MmuINT0010425 @ mm9
Intron Retention
Gene
ENSMUSG00000015143 | Actn1
Description
actinin, alpha 1 [Source:MGI Symbol;Acc:MGI:2137706]
Coordinates
chr12:81284380-81285886:-
Coord C1 exon
chr12:81285794-81285886
Coord A exon
chr12:81284611-81285793
Coord C2 exon
chr12:81284380-81284610
Length
1183 bp
Sequences
Splice sites
5' ss Seq
GATGTGGGT
5' ss Score
2.02
3' ss Seq
CCTCTGTTTTGCCACTGTAGCTG
3' ss Score
7.58
Exon sequences
Seq C1 exon
GCAGAAACAGCAGCCAATCGCATCTGCAAAGTGTTGGCGGTCAATCAAGAGAACGAGCAGCTTATGGAAGACTATGAGAAGCTGGCCAGTGAT
Seq A exon
GTGGGTACCCCTCTGTTCTACCTTGGCCCCAGCTAGGCCATGTATGACACCCTGAGAGAGTGAAGCTCCCAGGATCTGTACCTGTATTGTCATTCTGTGGGCACAGTCCCAGGCTGGTGTAGTGCATGATCCAATCACAGTTAACACAGGGCAGCTTGGTTCTGGGCCTCTGGGAGAGCAGAAGTGAAAACAGGAAAGATGGTCTCTGGGCTACAGTGGGCCTGGGAAATGCCTTCGCCTCTCTGGCTCTTGCTTTTTCTTTCACTTACTGAATGGGAGTTGAGACCTGGGATCTTAGAAGCATTTGCAGTCTGGTAAACTGCCCCTTGGGAAGTTTTGCCTGAACTACATAGTACAGGGCTATGCCAAGTACTTAGAAGACATGTGCCTGAGAGGGCTCAGTACTGTCTCAGGCTTGGTACTTAGCAGTACTTAGTACTTAGTAGTCAGGCCAGCAGGGGACAGGATGGGAAGCAGTCGATCAGCTGACCAGCTACCATTTGGGCTAAGGTGCTTCTTCCGTGACAGAATCCAGCCCTTTGACCTGCTCCCCTGGCCTTTCGGTGGCTTTGCCCTCCAGCTGAGTGAGAGCCAGTTGCCCTGGCTTTAATCCCTGCTTCACTGCTTCAGCCAGTCACCACAGCAGGCTGCGTGACCTGGCAGAGCCTTGGGCGCCTCCTCCATAGTGTGGGGGTGATAGTAGCACTTGACTATGTAGTATTCCTGTGAGTCACTTTGTGGGTCATGCCTGGCATCATGCAGGTGTTCGTATGCTTCCTGTCATCCATCCTGGATCTTCTTCCTCTCCCTCACCATGGCTCCAGGCTAGAAATATAGGCTGTCCCAGAAGCCAGCCTCTTTCTTTTGGAGCCAGAGGTTCCCATTCTATTACACCCCTGCTTGGTGTAGATGAAGAAACTGAGGCCTGGCTAGACTTAAGCTCAGGTCTCCTTGCTCTTAGAGAATCCTGTGGTTCTTTGGTTCTTCCCGTATCAGGGCAGAGAAGATGAGGGGTGTGGGCTCTGAATTGACCATATCCTGGTCAACTTGGAGGAAGCACCCAGAAGCCTTGCTGCAAGCCATGGTGAGGTCTTTGTAGGTAATTGGAAGGGAGAGTGGAAGAAAGGCAAGCTGGCCTTTGCGCATCCTTACCCTGTGCCTTTCCTCTGTTTTGCCACTGTAG
Seq C2 exon
CTGTTGGAGTGGATCCGCCGCACCATCCCATGGCTGGAGAATCGGGTGCCTGAGAACACCATGCATGCCATGCAGCAGAAGCTGGAGGACTTCCGAGACTATAGACGCCTGCACAAGCCGCCCAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTTAACACGCTGCAGACCAAGCTGCGGCTCAGCAACCGGCCTGCCTTCATGCCCTCCGAGGGCAGGATGGTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015143-Actn1:NM_134156:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.242 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PU(9.9=35.5)
A:
NA
C2:
PF0043516=Spectrin=FE(68.5=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:
GAAACAGCAGCCAATCGCATC
R:
GACCATCCTGCCCTCGGAG
Band lengths:
318-1501
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: