MmuINT0152670 @ mm10
Intron Retention
Gene
ENSMUSG00000022983 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:MGI Symbol;Acc:MGI:2146350]
Coordinates
chr16:90247170-90247745:-
Coord C1 exon
chr16:90247645-90247745
Coord A exon
chr16:90247284-90247644
Coord C2 exon
chr16:90247170-90247283
Length
361 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
CTGAGGTTCGGTTCTGTCAGATG
3' ss Score
4.04
Exon sequences
Seq C1 exon
TTTGTAGTACCACACTGTGGGTGGGACAACTGGACAAAAGGACTACTCAGCAGGATGTTGCCAGTCTCTTAGAAGAGTTTGGTCCAATTGAATCGATTAAT
Seq A exon
GTGAGTATTTATTGCCCTTAGGGTGCGGTGCTAACTAAGCAAGAAGTGCTCAGTTGTTTTGAGACTGAGGCCTTGAGCTCTCAGCTGCAGGCTCCCTTAACATTCTGTGCAGAAGATTCCTCTTGGACAACGGTGCTTACGTTGAACTACCTTTCTAGGAGAGTAACAAAATGTGCACACACGGTTTAAGAGCAAACTTGAATTGCCAGCGTCTGACCCCACAGGTTCTTACTTAGCCGTTTGCTGGTGGTGCTGGGGCTGCAAGGTTGTGCTTGCTACAGTGCTTGAGCTCTCCTGTGGACTCAAAGCACTGCTGAGAAGGAAGGGACGAGTGTTCTGACCTGAGGTTCGGTTCTGTCAG
Seq C2 exon
ATGATTCCTCCCAGGGGCTGTGCCTACATCGTCATGGTTCATAGACAAGATGCATACCGTGCCCTGCAGAAACTGAGCCGAGGAAACTACAAGGTGAACCAGAAATCCATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022983:ENSMUST00000039280:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(41.8=82.4)
A:
NA
C2:
PF0007617=RRM_1=FE(55.2=100)
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:
GTGGGACAACTGGACAAAAGGA
R:
TGGATTTCTGGTTCACCTTGT
Band lengths:
190-551
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