MmuINT0010411 @ mm10
Intron Retention
Gene
ENSMUSG00000015143 | Actn1
Description
actinin, alpha 1 [Source:MGI Symbol;Acc:MGI:2137706]
Coordinates
chr12:80174460-80176296:-
Coord C1 exon
chr12:80176156-80176296
Coord A exon
chr12:80174643-80176155
Coord C2 exon
chr12:80174460-80174642
Length
1513 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TCATGCCATGGTCTATCTAGGGA
3' ss Score
6.1
Exon sequences
Seq C1 exon
CGAACAGAGAAGCTGCTGGAAACCATCGACCAGCTCTACTTAGAGTACGCCAAGAGGGCTGCACCCTTCAACAATTGGATGGAGGGAGCCATGGAGGACCTGCAGGACACCTTCATCGTACATACCATCGAGGAGATCCAG
Seq A exon
GTGGGTAACTCCAAGAGTCTGGTCCTTCTTAGGATAAACTGAGGGGCAACGTCCTAAGGGTTCCATAGATTAATAGTGTTAGCATATGAGGTCACGCGTTTGTAAAGATTTCTTTATTTTTATGTTGTGTATATGGTTGTTTTGCCTGTCTGCATGCATGTACACCACTTACATATAGCACCCAGACTCCCCTGGTACTAGAGTCTCAGGTGGTTGTTGGTAGTCATATGTGTACCGGGAACGGAACATTGGCCCTCTGTAAGAGCAACAAGTGCTCTTAACTGCTGAGTCATCTTTCCAGCCTCTTACCCCTACAGGATCTTTGTATCCACTATGTGCTTCTGGGAAGTCTGGAGCACATTATCTATACCATGCTGGCCTCAAACTCACAGAAATCCTCCTGCCTCTGCTGCCCAAGTGCTGGGACTAAAGGAGTATGTCTTCATACCCAGTCCAGCACTTGAATTATTTTGATAAGGTATATATGTGTGTTGTGTGTGTGTGTGTGTGTGTGTGTAGTACAATATCTTTTTTTTAAAGATTTATTTATTATTTATTATATGTAAGTACACTGTATCTGTCTTCAGACACACCAGAAGAGGGAGTCAGATCTCGTTACGGATGGTTGTAAGCTACCATGTGGTTGCCAGGATTTGAACTCAGGACCTTCAGAAGAGCAGTCGGGTGCTCTTACCTGTTGAGCCATCTCACCAGCCCCGTAGTACAATATCTTAAAGATAAAGGGGTGCTAAGGCAAGGTTTCTTTCCCATAACTCTTTCTGGCCCCCTGTTCCCCTTTCCAGGGCTAAGTAGTATGATTAGAGTCTCTGTGTATACAGACAAATGCATTTATCTATGTGTTCTTTGTACCTTTTCTTTTGTGCACACAAAAATGTAGACTTTATTATATACCATATCCTAAATCTTGAGTTCTAACATTAACCTTGGAGCTCCCATTGGCTCCCATCTTCCTCAATCTTTTATGTCACTATAGAGTATTAGATTAAAAAGTTTGCAGGGACTAAGGATATAGCTCAGTTAGTAGCATGCTTGCCTAGCATACATGAAGCCCTGAGTTCAGTTCCAACCATTGCATAAAATGAGTATGTTGATGCATGTCTTTAATCCTAACATTCTCAAGGTAGAGGAAGGAAGAGGGATTTTTGCAGGAAGATGAAGGAGCTAGTGTTATAAGAGGTTCCCTAGGAAGCAGGGCTCGCCCCACCCCCACATGACTGATCTGATGGTATGGTGTTGAACATTCCCAGTGGTGACAACTGAGTGTACCAGCCCTCAACTCAGAACACAGCTGTTTCCTGGCTGGCTCTGCCTTTGCCTTTCTCAGGCTAGCCTGCCTTGCTGGTTCTCTGCCATAAGAACCTGGTTTGATGCCTCCAGCTCTTCACTAGGTGTGGGACTTGCTACCTCTTAGATTCACTTCGTTTACTGTGTCTGAGGAGAGGAGCCCTTCCTCCCTTGAGTCTCAGTACTAATCATGCCATGGTCTATCTAG
Seq C2 exon
GGACTGACCACAGCCCATGAGCAGTTCAAGGCCACCCTCCCGGATGCAGACAAGGAGCGCCTCGCCATTCTGGGCATCCACAATGAAGTGTCCAAGATCGTCCAGACCTATCATGTCAACATGGCAGGCACCAACCCCTATACAACCATCACGCCTCAGGAGATCAATGGCAAATGGGACCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015143:ENSMUST00000021554:14
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=0.213
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(0.1=0.0),PF0043516=Spectrin=PU(32.1=76.6)
A:
NA
C2:
PF0043516=Spectrin=FE(53.6=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:
CAGAGAAGCTGCTGGAAACCA
R:
TGGTCCCATTTGCCATTGATCT
Band lengths:
319-1832
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