Special

MmuINT0150538 @ mm10

Intron Retention

Gene
Description
sortilin-related receptor, LDLR class A repeats-containing [Source:MGI Symbol;Acc:MGI:1202296]
Coordinates
chr9:42002554-42004117:-
Coord C1 exon
chr9:42003986-42004117
Coord A exon
chr9:42002686-42003985
Coord C2 exon
chr9:42002554-42002685
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:ENSMUST00000060989:28
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:
PF0005713=Ldl_recept_a=WD(100=91.1)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=82.2)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
LOW PSI
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
  • 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