MmuINT0010414 @ mm10
Intron Retention
Gene
ENSMUSG00000015143 | Actn1
Description
actinin, alpha 1 [Source:MGI Symbol;Acc:MGI:2137706]
Coordinates
chr12:80171729-80173142:-
Coord C1 exon
chr12:80172963-80173142
Coord A exon
chr12:80171876-80172962
Coord C2 exon
chr12:80171729-80171875
Length
1087 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
GGCTTGATTCTTGCTTCTAGCAT
3' ss Score
6.09
Exon sequences
Seq C1 exon
GAGATTGGGAGGATTTCCATTGAGATGCACGGCACCCTGGAGGACCAACTCAGCCACCTGCGGCAGTATGAGAAGAGCATCGTCAATTACAAGCCAAAGATTGACCAGCTGGAGTGCGACCACCAGCTCATCCAGGAGGCACTTATCTTTGACAATAAGCACACCAACTACAACATGGAG
Seq A exon
GTAAATAGGCCTGGCCTCTTCCTAGCCTCCATTTGGGGTAGCATCTCCCAATGAATCAGGCTGGAGGAGGAGAAGGAGGGTTATGCTCTCTGCCCCTGAAACTCTGCACCTTCAATCTGCTGTACCTTCTGGATGCCAGACAACTTGTTGCAAGTATGCACATCTGGTCCCTAGCTGGAACTGAATGAGCCTTGGTTTGTAACAAGCACTCCCCAGTGATTATGATGCTATGGGCTCAAGACATCACTGGCTTAGGTACTTCCTAAATGATGTGAGCTCTTCATCCCTTAATAACAGGATATGTTCTGAGGTTTGCCTCGTTAAGTGGTCTCCTCTTTGTTCAAATATCAGAGTGTGCTTTCATTGGCTGCAGTGTTACCATGCAGCCACTTGAGACCACCGTGGTGTATTTGACTTGTCACTGATCAGAAGGCCATTATGTGGTGCCAGCTGTGTGGGTTTCCCTCAAAGGTTTATTTGTGGATGTATATGTCTGTATGTGTGGCTGCGGGGTAGGTCTTGCTGGGATGGGGGCATTCTGGTTTTTTAGCTTTTCCCACCACAAAATCTACCTTCCTTCACTAGCAGAGTTCCAATGGTAAATCCGGATCTTGTAGCTTTTTTTTTTTTTTTTTTTTTCAGGCAAAGGCCTGTTCTTTCTGGCCTCTTTCAGGCCTCCCATCCTGATAGGGTGTGATGTGTCCCTCCTGATGGTGATACTGTAACTATAGATAGAAGATCAAGTTAAATGTTTTTTTTGGTTTTTTTTTTTTTTTTGGTCTTTATCTTATGGCTATGAGTACTTTGCCTGAGTGAATGTCTGTGCACCGTGTCTGTTCCTGGTGCCGGAGAAGGCCAGAAGAGGATATATCCCCTGGAACTAGAAGTATAGATGGTTGTGAGCTGCCATAGGGGTCCTACAATTGAGCCTGGGTCCTCTGGAAAAGCAAGAAATGCTCTTAACCACTGAGACATCTCTCTAGCCCCTACTTCTGCCATGTTTGAGTTGGGAGGAGGGATAGTTAGTTGGACAGCCTGGAGCCCAGACCTGGCGCTCCTTTCTGATGGGCTTGATTCTTGCTTCTAG
Seq C2 exon
CATATCCGTGTGGGCTGGGAGCAGCTGCTCACCACCATTGCCAGGACCATCAATGAAGTGGAGAACCAGATCTTGACCCGGGATGCCAAAGGCATCAGCCAGGAACAGATGAACGAATTCCGCGCCTCTTTCAACCACTTTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015143:ENSMUST00000021554:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(56.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(20.2=42.9),PF134991=EF-hand_7=PU(31.3=53.1)
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:
ATTTCCATTGAGATGCACGGCA
R:
CAAAGTGGTTGAAAGAGGCGC
Band lengths:
310-1397
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