MmuINT0149665 @ mm9
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:95183505-95186001:+
Coord C1 exon
chr1:95183505-95183600
Coord A exon
chr1:95183601-95185884
Coord C2 exon
chr1:95185885-95186001
Length
2284 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TGGTGCTTTCCTGTTTCCAGGTA
3' ss Score
10.35
Exon sequences
Seq C1 exon
AACCCACCACTCCGGTGCCACTCAAGAACACAGAGGCCCCTGAGCAGGTCCATCTGGCCCTCCAGCTACCCAAGAACAGCAGCAAAGACACAGAAA
Seq A exon
GTAAGTCATGTGCGAGGGAGGGAAGGGGGCTGGTGGTTCTTCATAGCTACCACAGCGAGAGGCGCCACAGTGGGAAGCTGGGAGGCATAAGGTCTGCCCAGAGACAAATGGCACCCCAGTTGGGGCGCAATCCCCCAGTTCATGAGTGAGAGACCTGAGAACAGGACACACCCAGGATCTTAGAAAGGCTGTTCTATCCTCCTTATTTCCAGTAATCCCCCTCACCTTGCCCCTCACCCACCCTGGGGATCCACTTCAGGCCACCCAGCTCACTTCTTCATAGAGAAGGTACCAAGTCAGGTGGCAATCAGTGAAGAGTGGCCACTGAGTAAGTCCTAGCTTGAGGAGTGCCTCTCCAAGCTTGGCCACATGTAGGACTTGGCTTGGACTATTCTGTGCCCACACAGCACCAGGTGTGTTTCCAGCACCTCTAGCAAGCAGCTAGCAGCGCAAACAGATGCTCCTTCAACTGTCGGACTCTTGCTCTGTCCCTCTAGGGATTATGGGTTAGAGTTTCCTAGGGCCCCGAGGTCCTTCTTCCTTCTGAGTCACACCAGAGACTTAGAGTGTCTTCACCTAGCCCCACAGAAGATCAGAGTACATGGCAGAAGTGTAAACCCCAAGGTAACCTCACCTGGAAAACTGCCCTGGAAGGACACCTGTTAATATTAAGGGCATTACAATGCCTGAGGTACAGAGGGCCCACTGATCCCTGAATTCAGTATTCTCCTCAACCCGGGACCCCTGTGCCAGCTCTTGACCCTGCGCACACTGGGAGGGTGGTTGTGCATGCTGCAGCATCAAACACTCCTTACCACAGCTTGTGCTGCTGTTTGAGAGGATAGAACAGGCTCACTGAAGACCGTTACGTCGGCCCCTGTGAGTACCAAATGTCCCCTTTTATAAAGCCCAGAATAGTCTGTTTTCCCCGTGGAGTCAGTCTCCTGGGTTCCATCTCAAAAAGTCCAGGTGGCCTCAAGGCTACTGACATCCTGCAGTGGGGCACATTTCAGTGCTATCACAAGAAAAAGAATCTCTTAAGGCCTCAGACACAAAACTAATCATGACCTTTGGTTCATGACACACCCATGCTGTCTGTCCATCTGTTTGCCAGTTTGGCTGCCTTTGATAATTCTGGAGCCTGGCCCGTGCTAGAATCTGACAGGAAACTTTGTCTTGTGTTTTTTTTTTTTTTTCTCCTGGACTCTCCACGTGGCCCACCTCCATCCTGCGCTCTGTCTGAGTCCTTAGTCTTGGAATGAGTCACACACTACAATAGAGAGAGTCCTCTGTAAGGAACACGCTTTTATCCCAGCTCTCAGTCACCTGAATCAAGTGTCCAAACATGCATGGGTCCATCCTGGGCTATCTCCTTTGTTCCAGCATTTTCCCTCCCGTGAGCCATTTCCCCCACCTTAATGCCAGTGTGGCCTTAGTGTGAGTTTATACACTGTAGGACCTCTAAGGAGTCTCAATCTTTCTTTCAACTGTCCTTCATTATCTGTATGTTGGCTTTGTCTAGTGCAACAGGGTACTGGTACACAAGCTCCAAAGGCCATGCATGCCCATTGACATTTATCAGCCTTCTCATGTAAAGGATCCTTCAGCTGGACATAGGATGCCAGGTCTGGACTCCTCTCCCCACTGTCATCTGGTGTCCAGTCTTGTTCTTGTTTCCTTGTAGGTCATCTGATCCTTTTCTCTGGAAGAGTTGGACTTTTCTTCCTTGAGTAAAAGTGTTATCTATCCCCAAAAAGGCCCTCAGGAGTCCCTAAAGCACATTAATGCTTCCAAAGGTTGTTTCCTCACTGAACAACTTTCCAGGTCAAGGTTGTGCCTTCAAATCCCAGGAAGAATCTATGGGGAGGAGGAAGGTTCCCACAGCAGCCATCCTGGGATGGAGGGACCTCAAGGACAAAAGTGAAAGAGCAAATGCTAATCTAGATATTTAACCTGGTAGGAAGATTCATATTCCTGATATCAAAACATGCTATAAGTCCAGTGTGACACTCCTTAAGAGAGTCTAGAAAGAACCACATATCTATTGTTAAATGATTATGATGAGGGGACCAAGTCCACACCACAAGGAATAGTCAGTCTCCTCAATAAGCAGTTGAGACCCAGTCCAGACCCAGCCAGCACTGTTCGCAGCCCGCACCAGTGTCTGACAACAGGAGGAAGACAGGTTTGCCGCTGCTGTCCTTGTGTATCACTAAGGGATGCAGCCTACAGTAGCAGCAGGCTCCTCTGGACCCTGAAGCTGATGGTGCTTTCCTGTTTCCAG
Seq C2 exon
GTACCCCTGGCAGCTGTTCAGAAGATGCTTGTCAGAATGGAGGCACCTGTGTCCCAGGTGCCGATGCCCACAGCTGTGACTGCAGGCCTGGGTTCAAAGGCAGACACTGTGAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793-Sned1:NM_172463:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.076
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: