General information for g5267.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U4/U6 small nuclear ribonucleoprotein Prp3.
Parent gene
- The parent gene g5267 is located on chr_2: 8319502..8322200 (+ 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 | g5267 | g5267.t1 | TSS | g5267.t1 | 8317387 | 8317387 |
| chr_2 | g5267 | g5267.t1 | isoform | g5267.t1 | 8317631 | 8319502 |
| chr_2 | g5267 | g5267.t1 | exon | g5267.t1.exon1 | 8317631 | 8319502 |
| chr_2 | g5267 | g5267.t1 | cds | g5267.t1.CDS1 | 8317631 | 8319502 |
| chr_2 | g5267 | g5267.t1 | TTS | g5267.t1 | 8319604 | 8319604 |
Sequences
>g5267.t1 Gene=g5267 Length=1872
ATGAGTTTATCAAAAAGTCAAATTGATGAAATTAGGCCTGATTTAGAAAAGATATCAATT
AGAGTTGTTGGAACAGTGGATGACAGGATTATGTCAATATTTGATCGTGGGCTTTACAAT
GGATACGACAGAGAAAAATTTTTCAAAAAATTTTCTACTATAGTTGATGATAGACAAGCG
AAAAAGTTAGTAGAAAAACTTGATTCAATAATTGAGCATAATGCTCCGAAATCAAAAAAG
AGATCGTTTGAAGATAGTGAAGATAAAGACAGTAAAAGAGTAAAAACATCTCATTCAGAT
AGCACAAACGGAACTGATGCATCATCTGGAACTTTAACATCAGTTCAAATTCAGCAAATG
ATGGAACATGCACAGAAGCAAATTGAAGAGCGAAAAAGAAAACTTGAGGCTAGTAAAAGT
ACTATTCAAGCAGGAACACCGATTGTAAACGTTCTCGATATGAATGTTGACGAGAGACAG
AGAAAAATAGCAGAGCTACAAAGACAAATTCAAGCAAAATTGTCAGGATCAGTGGCAGTT
GCTGCTGGAATCACACCTATACCAATCAAACAAGCTGATAAACCTCGACCCCTTATATTA
GATTCAGAAGGAAGAACAGTAGATACAAGCGGTAGAGAAATCAACATTCAGACATTAACA
CCAACTTTAAAAGCAAACATTCGAGCAAAGAAGAAAGAAACTTTTAAACACCAACAAGCA
GAGAAGGTTGCAGATGAAGCAAGAACAGCAGAACTATCTTATTTTGATGAAAGAATACCA
ATAAAACCTGTCGTAAGAGGAAAGAGAGCTTTGCGCTTCCATGAGCCTGGTAAATTCGAA
TTAATGGCTGAACAGATGAGAATGAAAGCACAAATGGAAAGACTTCAAAATGAAATTTCT
CAAATTGCTCGTAAAACAGGAATCAGCAATGCTACACGTCTTGCTCTTATTGCTCCAAAA
ACAGATGTAAATAATGAAGAAGTGCCACAGCTAGAATGGTGGGATTCTGTCATTTGTGAT
GACTATAATAAAGTCGTTGATGGAAAAATTCCAATTCGTGTAAAAGCTATCACTAATTTG
ATTGAACATCCAGTGCAAGTGAGACCAGTTAATCCAATTCGTCCTGCTTATTTGCCAGTA
TTTTTGACTAAAAAAGAACGTAAAAAATTGCGAAGACAAAATAGAAGAGAAGCATGGAAA
GAAGAACAAGAGAAAATTCGCCTTGGCCTTGTTGATCCACCAGAGCCTAAATTAAAAATC
TCAAATTTGATGAGAGTACTCGGAACTGAAGCTGTTCAAGATCCAACAAAAATTGAAGCT
CATGTTCGCGAGCAAATGGCACGACGACAGAAAGCACATGAAGATGACAATCAAGCAAGA
AAATTGACAGACGAACAAAAACGTGAAAAGAAAATTAAAAAATTGAAAGAAGACACTTCA
ATGGGAGTAAATGTCTCAGTTTATAGAATCAAAGATTTAAGTAATCAATCGAAGAAATTT
AAAGTAGAAACAAATGCAAAACAACTCTTTATGACAGGAGTTGTCATACTTTTTCGTGAT
TGCTGTGTAGTTGTGGTTGAAGGTGGACCTAAACAACAAAAGAAATACAGGAGACTCATG
ATGCACCGAATAAAATGGGAGGAAGATATTGTCAAGTGTACTGAAGACAAGACCGAAGAT
AAAGAAGAACCAAATTCATGCAAATTAGTCTGGGAAGGGAAAGTTCCAAAACGATCATTT
GGAGAGATTAAATTTAAACAATTTACCATGGAAAAAGCTGTTCGTGAGTTCTTCCAAAAA
CATCATTGTGAACATTTATGGGATTTAGCTTATTCGGGTGCTGTTTTGGAAGTGTCAATG
GATGACATCTAA
>g5267.t1 Gene=g5267 Length=623
MSLSKSQIDEIRPDLEKISIRVVGTVDDRIMSIFDRGLYNGYDREKFFKKFSTIVDDRQA
KKLVEKLDSIIEHNAPKSKKRSFEDSEDKDSKRVKTSHSDSTNGTDASSGTLTSVQIQQM
MEHAQKQIEERKRKLEASKSTIQAGTPIVNVLDMNVDERQRKIAELQRQIQAKLSGSVAV
AAGITPIPIKQADKPRPLILDSEGRTVDTSGREINIQTLTPTLKANIRAKKKETFKHQQA
EKVADEARTAELSYFDERIPIKPVVRGKRALRFHEPGKFELMAEQMRMKAQMERLQNEIS
QIARKTGISNATRLALIAPKTDVNNEEVPQLEWWDSVICDDYNKVVDGKIPIRVKAITNL
IEHPVQVRPVNPIRPAYLPVFLTKKERKKLRRQNRREAWKEEQEKIRLGLVDPPEPKLKI
SNLMRVLGTEAVQDPTKIEAHVREQMARRQKAHEDDNQARKLTDEQKREKKIKKLKEDTS
MGVNVSVYRIKDLSNQSKKFKVETNAKQLFMTGVVILFRDCCVVVVEGGPKQQKKYRRLM
MHRIKWEEDIVKCTEDKTEDKEEPNSCKLVWEGKVPKRSFGEIKFKQFTMEKAVREFFQK
HHCEHLWDLAYSGAVLEVSMDDI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5267.t1 | Coils | Coil | Coil | 121 | 141 | - |
| 10 | g5267.t1 | Coils | Coil | Coil | 149 | 169 | - |
| 9 | g5267.t1 | Coils | Coil | Coil | 278 | 305 | - |
| 8 | g5267.t1 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 4 | 73 | 6.9E-11 |
| 6 | g5267.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 110 | - |
| 7 | g5267.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 99 | - |
| 5 | g5267.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 448 | 469 | - |
| 3 | g5267.t1 | PANTHER | PTHR14212 | U4/U6-ASSOCIATED RNA SPLICING FACTOR-RELATED | 88 | 613 | 2.1E-158 |
| 4 | g5267.t1 | PANTHER | PTHR14212:SF0 | U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP3 | 88 | 613 | 2.1E-158 |
| 2 | g5267.t1 | Pfam | PF08572 | pre-mRNA processing factor 3 (PRP3) | 254 | 463 | 8.5E-71 |
| 1 | g5267.t1 | Pfam | PF06544 | Protein of unknown function (DUF1115) | 487 | 610 | 8.3E-42 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5267/g5267.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5267.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0046540 | U4/U6 x U5 tri-snRNP complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12843 (U4/U6 small nuclear ribonucleoprotein PRP3)
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.
