing, via spliceosome BP
GO:0016567 protein ubiquitination BP
GO:0000974 Prp19 complex CC
GO:0004842 ubiquitin-protein transferase activity MF

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