MmuINT1030107 @ mm10
Intron Retention
Gene
ENSMUSG00000022466 | Rpap3
Description
RNA polymerase II associated protein 3 [Source:MGI Symbol;Acc:MGI:1277218]
Coordinates
chr15:97701068-97703369:-
Coord C1 exon
chr15:97703202-97703369
Coord A exon
chr15:97701212-97703201
Coord C2 exon
chr15:97701068-97701211
Length
1990 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TCTTCTCTTCTCCTGTCTAGAAT
3' ss Score
9.23
Exon sequences
Seq C1 exon
ACTTGGCAGGACACGATGACTTCGGCGAGTAAGGCAGTTGAGTTGCAGCTCCAGGTGAAACACAACGCAGAGGAGCTGCAGGACTTCATGAGGGACTTGGAGCACTGGGAGAAGGACATGAAGGAGAAGGACCTGGAGCTGAGAAGACAGGGTGGCGTTGCCGAGGAG
Seq A exon
GTGAGCGAAAGGTCTCTGCTCATGTGCAGCGGAACCTACTTATCATCAGTGTGTGTACCACGTGGGTGTGCATGTACAAACACACACACACACACACACACACACACCAGCATGCCACAGCACAGGATTACAAGTCAAAGGACAACCCCCTGGGGTTGGTTCTCTCTTGTGGGCTCCAGGAATCGAACTTGAGTCAACAGGCTTGCAACAAGCACTTTGACCTGCCCAGCCATGTTATCGTTAAATTTAAATTATAGAAATATTTAAAAATAAAGCATGGCCCTGTAAAATGTGCTGTCGAGTCCTGAGGTTGCCTGGAATCCTAGTAGTCGGGCAGTGGAGGCAGAAGGATCTAGAGTTTAAGTTAGGTGGTGGTGGCGGCGCACACTTTATCCTACCCAGCACTTGGGAGGCAGAAGCAGGCAGATCTCTGTAAGTTTGAAGCCAGCCTGATTTATAGAGCAAATGCCTGGACAGCCAAGACTACAAGGAGGAACCCTGTCTAGCCTGGGCTATATAAGATCTTGTTACATAAAAGTGCTGAGATCAGCCAGGCAGTGGTGGCACACGCCTTTAATCCCAGTATTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAAAAAAACAAAAACAAAAAATGCTGAGATTATAGTGGTTTGCATCATTGGAGACATTTTCAGAGATTCTGCTTCCTTACGGAGCTTTGAATAATTGTGTGTTAACCTATCAAAGTTATTCTAAGTCTTAGTGGGTATTTAGTGAGAGGATGGTCATGTGATAATACTTAAATAATCTCAAAATATGTAGGGGTGTCTGTATCTGAAAATAATATAATCATATATTTAATAATTTATAAACAGTATTGGCATTAAAATGCAGATAAGACTCTTGTTAAGCCAGTGTGTTGAAATCTGGCTAGGTTTTTATGTCGTATGTAGCCAGTGGAGGCATGCCAGGTTGTCTTTGAACATCGGCTCATTCGCCGTGCTAAGTGAGAATCGGGGAGTTTTTGAAGTTTGGATTTATAGCTGTGGATTTAAAGGCATAATTCAGATTTCATGTTAATGCTTTTCTTGTGACTGAACAGTGTGCAGCATTCATCAGTAGTGAGCTGAACTTATAAACATAATTACTCCTTTTTGTGGGGGGTGGGGTGGGGAGGTGTATGCCCACACGTGTGCACTTGTGTGTGTGTGCCCATGTGGTGCACACGGAGGTGCCTTCCTCCATTGCTCCGCACCTTATGTTTGGCGACAAGGTCTTTCTGTGAACTGACATACCCTGAAGGCTGACTGGCCCCAGGGCTCCTGGGATCTGCTTGTGTGTTTCCCACAGGATTGCAGGGTGTGTGGCCATGCCTGGCTTTTACCCGGGCGCTGGGGATTCAAACTCATGTCCTTTTGCTTGCACAGCCAGAGCTCCTATCCACTGAGCTGTGTCTCCAGTCCACATCATCAGTAGTAGAAAATGAACTTGAAAATTAAATTGAAAGAATTTCTTATTTGAAAATATTATTTAGTGCCAGGCAGTGGTGGCGCACGCCTTTAATCCTAGGGCTCAAGAGGCAAAGGCAGGCTGATCTTTTTTTCTTTTTGTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGCCCTGGAACTCACTCTGTAGACCAGACTGGCCTCATAAATTCGCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCATGCCCAGCTGTCAGCCTGATCTTTGAGTTTGGAGGCCAGCCTGGACTACACAGTGAGTTCCAGGGCATCCAGAGAAGCCCTGTCTCAGAAAAACCAAAAGAAACAAAAGAAACTATCATTTCAAACATTGTTAGTTATATAGAAGTAACAGAGCAAAATGCCAAAGCTTTTTTCTTTCTTTTTTTTCTTCTCTTCTCCTGTCTAG
Seq C2 exon
AATTTACCTCCTATTCGAAATGGGAATTTTAGAAAGAAGAAGAAGAAAGGCAAAGCTAAAGAGTCTTCCAGAAAAACCAAAGAAGAAAACACGAAAAACAGAATAAAATCTTACGACTATGATGCCTGGGCAAAACTTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022466:ENSMUST00000023104:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.725 A=NA C2=0.667
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGCAGGACACGATGACTT
R:
CACATCAAGTTTTGCCCAGGC
Band lengths:
311-2301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types