General information for g5267.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TSS | g5267.t2 | 8317387 | 8317387 |
| chr_2 | g5267 | g5267.t2 | isoform | g5267.t2 | 8317518 | 8318414 |
| chr_2 | g5267 | g5267.t2 | exon | g5267.t2.exon1 | 8317518 | 8317525 |
| chr_2 | g5267 | g5267.t2 | exon | g5267.t2.exon2 | 8317590 | 8318414 |
| chr_2 | g5267 | g5267.t2 | cds | g5267.t2.CDS1 | 8317631 | 8318413 |
| chr_2 | g5267 | g5267.t2 | TTS | g5267.t2 | 8318792 | 8318792 |
Sequences
>g5267.t2 Gene=g5267 Length=833
TCTTTTAGCCAAACGTTTTTAAACATCGTCAGATATTTATCCAACAAAAATGAGTTTATC
AAAAAGTCAAATTGATGAAATTAGGCCTGATTTAGAAAAGATATCAATTAGAGTTGTTGG
AACAGTGGATGACAGGATTATGTCAATATTTGATCGTGGGCTTTACAATGGATACGACAG
AGAAAAATTTTTCAAAAAATTTTCTACTATAGTTGATGATAGACAAGCGAAAAAGTTAGT
AGAAAAACTTGATTCAATAATTGAGCATAATGCTCCGAAATCAAAAAAGAGATCGTTTGA
AGATAGTGAAGATAAAGACAGTAAAAGAGTAAAAACATCTCATTCAGATAGCACAAACGG
AACTGATGCATCATCTGGAACTTTAACATCAGTTCAAATTCAGCAAATGATGGAACATGC
ACAGAAGCAAATTGAAGAGCGAAAAAGAAAACTTGAGGCTAGTAAAAGTACTATTCAAGC
AGGAACACCGATTGTAAACGTTCTCGATATGAATGTTGACGAGAGACAGAGAAAAATAGC
AGAGCTACAAAGACAAATTCAAGCAAAATTGTCAGGATCAGTGGCAGTTGCTGCTGGAAT
CACACCTATACCAATCAAACAAGCTGATAAACCTCGACCCCTTATATTAGATTCAGAAGG
AAGAACAGTAGATACAAGCGGTAGAGAAATCAACATTCAGACATTAACACCAACTTTAAA
AGCAAACATTCGAGCAAAGAAGAAAGAAACTTTTAAACACCAACAAGCAGAGAAGGTTGC
AGATGAAGCAAGAACAGCAGAACTATCTTATTTTGATGAAAGAATACCAATAA
>g5267.t2 Gene=g5267 Length=261
MSLSKSQIDEIRPDLEKISIRVVGTVDDRIMSIFDRGLYNGYDREKFFKKFSTIVDDRQA
KKLVEKLDSIIEHNAPKSKKRSFEDSEDKDSKRVKTSHSDSTNGTDASSGTLTSVQIQQM
MEHAQKQIEERKRKLEASKSTIQAGTPIVNVLDMNVDERQRKIAELQRQIQAKLSGSVAV
AAGITPIPIKQADKPRPLILDSEGRTVDTSGREINIQTLTPTLKANIRAKKKETFKHQQA
EKVADEARTAELSYFDERIPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5267.t2 | Coils | Coil | Coil | 121 | 141 | - |
| 5 | g5267.t2 | Coils | Coil | Coil | 149 | 169 | - |
| 4 | g5267.t2 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 4 | 73 | 1.7E-11 |
| 2 | g5267.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 110 | - |
| 3 | g5267.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 99 | - |
| 1 | g5267.t2 | PANTHER | PTHR14212 | U4/U6-ASSOCIATED RNA SPLICING FACTOR-RELATED | 87 | 259 | 8.3E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5267/g5267.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5267.t2.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 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.
