MmuINT0136469 @ mm9
Intron Retention
Gene
ENSMUSG00000022466 | Rpap3
Description
RNA polymerase II associated protein 3 [Source:MGI Symbol;Acc:MGI:1277218]
Coordinates
chr15:97516873-97518669:-
Coord C1 exon
chr15:97518542-97518669
Coord A exon
chr15:97516995-97518541
Coord C2 exon
chr15:97516873-97516994
Length
1547 bp
Sequences
Splice sites
5' ss Seq
GAGGTTAGT
5' ss Score
7.15
3' ss Seq
GATTGTATTGTGTTCAATAGATA
3' ss Score
6.52
Exon sequences
Seq C1 exon
GGCAACGGATTTTTCAAAGAGGGGAAATACGAGCAAGCAATTGAGTGCTACACCCGCGGGATAGCAGCGGACCGCACCAACGCCCTGCTGCCAGCTAACAGAGCGATGGCCTATCTCAAGATTCAGAG
Seq A exon
GTTAGTTCTGCCTCCATTTTGCTTTCAGGATGGACATTGACTGTAGATAAGCTAACTTTAGTTGATTTAGTATTTTTGCATCTATCTTCCGTGTTTGAATCCTCCTTCTTTCTTCTAGTTTCTATTTTTGCAGCAGTGCTAGGTTAGAGTTCAGGACCTCTTGAACACTAGAGAAGTGCTTCAGTGCTGAGCCGAGCCCCAGCAGGGATTTAGTAACTGTAATTTCCTCACAGTTAATGAGAGAGTGAAACGCAGAGAGAAGGAATGTGTGTGCATGTGGTACTGTATGTATCATGTGAGTGTTGTTATCTTTACATTCTTAATAGAATTGTACAGTGTGGAGTATATTGTGTGTTATTAAAAATTATTACATTTGTTTGTGTGGGTGGTATGTGTGGAAGGCAGAGGACAGGTTGCAGAAATTGGTTCTCTTTCTCCCACATTGGTTTGAGGATCAAACCTGGGTCATTATGTTTGTGGCAAGGACCTGTACTTGCTGAGTCTCCTTACTTTTGAGGTAGGGTCACATGTAGAGACATAGCAGGATATACTACTCTTACTTGTAATTTGTGTTTATTTTTCTGGTATTTGCTTTAGGGTCACACGGAGTATCACAAGCCTTCTGTACTTGGAGGGCAGTTTTACATATTAGAGTCTGATGTAGAACATAGAGTGCACGATCAGCTTTTGTTGAGGGAGCAGTCTTGTGGTTTGAGTTCCATGACTGTGTCTCGTTAGATGGATGGAGTGGGAAGTGGAGGGTGTGGGGTGGGGAGGGAGGCATGAGAGCCTTGCTTTGTATCCTACAACCCACATGAACCCACATGCTGCGGGGCGTGGCATCCCAGCCTTTAATCCCAGCCCTGGGAGGGGGTCTCAGGCTTGCCAGGCCAGGAGGCCAATCGGTTGGTGACCTCCACACTGAGCCAAAGACTCCTTCTCATAAAGGTGGAGAGTGACCACAGACAGACACTTCCTGCTGACCTCACACTCACACGTAGGAACATTTACCACACCCAGCAGAGAAAGAAAAAGAAAGACATCCAGGTTGTTAGTGTCGCTACTGTATGTAAGAAACATTGTATTCCTAGTGAGGCAAGCCTGAGTTACAGCGAGGAAGGGCCGGGGGGAGGGAAATTGTGGAGTGTGGTTTGGTAAGTGGTCAGCTTCAGAAGGTGATGAGGTACTGAGATAATAAAAGTGACAGACCTTGGAGGCAGGATTTTAGTACTGGAAGAGGGTGGATCCTGAACAAACTGGGTCCTCTTCTTGAGGTACCAGACTGCAGTAAAACCTACAAAAAGAACTCAGTAGTATGTTGGCTGTGGTGGTGTGTACCTTTAGCCCCAGCACTCGAGAGGAGGCATGGGAGGTGGAGGTCAGAGGTCAACTTTGACAACTTGGTTCTTTCCTTCCACCATGTGGGTCCCAGCAATGGATTCAGGTCATCAGGCTTGGTAACACTGAGCCGTCGTCTCGCCAGTCCCAGGATTCTGTTGTCTGTAAGCTTCTTGTTGTTCAGTTAGTGATTGTATTGTGTTCAATAG
Seq C2 exon
ATATGAAGAAGCTGAAAGAGACTGCACACAAGCTATCGTACTAGATGGCTCATACTCAAAAGCGTTTGCCAGAAGAGGAACAGCAAGGACATTTTTGGGAAAGATCAATGAGGCCAAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022466-Rpap3:NM_028003:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134141=TPR_11=FE(61.8=100)
A:
NA
C2:
PF134141=TPR_11=PD(23.5=38.1),PF0051523=TPR_1=PU(64.7=52.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACGGATTTTTCAAAGAGGGG
R:
GCTTGGCCTCATTGATCTTTCC
Band lengths:
246-1793
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: