MmuINT0010418 @ mm10
Intron Retention
Gene
ENSMUSG00000015143 | Actn1
Description
actinin, alpha 1 [Source:MGI Symbol;Acc:MGI:2137706]
Coordinates
chr12:80167547-80169016:-
Coord C1 exon
chr12:80168858-80169016
Coord A exon
chr12:80168481-80168857
Coord C2 exon
chr12:80167547-80168480
Length
377 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
TGACCATGCTTTCTCCGCAGAAT
3' ss Score
12.12
Exon sequences
Seq C1 exon
GGAGAGGCAGAGTTTGCCCGAATCATGAGCATTGTAGACCCCAACCGCTTGGGGGTAGTGACGTTCCAGGCCTTCATCGACTTTATGTCCCGAGAGACGGCAGATACTGATACTGCAGATCAGGTCATGGCTTCCTTCAAGATCCTGGCTGGAGATAAG
Seq A exon
GTAGGATGTGCTGACGCTGAGACAGTGGGTGGTTACTGTAAATCGGTAGGATGAATGAAAAAGTCCGAGTGAAATAGGTTTGGAAGGAAGTTGAAGTAGATACTAAAATGGAAAACGTGACGTGTTTAAAATACCATATACAAGTGATATATTACTTGTAAATATATAATATGCACTTAAATATATATATGTACATACACACGGATGTCTCTGTTATATGTATGCACGCACGTATTCTACAGATCAAGTAGAGCGAGGAAATTAGAACACGGGTACTTAACATTCCCGGCAAGTTTACGACCTAATAGTTGCGGCAACGCCGCGTTGCTTTCCGGCCGCTGCCGAGGTTTCCGACCCTGACCATGCTTTCTCCGCAG
Seq C2 exon
AATTACATCACAGAGGATGAGCTGCGCCGTGAGCTGCCCCCTGACCAAGCCGAGTACTGCATCGCAAGAATGGCCCCCTACGCGGGCCCCGACTCCGTGCCCGGTGCTTTAGACTACATGTCCTTCTCCACGGCACTGTATGGCGAGAGCGACCTCTAACCCGCCCCTGCCTCCCTCCACCACCCCCCCACCCCCGGCCTTCTGCGCGTGCGCCCCACCCTGCTCCTCCTCCTCCTCCGCCCAGTCTGGCTGGCTGGGTTCATTATTTTCAGCTCAGCCACCAAGGGGGCAGAGCTCCGACCCAGGCGGCATCAAGCCTCCCTGCCCACAAAGTGACAGTTTACAAAATTATTTTCTGCAAAAAAGGATAAAAAAAAAGTTACGTTAAAAAAAAATTTTAAAAAGAAAAAAAAAAACAAACAAAAAACTACATATTTTATTATAAAAAAAAAAGTATTTTTTTCTCCACCAGTCTTAAATGGAAAAGAGGAAAAATTAACTATTTGCACCGAAATGTTTTTGTTGTGACATAGGAAAATAACCAAGCACAAAGTTATATTCCATTCTTTTTACTGAAGTTTTTTCCTCCTACCTGTTCTGTCTGCTGTATTCATTTCTCTAATTTCATGCCCACTTGGGGGTGGGGTAGGTGGGTACTCTCATCAGAGGCACATTGGTGCATGTGTGTTTGCTAGCTCACTTGTCCATGAGAATATTTTATGATATTAAAGAAAACCTTTTGAAATGGCTGCTTTTCAAAGAAGATAATTCATGGCTTCTCATTTTTCAGTCTCTTCAAAAGTGTGGCTGGCCTGTTTTATGACTGCAGAGTTGTTATGTTTTTTAATTTTGAATATTGCCTATTAAAGATAGGACAAACTTGGAGATTATGATGTTGCTTGGCACAGACTGTATTAAAACAACACTCCCGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015143:ENSMUST00000021554:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.077
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(33.7=52.8),PF087265=EFhand_Ca_insen=PU(26.9=34.0)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(70.1=88.7)
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:
CGACTTTATGTCCCGAGAGACG
R:
TAATGAACCCAGCCAGCCAGA
Band lengths:
347-724
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