MmuINT0152671 @ mm10
Intron Retention
Gene
ENSMUSG00000022983 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:MGI Symbol;Acc:MGI:2146350]
Coordinates
chr16:90245381-90247283:-
Coord C1 exon
chr16:90247170-90247283
Coord A exon
chr16:90245538-90247169
Coord C2 exon
chr16:90245381-90245537
Length
1632 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TGTATTTCCACCAACTGTAGATT
3' ss Score
6.6
Exon sequences
Seq C1 exon
ATGATTCCTCCCAGGGGCTGTGCCTACATCGTCATGGTTCATAGACAAGATGCATACCGTGCCCTGCAGAAACTGAGCCGAGGAAACTACAAGGTGAACCAGAAATCCATAAAG
Seq A exon
GTACATTTTATCATTTACAAAAGGGTTTGATATGTAAATATACTGTTGTGGGGGGTTTTCTTTTCAACGATAATTTTACTGCTTGGGAATGGCTTAAGACATAAAAGCTACCCTGTAAAAATACGGTAACAACAATAACAAAGCAAAACGTTATTAGTTGACATAAAATTTTATGTAACAATTTTCTCAGGGTATTTATTTATTTATTTTATTTATATGAGTACACTGTAACTGTCTTCAGACATACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGCTTGCTGGGATTTGAACTCAGGACTTCTGGAAGAGCAGTCAGTCTCTTAACTTCTGAGCCATCTCTCCAGCTCTTCCAGATCCCACCTCCCTCCCTGACTCTCCATGCCCCTTCATCCCACCCCCCAACCCCCCACCTGGGACTGGAAAACAAGCAATAAAAGAGAGCAGAAAAGCACAGAAAACACCACACCCTCCTCAAAATCAGAAACCAAAACACACAAGCAAAAAGTCAGAGACAAAAATGCCCAAAGCAGCTGGAGAAAAAAGTCTACCCCCACCCCCAACAAAGAATTTGTTGAGTTGTCCGTGCACTACTGGGCATGGGCCTGCTCTGAGGGAAATAAATGCAGGGAAAACTAATTGGGAAAAACTCATGTTTCCTTGGCAAGCAGATGTCAGTTTCAGGAACCTCTTGGTTAGAGGTGGGAGCCTGAGCTGGCTTCTCCATTTCCGAGCTGGTACCTTATCTGGCTTGATCCGAGGCAGGACCTGTAGAAGCTGTCTCTGATTTTTGTTTTGTTTTGTTTTCGAGACAGGGTTTCTCTGTATAGTCTTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGACTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCCGGCTCCTCCCCACCCCCTTCTCTGATTTCATAGGTGCATCAGTACAATTGGAGTTACCCAGGCCCTTTGCACATAAGTTCCTGAACCCTGTGGGGAGGGTTTAAAGAAGGCAGCCCATTTAGGATGTTGGGTCTCTGTTATTTCCAATCACTTGCAGTGCCACATCTGTCTAGCTCTAATTGGTGCTTTAAAGATGTTTTCTAGTCAAATATTCTTGTATAAAAATGTGGATATTCCACAACCTAAGGTTTACCACTCCATCTTAGAATTAACTGTGAAAACAAAATCAGCAAAGGTAAAGAAAATTAGAAGTGCACCCTCTTAAAATTAGACAGCCACCCTCTGAGGAGTCGGGATTCGGTGCTGTTGTAGTTACTGCCCGGTTCTACTCTAATGTGGACTGGAAAAGGATGTTGCCCTCTCTGTAAAGTGGTCTTCAGTGTGCGGGCCTTCTCCTTGGTGAGCTCATTCCCTCTGCTGTGTGACTGCGTGACTGTGGGGAGGCAGAGTGGGAAGACAGCAGAGGCCTTACTCTGATCAGTGAGTACCTCAAGTGTGCAGGTCCAGCCAGGCCGTGCTGCTCCGCTGCCCTGTCCAGAGGAGTAGTGCTGGGGAGTGGGGAACTGAAGGTTCATGACCTTCCCCTTTCTATTGTGTATTTCCACCAACTGTAG
Seq C2 exon
ATTGCCTGGGCCTTGAACAAAGGAATAAAGGCGGATTATAAACAGTATTGGGATGTTGAACTTGGTGTCACTTACATTCCGTGGGACAAAGTCAAAGCTGAGGAGCTGGAGAGTTTCTGTGAAGGAGGCATGCTGGACAGTGACACACTTAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022983:ENSMUST00000039280:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.189
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(55.2=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGATTCCTCCCAGGGGCTG
R:
TGGGTTAAGTGTGTCACTGTCC
Band lengths:
270-1902
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