MmuINT0150528 @ mm10
Intron Retention
Gene
ENSMUSG00000049313 | Sorl1
Description
sortilin-related receptor, LDLR class A repeats-containing [Source:MGI Symbol;Acc:MGI:1202296]
Coordinates
chr9:42031669-42033656:-
Coord C1 exon
chr9:42033565-42033656
Coord A exon
chr9:42031916-42033564
Coord C2 exon
chr9:42031669-42031915
Length
1649 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
GTGGTCCCTGTATTGACCAGGGT
3' ss Score
5.76
Exon sequences
Seq C1 exon
GTAGCTAATCCAGATGGTGACTTCCGACTGACAATCGTCAATTCCTCTGTGCTTGATCGACCCAGGGCTTTAGTCCTTGTACCCCAAGAAGG
Seq A exon
GTAAGTGTTCCTTACGGGGAGTCAGCGTCACGCCCACTGCTGTAAGAGATGCTCATGAAAGTGAAAATGTGAGGCCAGGTTTCTGCTTCTGGTGATCATGGGGGAGATAACCTGTTGACTGAGGCTCTTGAAGCCATAGCTTGCTTGTCGTGGTCCGATAACTCTGTGTGTTTCATTAGAAAGCATCCGACTCTCTTATGGTCTCCAGATGTCTCACATCTGTGGGGTGTTTCAATAGAAAAGGTAACATGAAAGAGAGTCTTTGTAAACCAGTCAGGCCACTGATAAATTGTAAGGATTTTTTTTTTTTTTAATCTCGAGTTCCGTGAATCTCACAAACATTTAATTCGACCAGTCACTCTCACACACAGAACTCCCAGCGTGTGCAAGTTTTCTTACTTAAAATTACTGTGCACTTGGGGTACGCACGACTGCTTTTCACTAACTCCTTCATCACAGCAAAAATTACTAAGAAGGAAATGCTGTGCTAGCTTTTCTTTCTGTGTGTATTTATGATTGAGAATTAACACTATTCTTAAAAGGACACTCTAAAAGAAATCTATGGGCTTGGTTGCAGATATTAAAAGAGAAGACCTTGAAAGGATGCTTAAGTCTGCCCTGTTCTCATTCGTCACCCTTCATCCTCCTACATCCTCGGGATGCAATCACATCACTGTTACGTAATAGTCAGCATTACTCATGCATAATAGCCACAATTAATTTTTTGCTTGCATTATTCAGAGTCTTTTTACTGGTGTTCAATCATGATCATTAAATACAGCGCCCCTTAGTGACACACACGACTTGTCAGATAGAATCAGTCTGTTTGTGATTTCCTGCCAGTCAGCGGACATGCACATTGAGTGACAGCGGCTTATCAGAGCACACACAGCGGTTTAGTTGCTTCGGTAAGAACATGGATGAAAACCGAGGTGGCAGGAAGGAGTTTATTTTGCTCGCAGGTTATACTCCCTCCCTGAGGCAGTCTGAGGTAAGAACTGAAACAGAGACCACACTTACTGGATTGCTCCCAGTGGCTTGCTCAGCCGGCTTCCTGCCCAGGGTGGTACTGCCCACAGAGGTTTGGACCCTCCTGTATCAATCATGAATCCAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACTGGCCCACAGATTTTCTCCAGGCCAGTCTGATAAAGGCAGTTCCTTAATTGAAGTTTCTCCTTCTGAGGTGACTCTAGTTTGTGTCATTGTCAAAAACTAAGTAGCACATACAATAGATAGATTTCAAACTATTTTGGATACAATATTCTGGGGGCATTGCAGTAGGTATATTCTATTGTATAATACTACATATCACTTCCTCTGCCAATTAGCATTTAGATTAGCATGCATATATGTGGATCTCTTTGTATAGTATTGGAATAATGTGATTATAGGCAGACTTCAGTAGGTGAATTTTTGAGTCAAGTTCAACTACATTTCTGAATGAATCTCAAATATAGATGGTAGTAATAATGAGTGACTGCATGTCAAATATAGACAGGCAGTAGTGATAATGATGGCTTTGAGAGGTTACTTACCTCTGAGACGTAGAATCAAGGCTGGCCTGTGTCGTTCTGATGAGATTGTGTGGTCCCTGTATTGACCAG
Seq C2 exon
GGTGATGTTCTGGACTGACTGGGGGGACCTGAAGCCTGGGATTTACCGGAGCTACATGGACGGCTCTGCTGCCTACCGCCTTGTGTCAGAGGACGTGAAGTGGCCCAATGGCATCTCTGTGGACAGCCAGTGGATCTACTGGACGGATGCTTACCTGGACTGTATCGAGCGCATCACTTTCAGTGGCCAGCAGCGTTCAGTCATCCTTGACAGCCTCCCACACCCCTATGCCATCGCTGTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049313:ENSMUST00000060989:19
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:
PF0005812=Ldl_recept_b=PD(63.4=83.9),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=51.8),PF0005812=Ldl_recept_b=WD(100=48.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTAATCCAGATGGTGACTTCC
R:
AAAGACAGCGATGGCATAGGG
Band lengths:
334-1983
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