MmuINT0152679 @ mm10
Intron Retention
Gene
ENSMUSG00000022983 | Scaf4
Description
SR-related CTD-associated factor 4 [Source:MGI Symbol;Acc:MGI:2146350]
Coordinates
chr16:90258711-90260302:-
Coord C1 exon
chr16:90260141-90260302
Coord A exon
chr16:90258847-90260140
Coord C2 exon
chr16:90258711-90258846
Length
1294 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
CATTTTCTTACATATAACAGAGT
3' ss Score
4.22
Exon sequences
Seq C1 exon
TGTAAGCCAGAATATAAGGTTCCAGGCCTGTATGTCATCGACTCCATCGTGAGACAGTCTCGGCACCAGTTTGGAACTGATAAAGATGTTTTTGGGCCAAGATTCTCTAAAAATATAACTGCTACATTCCAGTATTTATATCTTTGTCCATCTGAAGATAAG
Seq A exon
GTATGGTTAAAACGTAACAAGCTAACATTTTGCATTTTGTCCAGCTTATTTCCTCTTTATATTTCTCACACAATGCTTACGTTCACGTTGTTGACACTTGTTATTTATGTTACTGGGTGATATCTTCATGTACTGATCTTGAATTGTAAGGTCAGTTTTTTCTACGGTGGTCATTTCCTATTCTTGCTTATATGTGAAATGGAGAAGTCACTTGGCCTCTGTACAAGGACTTTTATAATGTTGAATCATAGAAGGAGCCAGAGTTATAGATCCTGAGCAGAGCAGAGCAGAGCTTGCTGGCGAGTGAGGAGTGCCTTACCTCTGTGCATGGGAAGCCTCTTCTAAACGGCGTGGTAACAACAGCCAACAGCTAGGCGCTGTACACTACACATTTCATGTTACATATCCTGCAGTTAAAAGAAACTAGCAAAGGTTGTTCAGGAAGCATTATCTTTCCTTAAAGAACATATTGCTAGTGGGCATGGAGACACATATCCTTTGATCTCAGCACTTAGTGGGCAGATTGCTAATAACAGCAAGCTGAAGCTACAGAAGGAAGACAGACAACAACTCTGTGTGAGAGAAAATACTCACCAGGGTTTTGCATACTCTAGAAGACCCAGATTTGTTCTTCCCCAACATTCACACATGCAAGTGATTAATCTGCAGTAAGACTGCAACACACACATACATACACACACACACCACACACACATATACACCACACACACACATACACACACCACACACACACCACACACACACACCACACACACACCACACACCATACACACACACACACCACACACACAGTTTCACTGAAAGAAAGAAGGAACGAACATGAACGATACATGCATTCTAAATAGGTGGGAATTCACAGTAAACATCACTAACACTAACTTAACCTGCTGCTTTAGTTTCTCTTAATTCTTAAAGAAGTTATGTAACAGAAAAGGGAACTTGGTTTGGTCAAACCAGAGAGAGAGGGAAAGTGCCCGTGTCTGAGAGTAGCGACATTTGCATGAGGAGAGGCGTTGTGGGTTTGCAGAGTCTGTATAAGAGCATTAGAAATGGTTCTTGACGTGTTTACCTTCCTTTGTATTTGCTAGCTGTGTATTCTGTTTATATTCCTTTTCATTGGATCATACCACCGAGAAAAGGTTAATTTGAGTTTAACTGGGTAATAGTTCTGGTGGATTTTTTCCCTTATGAAACAGTAATTCTCTTTAAAATCAGATATGATACATTATTTCTATAAATATTTATTGTATGTTCATTTTCTTACATATAACAG
Seq C2 exon
AGTAAAATAGTTCGTGTGCTAAATCTTTGGCAAAAAAATGGAGTGTTCAAAATTGAAATTATTCAGCCTCTTTTGGACATGGCAGCAGGAACCAGTAATGCTGCTCCAGTAGCAGAAAATGTCACCAACAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022983:ENSMUST00000039280:4
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=0.261
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PU(72.7=88.9)
A:
NA
C2:
PF048188=CTD_bind=PD(24.2=34.8)
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:
AGCCAGAATATAAGGTTCCAGGC
R:
CTTCATTGTTGGTGACATTTTCTGCT
Band lengths:
294-1588
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