MmuINT0023255 @ mm10
Intron Retention
Gene
ENSMUSG00000047228 | A2ml1
Description
alpha-2-macroglobulin like 1 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128549783-128550800:-
Coord C1 exon
chr6:128550719-128550800
Coord A exon
chr6:128549940-128550718
Coord C2 exon
chr6:128549783-128549939
Length
779 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CTTTGTTGGTCCCATTACAGGCT
3' ss Score
7.35
Exon sequences
Seq C1 exon
GTTACCAAAATCACTTGTCTTTCAAAAACTATGATGGGTCCTACGATGTGTTCTGCCAGAGCAACCAGGAAGGGAGCACATG
Seq A exon
GTGAGCAATTAAAACTTTATTTTCCCCAATGGGAGGGGGTTCTCCAAGGAGAAGGAGAGAGAGCAATGGGGGGAGGGGTTTGTAAGGATGAGACTGGGAGGAGAGGAGCGAGGGGAGCTGTGATCGGGATGTACGTGAATTTAAAAATAGAAATAAGGAAGAAAAAGAAAGAAAGAAATTGAGGAGAAAGCCCTTTGTTTTCAATAATATAAGTTATTTTCTAAACAGGACTAGCAAGAAGCTGAGAGAAGCCAGGGCTCAGGGAGGGGTTTCCCAGCCAAGCGGGTTTTGAGAATAAAACCCACTGCAAACACTCACTACCAATAGCCTGATGCAGCAATATCCCCATCGTCTCACAAACTTGCTTGGCTGTCTGATCACTTAGTGACAGCTTTCTGTGATGACACAGCGTATGAGCTCCATGGCAAGTGTCACATCTTACTCTGTACCTCTCAGTCTCATTTAGATACTGGAAAGGGGAACTAGAAGGCCCCATAGTATCCTAGTTCTAGACCATACCAGTCCTGTTTCTGGGCATGTGTAATCAAATGGACTATACTGCCAGACCTTTGAGTGGCCAAAATCCACCTGCTCTATTTTCTACAGATTTGCTGTTCACCATATTTTATTGACCCCAATAAAAGAGCCACTGTCAATCAAGACTAGTTAAGTGTCAACATTAGACAAGTATGAATGCTTTACCAAAGGGAACAGTGCTGGTGAACCTGTGGCGTGGTGACATCTTCACTCTAACATTTGCTTTGTTGGTCCCATTACAG
Seq C2 exon
GCTCAGTGCCCTTTCTTTCAAGACAGTTGAGAAAATGAAGGAATATATTTTCATCGAAGAGACAGTCCCCAAACAGACGTTAATCTGGCTTGTAAAGAAACAGAAATCAAATGGATGCTTTAGAAGGGACGAGAAGCATGTCGACACGGCTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228:ENSMUST00000060574:25
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=0.170
Domain overlap (PFAM):
C1:
PF076789=A2M_comp=FE(10.9=100)
A:
NA
C2:
PF076789=A2M_comp=FE(21.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTACCAAAATCACTTGTCTTTCAAA
R:
CTCCTGAGCCGTGTCGACAT
Band lengths:
239-1018
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