General information for g8149.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-processing factor 19.
Parent gene
- The parent gene g8149 is located on chr_2: 28794782..28796549 (- 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_2 | g8149 | g8149.t1 | TTS | g8149.t1 | 28794672 | 28794672 |
| chr_2 | g8149 | g8149.t1 | isoform | g8149.t1 | 28794782 | 28796549 |
| chr_2 | g8149 | g8149.t1 | exon | g8149.t1.exon1 | 28794782 | 28794926 |
| chr_2 | g8149 | g8149.t1 | cds | g8149.t1.CDS1 | 28794782 | 28794926 |
| chr_2 | g8149 | g8149.t1 | exon | g8149.t1.exon2 | 28794986 | 28796198 |
| chr_2 | g8149 | g8149.t1 | cds | g8149.t1.CDS2 | 28794986 | 28796198 |
| chr_2 | g8149 | g8149.t1 | exon | g8149.t1.exon3 | 28796265 | 28796414 |
| chr_2 | g8149 | g8149.t1 | cds | g8149.t1.CDS3 | 28796265 | 28796414 |
| chr_2 | g8149 | g8149.t1 | exon | g8149.t1.exon4 | 28796531 | 28796549 |
| chr_2 | g8149 | g8149.t1 | cds | g8149.t1.CDS4 | 28796531 | 28796549 |
| chr_2 | g8149 | g8149.t1 | TSS | g8149.t1 | 28796650 | 28796650 |
Sequences
>g8149.t1 Gene=g8149 Length=1527
ATGTCTCTTATTTGTGCGATTTCAAACGAAGTTCCAGATGTTCCAGTCATTTCACCAAAT
TCGGGAGCTATATTTGAAAGAAGATTGATAGAGAAATACATTCAGGAGAATGGTGTTGAT
CCAATTTCAGGAAAAGATATGACGATTGAGGAGCTTATTGAAATAAAAACTCCACCCGTT
TTAAAACCAAAACCGCCCAGTGCTACAAGTATTCCAGCAATCTTAAAAATGATGCAAGAT
GAATGGGATGCACTTATGCTTCATTCTTTCACTCAGCGTCAACAACTTCAAACAGCAAGA
CAAGAATTATCTCATGCACTTTACCAACATGATGCTGCTTGTCGTGTAATTGCTCGTTTA
AATAAAGAAGTGACAGCGGCTCGTGAAGCTTTAGCAACTTTGAAACCGCAAGCTGGAATT
AGCACCACTATTCAGCAAACTGTTATTCAACAACCTGTTACTGCAAATGAAGCTCCTGGA
ATTGCTGCTGCTCTACCAGTTGAACAAGCTGGTATGAGTGATGAAATAATTCAGAAATTA
CAAGATAAAGCTACGGTACTCACACAAGAGAGAAAGAAAAAGGGAAAGACTGTTCCCGAA
GAGCTGGTTAGTGCGGAAAAGATCAGAAGCTTTCTCAATTTGGCATCACATCCAGGATTG
CATAGTGCAAGTGTACCTGGTATTTTAGCATTGGACATTAGTAATAGCGATAACAGCAAA
ATTTTAACAGGAGGAAATGACAAAAATGCTACAATTTTCAATAAAGATACAGAACAAGTC
GTAACGATCTTGAAAGGACATTCGAAAAAAGTTACAAAAGTTATATATCATCCAGATGAG
TCTACTGTTATCACCGCCTCTCCAGACACTACAATTCGTGTTTGGAATGTGCCAACATCT
CAAACTACTCTTTTGCTGCGTTGTCACGAAGGACCAGTTACTGGTTTATCATTGCATCCG
ACTGGTGACTATATTCTTTCAACATCTCAAGATAAAAATTGGGCATTCTCTGATATAAGA
ACTGGACGTTTATTAACAATGAAAATTGATTCTGCTGATTGTGGCTTGACAGCTGCACAA
TTTCATCCTGATGGACTTATTTTCGGAACAGGAACTGAAGATGCTCAAGTTCGTATTTGG
GATTTGAAGGAACAAAGCAATGTTGCAAACTTTCCAGGACATATTGGAGAAATTAGTGCC
ATTTCATTTTCTGAAAATGGTTACTATCTTGCTACTGCTGCTTCCGATTCATGCGTAAAA
TTGTGGGATTTAAGAAAATTGAAGAATTTCAAAACAATTCAACTTGAAGATGGCTATGAA
GTCAAAGACTTGTGTTTTGATCAAAGTGGAACATATCTGGCAATTGCAGGCACTGATATT
AGAGTTTATTTGTGTAAACAATGGACAGAATTAAAAGTTTTTAATGATCATACTGCGACA
TCAACTGGTGTACGTTTTGGAAGGCATGCTCAATGGCTCGCATCAACTAGTATGGATCGA
ACACTTAAACTCTATGGTATTGAATGA
>g8149.t1 Gene=g8149 Length=508
MSLICAISNEVPDVPVISPNSGAIFERRLIEKYIQENGVDPISGKDMTIEELIEIKTPPV
LKPKPPSATSIPAILKMMQDEWDALMLHSFTQRQQLQTARQELSHALYQHDAACRVIARL
NKEVTAAREALATLKPQAGISTTIQQTVIQQPVTANEAPGIAAALPVEQAGMSDEIIQKL
QDKATVLTQERKKKGKTVPEELVSAEKIRSFLNLASHPGLHSASVPGILALDISNSDNSK
ILTGGNDKNATIFNKDTEQVVTILKGHSKKVTKVIYHPDESTVITASPDTTIRVWNVPTS
QTTLLLRCHEGPVTGLSLHPTGDYILSTSQDKNWAFSDIRTGRLLTMKIDSADCGLTAAQ
FHPDGLIFGTGTEDAQVRIWDLKEQSNVANFPGHIGEISAISFSENGYYLATAASDSCVK
LWDLRKLKNFKTIQLEDGYEVKDLCFDQSGTYLAIAGTDIRVYLCKQWTELKVFNDHTAT
STGVRFGRHAQWLASTSMDRTLKLYGIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g8149.t1 | CDD | cd16656 | RING-Ubox_PRP19 | 4 | 56 | 1.82976E-29 |
| 15 | g8149.t1 | CDD | cd00200 | WD40 | 214 | 505 | 1.7081E-58 |
| 14 | g8149.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 2 | 58 | 9.1E-20 |
| 13 | g8149.t1 | Gene3D | G3DSA:2.130.10.10 | - | 199 | 507 | 8.0E-113 |
| 6 | g8149.t1 | PANTHER | PTHR43995:SF1 | PRE-MRNA-PROCESSING FACTOR 19 | 1 | 506 | 0.0 |
| 7 | g8149.t1 | PANTHER | PTHR43995 | PRE-MRNA-PROCESSING FACTOR 19 | 1 | 506 | 0.0 |
| 10 | g8149.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 283 | 297 | 4.2E-6 |
| 9 | g8149.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 368 | 382 | 4.2E-6 |
| 8 | g8149.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 410 | 424 | 4.2E-6 |
| 1 | g8149.t1 | Pfam | PF08606 | Prp19/Pso4-like | 68 | 133 | 4.2E-30 |
| 5 | g8149.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 259 | 296 | 9.4E-6 |
| 4 | g8149.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 305 | 332 | 0.07 |
| 2 | g8149.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 387 | 423 | 1.4E-5 |
| 3 | g8149.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 470 | 505 | 0.052 |
| 18 | g8149.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 283 | 297 | - |
| 17 | g8149.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 410 | 424 | - |
| 27 | g8149.t1 | ProSiteProfiles | PS51698 | U-box domain profile. | 1 | 72 | 15.172 |
| 28 | g8149.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 221 | 508 | 43.977 |
| 32 | g8149.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 264 | 305 | 15.989 |
| 30 | g8149.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 349 | 390 | 11.812 |
| 29 | g8149.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 391 | 432 | 15.621 |
| 31 | g8149.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 474 | 508 | 9.472 |
| 19 | g8149.t1 | SMART | SM00504 | Ubox_2 | 2 | 68 | 4.3E-23 |
| 22 | g8149.t1 | SMART | SM00320 | WD40_4 | 204 | 254 | 6.0 |
| 26 | g8149.t1 | SMART | SM00320 | WD40_4 | 257 | 296 | 3.8E-9 |
| 25 | g8149.t1 | SMART | SM00320 | WD40_4 | 299 | 338 | 0.0022 |
| 21 | g8149.t1 | SMART | SM00320 | WD40_4 | 342 | 381 | 0.04 |
| 20 | g8149.t1 | SMART | SM00320 | WD40_4 | 384 | 423 | 4.3E-8 |
| 23 | g8149.t1 | SMART | SM00320 | WD40_4 | 426 | 466 | 10.0 |
| 24 | g8149.t1 | SMART | SM00320 | WD40_4 | 467 | 506 | 0.016 |
| 11 | g8149.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 3 | 55 | 1.06E-11 |
| 12 | g8149.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 227 | 505 | 1.4E-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:0016567 | protein ubiquitination | BP |
| GO:0000974 | Prp19 complex | CC |
| GO:0004842 | ubiquitin-protein transferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10599 (pre-mRNA-processing factor 19)
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.
