MmuINT0023260 @ mm10
Intron Retention
Gene
ENSMUSG00000047228 | A2ml1
Description
alpha-2-macroglobulin like 1 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128578734-128580479:-
Coord C1 exon
chr6:128580323-128580479
Coord A exon
chr6:128578787-128580322
Coord C2 exon
chr6:128578734-128578786
Length
1536 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CAGTATCCCCTTTTCCTTAGTTC
3' ss Score
5.5
Exon sequences
Seq C1 exon
GTGTCTCAGATGTCCTCAGAGCAGTTGGCCTTTGTGGCATTACTTGTTCAGGGAAACACTCTTAAAATCTCTGAGAGAAGATCTGTGGCCATCGCTGCTGAGGAGAACGCCACTTTTGTGCAGACAGACACACCGGTCCATAAACCTGGAGACACAG
Seq A exon
GTAAGTTACTTTAAAAAAAAAAACACTTTCTCCAAGTTAATGTGTAAAATTGAGTAAAACTTGTCTTTATCATCACTGACTGCTGCATTTCCATAGTTCCTATAGCTATGAGACAGTGCTGTTAGAGCCGGGAGCTTGGGCATGGCTTCATAAGACTCTGTGTGTTCTTTGATTGTACACAAATCCTACTGACAAGGCTTCATAGTACAGTGGTTACCAGAATGCAGAGTTATAATTGTTTGATCTAAACCAAAGATCCATTACATACCCATTGGACAAGCTCATTAATTCTCCTTTTCAAGCCAATTATTCCATTCTTAAGGTAGAGATAATGAAAGTTTCTTTGAACTTTCAGGGAAGAAATGAGAGTCATTGTAAAAAAAAAAAAAAATAGTGCCAATAACAGCAAAGACCTCACCAGCAACATTTAGGAATTCTACTGTTCCATTTTTATGTCAATTGGTCTAGCAGGAGAAAGTCAGCCAGAGCCTTCCGCTTTCTTAACTATTGTTCTAAGCAGAATGTGCCATAAAGAATACCAAGCTAGAATTCAAAGCCTCTTGCTTCAAAGCTTAGCTCTGTTGACCAGTGATTGACTCTTGGCAAGTAAATTCTGGTCCTTGAGATATAATTTCTTCATCTGTAAAATGAAAGGGCTAGAGATGAAAAAGCCTGTGCATTGTATCCTGATTCATATTGTCTATGACTTAAAAAAAAAAAAAGAAAGAAACAAAAGACTGAAAGTAGAATTTATTTTGGCTTAAACAATAGACACATAGACACATACTTCTGGCAGCTGAAGAAACTGCCGATATGAAAGTGCCGGGGGTTGTTTCCTCCAAAGATTCTCTGCTGTACTCTGACTGATGTGACTGTGTCTGAGGCAGGGGAATTCCTCCAAGGAGTCTGTACTGTACTATAAACGGCCGGCTTATGAAGGCTTCTTTCCTTTTTCTTTTATAATTATTTTTAAGTCAGCTCACAAAGCAGTGCATTTCATTATGATATTTTCACATTTAATATTGCAAAGATAATTCTTAAAGGGAGATTTTTACTTCCTGATACTCCCTTTTCTGCTCTTGTTAAAATATTAGAATAAACTGTATATTTTAAAGAACCGACATCTTTTGTAGTTCTGCTAAAATAGCTTAATTTTGCTAGCATTGTTCTCAAGGAAAATTATACTTGTTCATTTCCATAAATGTCTGACATTTATGCTTCTATGGATAAGTCTGTCACTAATTCTGTTCCAGGCTATCTCAGTCTATGTCTGATAGGGTAAAAGCTTCTAAGGGCAGCATTGGGGACAACAAGAATCATTAAGAGAGGAATAATAAATACAAGTTGATATTTTCCCCCAATGAACTCCTAACCTGAAAAGGTGAAATCAGAGCTAGAGGGAAAGGAATGTGACGGGCAAGCTTGCCCATCTTGTGATGGGCAAGCAATTACTTATGTATATATCTTAAAGCAATCATCGCTATAAGGTGGGGATCACAAGAAATCCACTTTACAGCAGTATCCCCTTTTCCTTAG
Seq C2 exon
TTCACTTTCGCGTTGTGACACTGAACATCTGGCTGAAGCCTGTTGATGACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228:ENSMUST00000060574:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0183514=A2M_N=PU(17.0=30.2)
A:
NA
C2:
PF0183514=A2M_N=FE(18.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCTCAGATGTCCTCAGAGCA
R:
CAAGTCATCAACAGGCTTCAGC
Band lengths:
209-1745
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