General information for g11613.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U4/U6 small nuclear ribonucleoprotein Prp4.
Parent gene
- The parent gene g11613 is located on chr_1: 17447233..17455950 (- strand)
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.t6 | isoform | g11613.t6 | 17447233 | 17448559 |
| chr_1 | g11613 | g11613.t6 | exon | g11613.t6.exon1 | 17447233 | 17448310 |
| chr_1 | g11613 | g11613.t6 | cds | g11613.t6.CDS1 | 17447233 | 17448310 |
| chr_1 | g11613 | g11613.t6 | exon | g11613.t6.exon2 | 17448366 | 17448559 |
| chr_1 | g11613 | g11613.t6 | cds | g11613.t6.CDS2 | 17448366 | 17448559 |
| chr_1 | g11613 | g11613.t6 | TSS | g11613.t6 | 17448621 | 17448621 |
| chr_1 | g11613 | g11613.t6 | TTS | g11613.t6 | NA | NA |
Sequences
>g11613.t6 Gene=g11613 Length=1272
ATGTCTGATGACGAAGAAGTTTTATATGTAAAAAGACAAAAAACAATTCATTATGGATCA
CTTGAAGAAACCATGGAAAATCGTGTTAAACATGCAAGAATTGAAACAGAAAGCAGCAAT
GCAGTACCAACAGCGGCTTCAAATTCTTCAAACAATTCTCAACTTCCAGAATATTTTGAT
ATCGAAAATGAAATGGAAAAAGATAAAATGGCTTTATTGGAAGAATTTGAAAGGAAAAAG
AAAGCAAGACAGATAAACGTTTCAACTGATGATGCTGAAATCAAGAAAAATTTGCGTGCT
TTAAATGAACCTATAGTGCTTTTCGGTGAAGGACCAGCAGATAGACGTATTAGATTGAGA
GAATTGATTGCAATGTTAGGCGATAATGCAATCAAAAAAACGGATGATGAAGACAAGAGA
ATATCAACAAAAGAACAACAGCAACAACAACAGCAGGATTCTAATCAAACTTGGTTTCAT
GAAGCACCAGATACGCTTAGAGTAGCGCGTCTTTGGATTGCAGATTATTCATTGCCTAGA
GCAAGAAAAAGATTAGAAGAAGCAAGAGAACAAAGTCAAATTCCAAGTGCTACCAAAGCA
AGCAGGATTGTAGAACTTCAGAAAAAAATTCAAGCACTTATGCCACAGTGTTCTCAAATT
GGAGACACTAGACCGATTTCTGCATGCAGTTTTAATAGTGATTCAACTCTCTTGTTGACT
GCAAGTTGGTCTGGTTTATGCAAAGTTTGGAGTGTTCCAGATTGTGAACTTGTTCAAGTG
CTTCGTGGTCATGCAAACAATGTTGGGGGTGTTGCATTTAGAAATAATGTAACAACAGAT
TGTTTTGCTGAAGTTTCAATGGCAACTTGCTCTGCAGATGGTATGGTAAAATTATGGAGC
TTCAAAAGTGAAGAATCTGTAGCAGATATCACTGGACATATGCCGCATCGTGTTTCACGA
CTTGCTTTTCACCCATCTGGTCGATTTTTGGGAACTGCATGTTATGATGCATCATGGCGT
TTGTGGGATTTAGAACAGAGACAAGAAGTATTACATCAAGAAGGTCACGCAAAAGCTGTG
CATGCTATTGCATTTCAACATGATGGAAGTGTTGCATTAAGCGGTGGTTTAGATGCTTTC
GGTCGTGTATGGGATTTAAGAACTGGACGTTGTATTATGTTTCTTGACGGTCATATGGGA
AATATATATGCTGTAGATTTTTCATCAAATGGTTATCATATGATAACTGGAAGTGAAGAC
CATACTTGCAAA
>g11613.t6 Gene=g11613 Length=424
MSDDEEVLYVKRQKTIHYGSLEETMENRVKHARIETESSNAVPTAASNSSNNSQLPEYFD
IENEMEKDKMALLEEFERKKKARQINVSTDDAEIKKNLRALNEPIVLFGEGPADRRIRLR
ELIAMLGDNAIKKTDDEDKRISTKEQQQQQQQDSNQTWFHEAPDTLRVARLWIADYSLPR
ARKRLEEAREQSQIPSATKASRIVELQKKIQALMPQCSQIGDTRPISACSFNSDSTLLLT
ASWSGLCKVWSVPDCELVQVLRGHANNVGGVAFRNNVTTDCFAEVSMATCSADGMVKLWS
FKSEESVADITGHMPHRVSRLAFHPSGRFLGTACYDASWRLWDLEQRQEVLHQEGHAKAV
HAIAFQHDGSVALSGGLDAFGRVWDLRTGRCIMFLDGHMGNIYAVDFSSNGYHMITGSED
HTCK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11613.t6 | CDD | cd00200 | WD40 | 225 | 424 | 8.21738E-50 |
| 12 | g11613.t6 | Gene3D | G3DSA:1.10.720.150 | - | 62 | 127 | 6.8E-8 |
| 11 | g11613.t6 | Gene3D | G3DSA:2.130.10.10 | - | 351 | 424 | 1.6E-19 |
| 21 | g11613.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 134 | 158 | - |
| 7 | g11613.t6 | PANTHER | PTHR19846 | WD40 REPEAT PROTEIN | 47 | 424 | 3.8E-131 |
| 8 | g11613.t6 | PANTHER | PTHR19846:SF0 | U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 | 47 | 424 | 3.8E-131 |
| 1 | g11613.t6 | Pfam | PF08799 | pre-mRNA processing factor 4 (PRP4) like | 94 | 122 | 3.0E-12 |
| 6 | g11613.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 225 | 251 | 0.074 |
| 3 | g11613.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 256 | 300 | 0.0036 |
| 2 | g11613.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 308 | 343 | 0.0024 |
| 5 | g11613.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 349 | 385 | 0.018 |
| 4 | g11613.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 389 | 424 | 5.0E-5 |
| 14 | g11613.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 330 | 344 | - |
| 22 | g11613.t6 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 219 | 424 | 38.441 |
| 26 | g11613.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 261 | 309 | 9.606 |
| 25 | g11613.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 318 | 352 | 10.041 |
| 23 | g11613.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 353 | 394 | 13.416 |
| 24 | g11613.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 395 | 424 | 10.475 |
| 20 | g11613.t6 | SMART | SM00500 | pr04_2 | 89 | 138 | 5.0E-12 |
| 19 | g11613.t6 | SMART | SM00320 | WD40_4 | 212 | 251 | 5.9E-4 |
| 18 | g11613.t6 | SMART | SM00320 | WD40_4 | 254 | 300 | 0.021 |
| 16 | g11613.t6 | SMART | SM00320 | WD40_4 | 303 | 343 | 1.7E-4 |
| 17 | g11613.t6 | SMART | SM00320 | WD40_4 | 346 | 385 | 0.0014 |
| 15 | g11613.t6 | SMART | SM00320 | WD40_4 | 388 | 423 | 0.059 |
| 10 | g11613.t6 | SUPERFAMILY | SSF158230 | PRP4-like | 72 | 125 | 2.09E-15 |
| 9 | g11613.t6 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 214 | 424 | 1.83E-50 |
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
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.
