MmuINT0150538 @ mm9
Intron Retention
Gene
ENSMUSG00000049313 | Sorl1
Description
sortilin-related receptor, LDLR class A repeats-containing [Source:MGI Symbol;Acc:MGI:1202296]
Coordinates
chr9:41810637-41812200:-
Coord C1 exon
chr9:41812069-41812200
Coord A exon
chr9:41810769-41812068
Coord C2 exon
chr9:41810637-41810768
Length
1300 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CGACAGTTCTCGCCCTCTAGCGC
3' ss Score
5.18
Exon sequences
Seq C1 exon
AGCCCTTCTGCACGCGCTTCATGGACTTCGTGTGTAAGAACCGTCAGCAGTGTCTGTTCCACTCCATGGTGTGTGACGGGATCGTCCAGTGCCGAGATGGCTCTGATGAGGATGCGGCCTTCGCTGGATGCT
Seq A exon
GTGAGTGGATGCATGCGTGAATGCATGCGGAAGCCGGCCACTCTGTGGGGCACCTAAGACTTGGATGCAGGTCATGTCTCAGTGCCTGGGCCTGCATTTGTTGTTCCTTTTCCCACAGAAGCACTGATGCGTTGTCTATTTTAGTTATAAATGGATGTGATGAGGCTGGGGAGTGACCAGGACCTTGTCACGTGTCACCTTCTGGGAGAGACTGGCTTTCCGATGATATTTACAGGCTAATCTCTCTGTAACACAGCTTTGCTCCAGCAGTCTTCCTGGCACGGATCCTCGCTTTGTATACTTTCTCTTACAGCCAACCTCTCCTGCTGCAGAATATCCTTAGGTGTCCCTTTTGTGACCGAATAGCCGGCAGAAACAGCTTAAAGAGGAAGGCTTTACTTTGGCTCATGGTGCCATAGGGTTTGGTCCCTGGTTGCTTGGCATCATATGCTTGGACAGAATATTGGGGTGGTGGCAGTGTGGACAGGGAGAGCATTTTACTGCATGACACATGGGAGGCAGAGTGAAAAGGTCCCTGAGGACCCAGTGCGACCTTCAAAGGCCCAGCCCCAGAGACTTACTTTCCCTACTGATATTCCACGTCCCAGCCAGAGTTCCCAGAGCCTCCCAAAATAGTGGCACTGAGTAGGGACCAAGTGTTCAAACATAAACCTGTTGGGTACATTTCATATTCAAAGCATAGCACTAGGGCTGTGCATGCCTTAAGCTATCATAGCAAAGCCCAGTAGACTGACTGTGTGCTTCAACCAACAGAAACTGTTGTCCACTCTTGAGGTGTTGGGAGCACTATCCGGGGCCTCCCTCCCCACCTAGTGGGTGCTGTCTTTACCTATGTCGTCACGTGATCGTTCTCCTGTATGCATCTGTGTCTCAATTTCCACTGTTGTATATTTTAATTTAAAGAAACAGGGTCCTGCCATGTTGCCCAGGTTGGCATCAAAAACCTGGGCTTCAGGGGCAATCTTTTCCTAAGGACACTAGTCAATACTAGACTAGAGCCCACCTTGATGACTCTATTTGAATGTAAATTTCCTCATTGAAAGTGTTATCTCTAAAGCAGGCACAGTATTGGAGCTCAGGGATTTGGCCCTGTCCATGCCCCATGTGAGTGTGCGGAATGGATTAGTTATTGTGTGCTCTGCTGAGACCCGGTCCCGCCTTGATTTCTCAGGGCTCCCTTAGCTCTCAGCGTAGGACCTTAGCTACCAAGGAGCCCTGCTGCTCTGAACTCTCCAGCGTGGAAGTAACCTGGGCTTGACCGACAGTTCTCGCCCTCTAG
Seq C2 exon
CGCAAGACCCCGAGTTCCACAAGGAGTGCGATGAGTTCGGCTTCCAGTGTCAGAACGGAGTGTGCATCAGCTTGATTTGGAAATGCGATGGGATGGATGACTGCGGGGACTACTCTGACGAGGCCAACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049313-Sorl1:NM_011436:28
Average complexity
IR-S
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:
PF0005713=Ldl_recept_a=WD(100=91.1)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=82.2)
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:
CCCTTCTGCACGCGCTTC
R:
CACAGTTGGCCTCGTCAGAGT
Band lengths:
262-1562
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: