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.t3 TTS g8149.t3 28794672 28794672
chr_2 g8149 g8149.t3 isoform g8149.t3 28794782 28796192
chr_2 g8149 g8149.t3 exon g8149.t3.exon1 28794782 28794926
chr_2 g8149 g8149.t3 cds g8149.t3.CDS1 28794782 28794926
chr_2 g8149 g8149.t3 exon g8149.t3.exon2 28794986 28796192
chr_2 g8149 g8149.t3 cds g8149.t3.CDS2 28794986 28796139
chr_2 g8149 g8149.t3 TSS g8149.t3 28796650 28796650

Sequences

>g8149.t3 Gene=g8149 Length=1352
CCGTTTTAAAACCAAAACCGCCCAGTGCTACAAGTATTCCAGCAATCTTAAAAATGATGC
AAGATGAATGGGATGCACTTATGCTTCATTCTTTCACTCAGCGTCAACAACTTCAAACAG
CAAGACAAGAATTATCTCATGCACTTTACCAACATGATGCTGCTTGTCGTGTAATTGCTC
GTTTAAATAAAGAAGTGACAGCGGCTCGTGAAGCTTTAGCAACTTTGAAACCGCAAGCTG
GAATTAGCACCACTATTCAGCAAACTGTTATTCAACAACCTGTTACTGCAAATGAAGCTC
CTGGAATTGCTGCTGCTCTACCAGTTGAACAAGCTGGTATGAGTGATGAAATAATTCAGA
AATTACAAGATAAAGCTACGGTACTCACACAAGAGAGAAAGAAAAAGGGAAAGACTGTTC
CCGAAGAGCTGGTTAGTGCGGAAAAGATCAGAAGCTTTCTCAATTTGGCATCACATCCAG
GATTGCATAGTGCAAGTGTACCTGGTATTTTAGCATTGGACATTAGTAATAGCGATAACA
GCAAAATTTTAACAGGAGGAAATGACAAAAATGCTACAATTTTCAATAAAGATACAGAAC
AAGTCGTAACGATCTTGAAAGGACATTCGAAAAAAGTTACAAAAGTTATATATCATCCAG
ATGAGTCTACTGTTATCACCGCCTCTCCAGACACTACAATTCGTGTTTGGAATGTGCCAA
CATCTCAAACTACTCTTTTGCTGCGTTGTCACGAAGGACCAGTTACTGGTTTATCATTGC
ATCCGACTGGTGACTATATTCTTTCAACATCTCAAGATAAAAATTGGGCATTCTCTGATA
TAAGAACTGGACGTTTATTAACAATGAAAATTGATTCTGCTGATTGTGGCTTGACAGCTG
CACAATTTCATCCTGATGGACTTATTTTCGGAACAGGAACTGAAGATGCTCAAGTTCGTA
TTTGGGATTTGAAGGAACAAAGCAATGTTGCAAACTTTCCAGGACATATTGGAGAAATTA
GTGCCATTTCATTTTCTGAAAATGGTTACTATCTTGCTACTGCTGCTTCCGATTCATGCG
TAAAATTGTGGGATTTAAGAAAATTGAAGAATTTCAAAACAATTCAACTTGAAGATGGCT
ATGAAGTCAAAGACTTGTGTTTTGATCAAAGTGGAACATATCTGGCAATTGCAGGCACTG
ATATTAGAGTTTATTTGTGTAAACAATGGACAGAATTAAAAGTTTTTAATGATCATACTG
CGACATCAACTGGTGTACGTTTTGGAAGGCATGCTCAATGGCTCGCATCAACTAGTATGG
ATCGAACACTTAAACTCTATGGTATTGAATGA

>g8149.t3 Gene=g8149 Length=432
MMQDEWDALMLHSFTQRQQLQTARQELSHALYQHDAACRVIARLNKEVTAAREALATLKP
QAGISTTIQQTVIQQPVTANEAPGIAAALPVEQAGMSDEIIQKLQDKATVLTQERKKKGK
TVPEELVSAEKIRSFLNLASHPGLHSASVPGILALDISNSDNSKILTGGNDKNATIFNKD
TEQVVTILKGHSKKVTKVIYHPDESTVITASPDTTIRVWNVPTSQTTLLLRCHEGPVTGL
SLHPTGDYILSTSQDKNWAFSDIRTGRLLTMKIDSADCGLTAAQFHPDGLIFGTGTEDAQ
VRIWDLKEQSNVANFPGHIGEISAISFSENGYYLATAASDSCVKLWDLRKLKNFKTIQLE
DGYEVKDLCFDQSGTYLAIAGTDIRVYLCKQWTELKVFNDHTATSTGVRFGRHAQWLAST
SMDRTLKLYGIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8149.t3 CDD cd00200 WD40 138 429 7.36637E-58
12 g8149.t3 Gene3D G3DSA:2.130.10.10 - 123 431 4.9E-113
6 g8149.t3 PANTHER PTHR43995:SF1 PRE-MRNA-PROCESSING FACTOR 19 1 430 2.2E-275
7 g8149.t3 PANTHER PTHR43995 PRE-MRNA-PROCESSING FACTOR 19 1 430 2.2E-275
8 g8149.t3 PRINTS PR00320 G protein beta WD-40 repeat signature 207 221 2.8E-6
10 g8149.t3 PRINTS PR00320 G protein beta WD-40 repeat signature 292 306 2.8E-6
9 g8149.t3 PRINTS PR00320 G protein beta WD-40 repeat signature 334 348 2.8E-6
1 g8149.t3 Pfam PF08606 Prp19/Pso4-like 2 57 3.2E-24
3 g8149.t3 Pfam PF00400 WD domain, G-beta repeat 183 220 7.6E-6
2 g8149.t3 Pfam PF00400 WD domain, G-beta repeat 229 256 0.057
4 g8149.t3 Pfam PF00400 WD domain, G-beta repeat 311 347 1.1E-5
5 g8149.t3 Pfam PF00400 WD domain, G-beta repeat 394 429 0.042
14 g8149.t3 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 207 221 -
15 g8149.t3 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 334 348 -
23 g8149.t3 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 145 432 43.977
27 g8149.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 188 229 15.989
26 g8149.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 273 314 11.812
24 g8149.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 315 356 15.621
25 g8149.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 398 432 9.472
22 g8149.t3 SMART SM00320 WD40_4 128 178 6.0
19 g8149.t3 SMART SM00320 WD40_4 181 220 3.8E-9
17 g8149.t3 SMART SM00320 WD40_4 223 262 0.0022
18 g8149.t3 SMART SM00320 WD40_4 266 305 0.04
21 g8149.t3 SMART SM00320 WD40_4 308 347 4.3E-8
20 g8149.t3 SMART SM00320 WD40_4 350 390 10.0
16 g8149.t3 SMART SM00320 WD40_4 391 430 0.016
11 g8149.t3 SUPERFAMILY SSF50978 WD40 repeat-like 151 429 8.88E-64

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:0000974 Prp19 complex CC

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