MmuINT0139099 @ mm9
Intron Retention
Gene
ENSMUSG00000038095 | Sbno1
Description
sno, strawberry notch homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2384298]
Coordinates
chr5:124855578-124857196:-
Coord C1 exon
chr5:124857100-124857196
Coord A exon
chr5:124855739-124857099
Coord C2 exon
chr5:124855578-124855738
Length
1361 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
TTTTAAAATCTTTTGTTTAGTAA
3' ss Score
4.85
Exon sequences
Seq C1 exon
AAGGTACCTGTTGTTAAAGAGGAAGATGAACCAGAAGAAGAAGATGAGGAAGAAATGGGTCATGCAGAGACCTACGCAGAGTATATGCCAATAAAAT
Seq A exon
GTATGTTTTTTGGATTTGTCAAAACGATGGACTCAAGTTCCTCTTGAACTTGTCTTAAACCACTATATGTTAGTGCCTATCAATGTCAGGTGCTTCAGGATTTGACAGACGTGAACTATGAATAGTTTTTCTTTCCTCGCTCGTCTACCCTACCTGTCTGACTCGCTGTCTGTCTCTCTTTCTGTCTCTTAATCTCTCTTCCCCCCTTTTCTCTCTCTGTCTCTGTCTCACACATACACACACACACACACACACACACACACACACACACACAGAGTTGCTGGGTGGAATTTACCTTTGGCAAATTTCACTGTTTTCCCCCTTTTAGCCAATTTTAGAACCTTGTTTGGGGCTAAAGGTTTAAAAGCCATGACAGTAAATCCTTGGGTTTGTTTATTTTGTTGCTGGCTAGTTTTTCTTACATAAGTATTGATTAAAAATTTTTTTTAAGGTGAATTATGGAGATAACAAATGTACATTGTGAATTTACACTAGTTTTAACACCTTATCCAAATCATAGGCACATTGAAACCTTCTTTTGATTCTTGGGGGTTTTGATGTTTATTTTTTTTTTTTGAGACAGGTTCTCCAGTACTTAAAATTTTCAGCTAGGCTAGCTTCAAATTCGGAGAGATCTACTGTCTCATTACTTGGAGTGCTGAGCTTAAAGGTGTGAGCTGCCCTGCCTGGGATTCATAGCCTTTTGTTTTGGCTTTGCTGAGATAGTCTTTGCTTTAAGCTTATACTTGCTTTGATCCTGTATCAATCCTGTTCTAGGATTGCCGTCAAGAGTCTCTAGGCTTGACGTCATTGGTTTTTATTAATGCTATTTTCCTGCCTTTTTTGTAATGTGAATAACTTCTCGGTTGAACTTTATATGAGGTTGAAAGTTAACTTTTAGCTTTTGTATGGAAATTTAAACCTCTTTGCTACATTAAGAATAATAATAGATTTTTTTTAACCTTTTGATATCTGGTTTCCTTGTATTCAGTTTGGCCTTCATCTCATGGTCTCAACTGATCGTACCATGTCATTTCTTATGGTAGATGAGACTGGTGGTGTGCAGTACCATATCTAGTTATGTTTGGATATGTGGGGGCTGGATAGAAAACTGCCTGCCTGTGCTTCCTAAGCAGGTCTGCTTTTTAACTAGATCTTTTCATCATCTATCTCTAAACTGTGTAGTTAGGTAATTTTTGTCAAATTTGAGAAGTACGTTACAATTAGTAACTTTATATAGAAGCTGGAAGTGAGTAGTTAGTGTTTATTCTGTCAAAAGACAAAGAATGTACTATCTTGTAATAAGCCTGGAAATGTTACTCAAATGACTTAAATGAAACATTTTAAAATCTTTTGTTTAG
Seq C2 exon
TAAAAATTGGCCTGCGTCACCCTGATGCAGTGGTGGAGACTAGCTCTCTGTCCAGTGTCACTCCTCCTGATGTTTGGTACAAAACCTCCATCTCTGAAGAGACCATTGATAATGGCTGGCTGTCTGCATTGCAGCTTGAGGCAGTTACCTATGCGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038095-Sbno1:NM_001081203:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138721=AAA_34=PU(16.2=92.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTGTTAAAGAGGAAGATGAACCA
R:
CTGGGCCGCATAGGTAAC
Band lengths:
250-1611
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: