Gene loci information

Transcript annotation

  • This transcript has been annotated as U4/U6 small nuclear ribonucleoprotein Prp4.

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_1 g11613 g11613.t1 isoform g11613.t1 17447010 17448559
chr_1 g11613 g11613.t1 exon g11613.t1.exon1 17447010 17447171
chr_1 g11613 g11613.t1 cds g11613.t1.CDS1 17447010 17447171
chr_1 g11613 g11613.t1 exon g11613.t1.exon2 17447233 17448310
chr_1 g11613 g11613.t1 cds g11613.t1.CDS2 17447233 17448310
chr_1 g11613 g11613.t1 exon g11613.t1.exon3 17448366 17448559
chr_1 g11613 g11613.t1 cds g11613.t1.CDS3 17448366 17448559
chr_1 g11613 g11613.t1 TSS g11613.t1 17448621 17448621
chr_1 g11613 g11613.t1 TTS g11613.t1 NA NA

Sequences

>g11613.t1 Gene=g11613 Length=1434
ATGTCTGATGACGAAGAAGTTTTATATGTAAAAAGACAAAAAACAATTCATTATGGATCA
CTTGAAGAAACCATGGAAAATCGTGTTAAACATGCAAGAATTGAAACAGAAAGCAGCAAT
GCAGTACCAACAGCGGCTTCAAATTCTTCAAACAATTCTCAACTTCCAGAATATTTTGAT
ATCGAAAATGAAATGGAAAAAGATAAAATGGCTTTATTGGAAGAATTTGAAAGGAAAAAG
AAAGCAAGACAGATAAACGTTTCAACTGATGATGCTGAAATCAAGAAAAATTTGCGTGCT
TTAAATGAACCTATAGTGCTTTTCGGTGAAGGACCAGCAGATAGACGTATTAGATTGAGA
GAATTGATTGCAATGTTAGGCGATAATGCAATCAAAAAAACGGATGATGAAGACAAGAGA
ATATCAACAAAAGAACAACAGCAACAACAACAGCAGGATTCTAATCAAACTTGGTTTCAT
GAAGCACCAGATACGCTTAGAGTAGCGCGTCTTTGGATTGCAGATTATTCATTGCCTAGA
GCAAGAAAAAGATTAGAAGAAGCAAGAGAACAAAGTCAAATTCCAAGTGCTACCAAAGCA
AGCAGGATTGTAGAACTTCAGAAAAAAATTCAAGCACTTATGCCACAGTGTTCTCAAATT
GGAGACACTAGACCGATTTCTGCATGCAGTTTTAATAGTGATTCAACTCTCTTGTTGACT
GCAAGTTGGTCTGGTTTATGCAAAGTTTGGAGTGTTCCAGATTGTGAACTTGTTCAAGTG
CTTCGTGGTCATGCAAACAATGTTGGGGGTGTTGCATTTAGAAATAATGTAACAACAGAT
TGTTTTGCTGAAGTTTCAATGGCAACTTGCTCTGCAGATGGTATGGTAAAATTATGGAGC
TTCAAAAGTGAAGAATCTGTAGCAGATATCACTGGACATATGCCGCATCGTGTTTCACGA
CTTGCTTTTCACCCATCTGGTCGATTTTTGGGAACTGCATGTTATGATGCATCATGGCGT
TTGTGGGATTTAGAACAGAGACAAGAAGTATTACATCAAGAAGGTCACGCAAAAGCTGTG
CATGCTATTGCATTTCAACATGATGGAAGTGTTGCATTAAGCGGTGGTTTAGATGCTTTC
GGTCGTGTATGGGATTTAAGAACTGGACGTTGTATTATGTTTCTTGACGGTCATATGGGA
AATATATATGCTGTAGATTTTTCATCAAATGGTTATCATATGATAACTGGAAGTGAAGAC
CATACTTGCAAAATTTGGGATTTGAGAAAAAGACAAATTTTATATACAATTCCTGCACAT
GTTAATATCGTCTCAGATGTCAAGTATCAAAAAAATGGTGGTCATTTTATAGTTTCATCA
AGTTATGATAATACAGTTAAGGTAAGTTTTTTTACAAAATTTTATTTCAAATGA

>g11613.t1 Gene=g11613 Length=477
MSDDEEVLYVKRQKTIHYGSLEETMENRVKHARIETESSNAVPTAASNSSNNSQLPEYFD
IENEMEKDKMALLEEFERKKKARQINVSTDDAEIKKNLRALNEPIVLFGEGPADRRIRLR
ELIAMLGDNAIKKTDDEDKRISTKEQQQQQQQDSNQTWFHEAPDTLRVARLWIADYSLPR
ARKRLEEAREQSQIPSATKASRIVELQKKIQALMPQCSQIGDTRPISACSFNSDSTLLLT
ASWSGLCKVWSVPDCELVQVLRGHANNVGGVAFRNNVTTDCFAEVSMATCSADGMVKLWS
FKSEESVADITGHMPHRVSRLAFHPSGRFLGTACYDASWRLWDLEQRQEVLHQEGHAKAV
HAIAFQHDGSVALSGGLDAFGRVWDLRTGRCIMFLDGHMGNIYAVDFSSNGYHMITGSED
HTCKIWDLRKRQILYTIPAHVNIVSDVKYQKNGGHFIVSSSYDNTVKVSFFTKFYFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11613.t1 CDD cd00200 WD40 225 468 6.84984E-62
13 g11613.t1 Gene3D G3DSA:1.10.720.150 - 62 126 8.8E-8
12 g11613.t1 Gene3D G3DSA:2.130.10.10 - 350 473 5.5E-33
24 g11613.t1 MobiDBLite mobidb-lite consensus disorder prediction 134 158 -
8 g11613.t1 PANTHER PTHR19846 WD40 REPEAT PROTEIN 48 468 3.1E-155
9 g11613.t1 PANTHER PTHR19846:SF0 U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 48 468 3.1E-155
1 g11613.t1 Pfam PF08799 pre-mRNA processing factor 4 (PRP4) like 94 122 3.5E-12
6 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 225 251 0.086
3 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 256 300 0.0042
2 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 308 343 0.0028
5 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 349 385 0.021
7 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 389 427 1.7E-8
4 g11613.t1 Pfam PF00400 WD domain, G-beta repeat 432 468 0.056
15 g11613.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 330 344 -
16 g11613.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 414 428 -
25 g11613.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 219 468 46.798
29 g11613.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 261 309 9.606
28 g11613.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 318 352 10.041
26 g11613.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 353 394 13.416
27 g11613.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 395 436 15.956
23 g11613.t1 SMART SM00500 pr04_2 89 138 5.0E-12
22 g11613.t1 SMART SM00320 WD40_4 212 251 5.9E-4
21 g11613.t1 SMART SM00320 WD40_4 254 300 0.021
17 g11613.t1 SMART SM00320 WD40_4 303 343 1.7E-4
19 g11613.t1 SMART SM00320 WD40_4 346 385 0.0014
20 g11613.t1 SMART SM00320 WD40_4 388 427 2.5E-10
18 g11613.t1 SMART SM00320 WD40_4 430 470 0.014
11 g11613.t1 SUPERFAMILY SSF158230 PRP4-like 72 125 2.62E-15
10 g11613.t1 SUPERFAMILY SSF50978 WD40 repeat-like 214 468 3.3E-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:0005515 protein binding 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