MmuINT0010413 @ mm10
Intron Retention
Gene
ENSMUSG00000015143 | Actn1
Description
actinin, alpha 1 [Source:MGI Symbol;Acc:MGI:2137706]
Coordinates
chr12:80172963-80174214:-
Coord C1 exon
chr12:80174080-80174214
Coord A exon
chr12:80173143-80174079
Coord C2 exon
chr12:80172963-80173142
Length
937 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CATCTCCTTCTGATGAGCAGGAG
3' ss Score
2.79
Exon sequences
Seq C1 exon
GTACGGCAGCTAGTGCCCCGGAGGGACCAGGCTCTCACAGAGGAACATGCAAGGCAGCAGCACAATGAGAGGCTACGCAAACAGTTTGGCGCACAAGCCAATGTCATTGGGCCCTGGATCCAGACCAAGATGGAG
Seq A exon
GTGAGTTTTACATTGGGAAGCAGGCTGGAAATGTTCTTTCTCTTCCTACTTAACACCATTACAGCCAGTCACCTGCTTACTAGGAAGGACCATGATGTCCCAGGTCCAAGCCTGTGATTATTCAGTTGCAGGGGATGCTGACTGCTGACAGTTTGCTCCCTTTGTCAGATTGGAGCAAAGTAGGACACTATTAAGGAACTACCTATGAAAATTCCACAGGAAGAGCAACTGAGTACCTTGGTCAGCTCAGGCCCTCTCTGGGTTTTCTTGTCTCTATTACCGCTCTCCTGTCAGTGAGCATGATTCTTTTCAGAGAGCCGAGCCTCTCGACAAGTATAGAAATATTTCGTAGGATGGAGAGGATCGATCAGGGAAGGAGTGTAGCCAGGATGTGATCACTGAACATCTTGTACACAGCGTCCATGCCAAGTTTGTGTGGGTGTACACATACGCACATACATGCACACACGCTCATGGACATGGATCCCCAAGACTCTACTTGTAAATGCTTGATAAGTTTTTAACAGGACTGAGCCGAATGAACAAAACTGCCTTCACCAAGAACCACTTAAATGAGTGAGTGGCTGGCAGAAGTATGCATTAGGCCTGGCACCCGGGGACGAATGGGGATCAGTAGGAATTGGACATCCATCCTAGGAGGCAAAACAGCAGGGTTATAGAGAAGACCCATCAGGGGAACTGAGAAATAAGAGGGGCCCTGCTCAACATAGATAGATGGGAGATGGTTGGGTATAAGTATAGGATGCAGCTTCCCTATCAAGGAACGTCCACGCTAAATAGCTTTCCCTGCTCTGTATTGCCAGTGCTAACCTCTTTAGGGCTTGGAAGATAGCTAGGAGAGGTGACTAGGGACTGGTCCCTGCCCCAGGAGTGCAGAGTAGGCTGGTATGACAAGACATCTCCTTCTGATGAGCAG
Seq C2 exon
GAGATTGGGAGGATTTCCATTGAGATGCACGGCACCCTGGAGGACCAACTCAGCCACCTGCGGCAGTATGAGAAGAGCATCGTCAATTACAAGCCAAAGATTGACCAGCTGGAGTGCGACCACCAGCTCATCCAGGAGGCACTTATCTTTGACAATAAGCACACCAACTACAACATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015143:ENSMUST00000021554:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.444 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(11.6=28.9),PF0043516=Spectrin=PU(20.2=46.7)
A:
NA
C2:
PF0043516=Spectrin=FE(56.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTAGTGCCCCGGAGG
R:
TCCATGTTGTAGTTGGTGTGCT
Band lengths:
308-1245
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