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.t4 TTS g8149.t4 28794672 28794672
chr_2 g8149 g8149.t4 isoform g8149.t4 28794782 28796414
chr_2 g8149 g8149.t4 exon g8149.t4.exon1 28794782 28794926
chr_2 g8149 g8149.t4 cds g8149.t4.CDS1 28794782 28794926
chr_2 g8149 g8149.t4 exon g8149.t4.exon2 28794986 28796198
chr_2 g8149 g8149.t4 cds g8149.t4.CDS2 28794986 28796198
chr_2 g8149 g8149.t4 exon g8149.t4.exon3 28796265 28796414
chr_2 g8149 g8149.t4 cds g8149.t4.CDS3 28796265 28796295
chr_2 g8149 g8149.t4 TSS g8149.t4 28796650 28796650

Sequences

>g8149.t4 Gene=g8149 Length=1508
TTTCAAACGAAGTTCCAGATGTTCCAGTCATTTCACCAAATTCGGGAGCTATATTTGAAA
GAAGATTGATAGAGAAATACATTCAGGAGAATGGTGTTGATCCAATTTCAGGAAAAGATA
TGACGATTGAGGAGCTTATTGAAATAAAAACTCCACCCGTTTTAAAACCAAAACCGCCCA
GTGCTACAAGTATTCCAGCAATCTTAAAAATGATGCAAGATGAATGGGATGCACTTATGC
TTCATTCTTTCACTCAGCGTCAACAACTTCAAACAGCAAGACAAGAATTATCTCATGCAC
TTTACCAACATGATGCTGCTTGTCGTGTAATTGCTCGTTTAAATAAAGAAGTGACAGCGG
CTCGTGAAGCTTTAGCAACTTTGAAACCGCAAGCTGGAATTAGCACCACTATTCAGCAAA
CTGTTATTCAACAACCTGTTACTGCAAATGAAGCTCCTGGAATTGCTGCTGCTCTACCAG
TTGAACAAGCTGGTATGAGTGATGAAATAATTCAGAAATTACAAGATAAAGCTACGGTAC
TCACACAAGAGAGAAAGAAAAAGGGAAAGACTGTTCCCGAAGAGCTGGTTAGTGCGGAAA
AGATCAGAAGCTTTCTCAATTTGGCATCACATCCAGGATTGCATAGTGCAAGTGTACCTG
GTATTTTAGCATTGGACATTAGTAATAGCGATAACAGCAAAATTTTAACAGGAGGAAATG
ACAAAAATGCTACAATTTTCAATAAAGATACAGAACAAGTCGTAACGATCTTGAAAGGAC
ATTCGAAAAAAGTTACAAAAGTTATATATCATCCAGATGAGTCTACTGTTATCACCGCCT
CTCCAGACACTACAATTCGTGTTTGGAATGTGCCAACATCTCAAACTACTCTTTTGCTGC
GTTGTCACGAAGGACCAGTTACTGGTTTATCATTGCATCCGACTGGTGACTATATTCTTT
CAACATCTCAAGATAAAAATTGGGCATTCTCTGATATAAGAACTGGACGTTTATTAACAA
TGAAAATTGATTCTGCTGATTGTGGCTTGACAGCTGCACAATTTCATCCTGATGGACTTA
TTTTCGGAACAGGAACTGAAGATGCTCAAGTTCGTATTTGGGATTTGAAGGAACAAAGCA
ATGTTGCAAACTTTCCAGGACATATTGGAGAAATTAGTGCCATTTCATTTTCTGAAAATG
GTTACTATCTTGCTACTGCTGCTTCCGATTCATGCGTAAAATTGTGGGATTTAAGAAAAT
TGAAGAATTTCAAAACAATTCAACTTGAAGATGGCTATGAAGTCAAAGACTTGTGTTTTG
ATCAAAGTGGAACATATCTGGCAATTGCAGGCACTGATATTAGAGTTTATTTGTGTAAAC
AATGGACAGAATTAAAAGTTTTTAATGATCATACTGCGACATCAACTGGTGTACGTTTTG
GAAGGCATGCTCAATGGCTCGCATCAACTAGTATGGATCGAACACTTAAACTCTATGGTA
TTGAATGA

>g8149.t4 Gene=g8149 Length=462
MTIEELIEIKTPPVLKPKPPSATSIPAILKMMQDEWDALMLHSFTQRQQLQTARQELSHA
LYQHDAACRVIARLNKEVTAAREALATLKPQAGISTTIQQTVIQQPVTANEAPGIAAALP
VEQAGMSDEIIQKLQDKATVLTQERKKKGKTVPEELVSAEKIRSFLNLASHPGLHSASVP
GILALDISNSDNSKILTGGNDKNATIFNKDTEQVVTILKGHSKKVTKVIYHPDESTVITA
SPDTTIRVWNVPTSQTTLLLRCHEGPVTGLSLHPTGDYILSTSQDKNWAFSDIRTGRLLT
MKIDSADCGLTAAQFHPDGLIFGTGTEDAQVRIWDLKEQSNVANFPGHIGEISAISFSEN
GYYLATAASDSCVKLWDLRKLKNFKTIQLEDGYEVKDLCFDQSGTYLAIAGTDIRVYLCK
QWTELKVFNDHTATSTGVRFGRHAQWLASTSMDRTLKLYGIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8149.t4 CDD cd00200 WD40 168 459 1.46203E-58
12 g8149.t4 Gene3D G3DSA:2.130.10.10 - 153 461 6.0E-113
6 g8149.t4 PANTHER PTHR43995:SF1 PRE-MRNA-PROCESSING FACTOR 19 2 460 2.5E-297
7 g8149.t4 PANTHER PTHR43995 PRE-MRNA-PROCESSING FACTOR 19 2 460 2.5E-297
9 g8149.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 237 251 3.3E-6
8 g8149.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 322 336 3.3E-6
10 g8149.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 364 378 3.3E-6
1 g8149.t4 Pfam PF08606 Prp19/Pso4-like 22 87 3.6E-30
5 g8149.t4 Pfam PF00400 WD domain, G-beta repeat 213 250 8.3E-6
4 g8149.t4 Pfam PF00400 WD domain, G-beta repeat 259 286 0.062
3 g8149.t4 Pfam PF00400 WD domain, G-beta repeat 341 377 1.2E-5
2 g8149.t4 Pfam PF00400 WD domain, G-beta repeat 424 459 0.046
14 g8149.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 237 251 -
15 g8149.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 364 378 -
23 g8149.t4 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 175 462 43.977
27 g8149.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 218 259 15.989
26 g8149.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 303 344 11.812
24 g8149.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 345 386 15.621
25 g8149.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 428 462 9.472
20 g8149.t4 SMART SM00320 WD40_4 158 208 6.0
17 g8149.t4 SMART SM00320 WD40_4 211 250 3.8E-9
18 g8149.t4 SMART SM00320 WD40_4 253 292 0.0022
22 g8149.t4 SMART SM00320 WD40_4 296 335 0.04
19 g8149.t4 SMART SM00320 WD40_4 338 377 4.3E-8
16 g8149.t4 SMART SM00320 WD40_4 380 420 10.0
21 g8149.t4 SMART SM00320 WD40_4 421 460 0.016
11 g8149.t4 SUPERFAMILY SSF50978 WD40 repeat-like 181 459 1.07E-63

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