MmuINT0132610 @ mm10
Intron Retention
Gene
ENSMUSG00000046201 | Scaf8
Description
SR-related CTD-associated factor 8 [Source:MGI Symbol;Acc:MGI:1925212]
Coordinates
chr17:3162959-3164277:+
Coord C1 exon
chr17:3162959-3163112
Coord A exon
chr17:3163113-3164146
Coord C2 exon
chr17:3164147-3164277
Length
1034 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
TGTGATGTCTTTTCTAAAAGGAA
3' ss Score
7.48
Exon sequences
Seq C1 exon
AGTAAAATAGTGAGAGTATTAAACTTATGGCAGAAGAATAATGTTTTTAAGAGTGAGATTATCCAGCCTCTTCTGGATATGGCGGCAGGGATTCCTCCCCCAGTTGTCACGCCTGTTTTGGCCAGCACCACTGCAGCTATGAGCAACACTCCAG
Seq A exon
GTACGTGCCTGTTGTACAGACTTGTTGGAGACTCAAGTTACACTGCTTACCCAATGTTCACACGCTATAGGGCAGAGGAGTTTGTCCAGTGTTAAGAGACTTGAAGGCTGAGTGTGGTGGCAAGTGCCAACTGTTAGTCCTTACACTGGGCAGACAGGCAGGTGTATCTCTTTATGTTCATGAAATAAAATACTGTGGTTTTGCTCTTAATCTAAAATTTAGAAAACAATTTTTAAAAATTGCTTTTATTTCTTTTTTTCTATCACCCAAAACATTTTGGAAAATGTCTATGTCACAGTTCATTTTTGTTTTGTTTAGCACTATGATTGATTGAACTCGGGGCCCAGCATATGCTGGGCAAGGACTTTTGCACTGAGCCACATCCCCAGTTCTCAATGAGCGTTTTCTTGATTTAGGTTGTCTATAACTCCTTAAACATGTATATGTAACTTAACTTGTTTACAGGTTATTTGGGGAATGTCATTTTTTAAGAAAAACTCCAAAATCGCTTAATAAAGCCAAGATTGCTTTAATGTAATTATCTAAAAATTTTATTGCTTGGGATATTTTAAATATTTCAGCTTTTACTCTGAACCCAACATTCGTTAACTTTTTGGTATGTAGTTCTTGTTGTACACCTGTCTACAAACATCTGTGTATAAACAAGAGTTTTGAAAAAAAAATAGTTTCATCTTACAGATACAGATTTTACCAGGAAAGATTGTATTTTTGTTATTTCCCCCTGTTAAAGAATTTTCTGTAGTAAAACTTTGCTGACAGGTTTCATTGAAGTGGTAGCTTAGTTTAAGATAAGTATAGACAGATCGCATGGGGCTTGGAGTGGGGAATTGCCTTCCTGTTTGTAAAGTTACCTAACTACATAAAGGCTGTAAGTCGTTTTCAAGATGGAGGCAGTAAAGTGAAAGCATACTATCTGCTTATGTTTTATATGTTAGCTGAATAAATCTTTGTACCTTTTTAAAGTATCATTTACTTGTTTCCTTCTTTGGTCCGTGTGATGTCTTTTCTAAAAG
Seq C2 exon
GAACACCCGTGACACCTGTTACTCCAGCCAATGTGGTCCAAGGCTTACCTGATCCATGGGTATCTCAGATAGCAAACACAGACACACTGGCAGCTGTTGCTCAGATCCTACAAAGTCCTCAAGGTCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000046201:ENSMUST00000076734:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.227
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PD(24.2=30.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAGAGTATTAAACTTATGGCAGA
R:
CTGTTGACCTTGAGGACTTTGT
Band lengths:
277-1311
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