MmuINT0139061 @ mm10
Intron Retention
Gene
ENSMUSG00000038371 | Sbf2
Description
SET binding factor 2 [Source:MGI Symbol;Acc:MGI:1921831]
Coordinates
chr7:110461137-110462966:-
Coord C1 exon
chr7:110462856-110462966
Coord A exon
chr7:110461243-110462855
Coord C2 exon
chr7:110461137-110461242
Length
1613 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TTGTTTCTTTCATTCTGCAGAAG
3' ss Score
10.1
Exon sequences
Seq C1 exon
GCCTGCCTGGGTTTGATCTATACTGTGTATGTGGACAGCATGAGTGTCTCCTTGGAAAGTCTCATCGCAAATCTTTGTGCTTGCCTTGTCCCAGCTGCTGGAGGGTCTCAG
Seq A exon
GTAAATAGAACACATTTATTCTGGGTGATTTAATTTATGACAAAAAAGAAAGAATTCTTCAAATATTTTTTGTTTTAGGTAGGATCCTACTTTAGGTAAACCTTGTCCCTATGATGTACCTTCTAGACACCTAAGATTCCATTCTTTTCATAGGTCAAGAGGCTGATTTCAAGGGCTTGAGACATGGCTCAGTGGCTAAGAGAACATCTAGCATCTACACCACATAGCTTACAACCGTCTGTAAGCCCAACTCCAGGGACACCTGACCTTAGTAGCCACTTGTATGCATGTTCATGGACTCACCCCACACACATATACATAATTAAAATAATGAAAAGAAATCTTTAAAAAAAAAAAGGAGCCCATTTTCAGACTGAGTTCCCCTTTAGGTGGCATAATTAGCAGACATACTTGACCCACCTTCAAACCTACTTTTGACCTTTGTGGACATATCTTTCTTTAGAAAGAATTTTTCAATATGATTCTGCTGCTTTTTTATTTTTGTATATAGTTATACCTCAATTATACTAAGTAAAAAAAAATGACCAAAATTAGAAGACAAAATTGAGTAAACTCTTTTTGTAACATTGTAACTTTTTAAAAATAGATCCCTTTTTGTCTGTATCTTGATGCTTAAAAATATTATCTTAGAAGCAGAAAAATAAGAATCTTTGCTTCCATGGTTTATTTATTGTTTCTAGGTCAACCATCTTTAAAAGCACTGGAGCTAGAAATGCAGCCCTGGTGAGAGAGAGCACGTGCTCACCATGTGCAAGGCCTTCCTATCAATTCTAGTGCCAGACAGAGCAGACGGCTTGTCTTCTTAGACCTTAAAGACATCTAGTTGGCCATGTATTTTGCTTTTTATATATCGAGTAAGAGAGACCACACTTCGAAAAGTCACACCACTTGTCCTTTAGTCTGTCAAAAATGGTAAAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGCGCGTGCATGCTCATACATGCATCCATGCATGCTGTTGTCCAAGGAGTTCAGAGGCAGCAGATCCTTACTGTTAGAGTTCAAAATGGTTGCAAGCCTCCTGACATGGATGCTAGGAACTAGACTCAGATGCTCTGAAAGAGTTGCAAGTCCTCTTACCTGAGCCATCTCTCCAGCCCCTGAAAAATGTTAAATTTGAAAAAGAAAAGATGCTACTTATAGGGTAATTAGCATTTTAACTCTCTTCTTTCTCAACTTCTTTTGTCTTAAATTACCTCCTCTCTTCTTTTTTCCTTCTTCTTCTTCTTCTCCCTCCTCTTCTTCTTCTTCCTTTTCTCTTCTTCCTCTATGGTGTTCTAAAGACAGAATCTTAAAGGTGGCCTTGGCCTCTCAGGCCTTTCCATCGAAGAAGCAGATGGTTCTGTACACAAGATGGTTATGTAACACAAGTTAACATAGTTTTGGTCAGTTATAATTGTTAGTGATATTTGCTCCTATCTACTGAGGTTTCAACTTCCATGGAATGAATTTTCTGGTATCATTTTGATTTGTACACAACATAACTTGTATGTTTTAGGTTATATGTTTCTGTTTTTTGTCTCTTATGACTTTATATTTGTTTCTTTCATTCTGCAG
Seq C2 exon
AAGCTATTTTCCTTGGGTGCAGGAGACAGACAACTGATCCAGACACCTTTGCATGACAGCCTTCCTGTCACAGGCACTAGTGTGGCTCTTTTATTTCAGCAATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038371:ENSMUST00000164759:5
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=0.000
Domain overlap (PFAM):
C1:
PF0214116=DENN=PU(16.4=96.2)
A:
NA
C2:
PF0214116=DENN=FE(19.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGCCTGGGTTTGATCTAT
R:
ATTGCTGAAATAAAAGAGCCACACT
Band lengths:
214-1827
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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