MmuINT0094291 @ mm10
Intron Retention
Gene
ENSMUSG00000028649 | Macf1
Description
microtubule-actin crosslinking factor 1 [Source:MGI Symbol;Acc:MGI:108559]
Coordinates
chr4:123395913-123397907:-
Coord C1 exon
chr4:123397748-123397907
Coord A exon
chr4:123395998-123397747
Coord C2 exon
chr4:123395913-123395997
Length
1750 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ATGCTCTTCTTTCCTTTCAGGCT
3' ss Score
11.34
Exon sequences
Seq C1 exon
GCAAAAACAGCTGGAAGATATCTTGGTTCTGGCTAAACAATTCCATGAGACAGCTGAGCCTATTTCTGACTTCTTATCTGTCACAGAGAAAAAGCTTGCTAACTCGGAACCTGTTGGCACTCAGACTGCCAAAATACACCAGCAGATTATTCGTCACAAG
Seq A exon
GTAGGAAAGTGCTGCCATAGATGAAACAGAGCCAGAGGTAGAGACTGAAAAACTGCAGCATTCTCTAGAAGATGTTTTGTGGAGTTTTTAGTTTAAGATGAGGTCATATTAGTTGGAGAAGTTACACTGGGTTGAAGTAAAGTAGACATTGACTAATAGCTGAACATCAAAGGGGAGAGGAGCAGCTTGTGTGTTACTTCTCATATTGTTTTTGCTGTGCAGCAGGTGAATTTTTATTTTAATTTGTTCTGTTATTTGTTATTCATTGTTTCATGTTTGTTTTTCATTTACTTTTTTGTTACTCATTTTTTCCATCTGGATTTCCAGGCTCTAGAGGAAGAAATAGAAAACCATGCAACAGATGTGCACCAGGCAGTTAAAATTGGGCAGTCCCTCTCCTCCCTGACATGTCCGGCAGAGCAGGGCATCATGTCAGAAAAGCTAGACTCATTGCAGGCCCGATACAGTGAAATTCAAGACCGGTGCTGTCGGAAAGCATCCCTGCTCGAGCAGGCCCTGTTCAATGCTAGGCTGTTCGGGGAGGATGAGGTGGAGGTGCTCAACTGGCTGGCTGAGGTTGAGGACAAGCTCAGTACAGTGTTCGTAAAGGATTACAGACAGGATGTCCTGCAGAAACAGCATGCCGACCACCTGGTATTTGTGTTTTCATTCTTATGTTACTGAATTATTTTGTCATTCTGATATGTGTTCCTTTTCATTTCTTTTTCTTTTAATTTCTTTTTTCCCCTTCATTCCAAACACTTCAGCTTTATTGTGTGCATAGAATATTTATACATATACATAGTTGAGTTGTTGCCAAGTACTAGTCCTTTTTGGATAGGTCCATGAATAAATACTCGTATTTAACAAGTGAACTAATGATTCTACATTATACAGGTAAGAGGCAGGTCCATCTCAGTTGCACATTGGGTAGGTACATCAATGGATCAGTAGGTTTTCATTTGAGTAGATGAGAGCATTCTGTAACGAAACCACATATATCTGAATGGTGTCCATAATCTCATCGTGTACTTGTAACTTAATATTTGTGAAATCCAAGACATTCTGTATTGTCTTATACAATATGTCTGTTTTGATTTTTTTTAAAGATTTACTTATTTATTTATTATATGTAAGTACATACACTGTAGCTGTCTTCAGACTCTCCAGAAGAAGTTTCAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATCTGAACGCAGGACCTTCAGAAGAGCAGTTGGCGCTCTTAACCACTGAGCCATCTCTCCAGCCCTTGATCTTTTTTCAATTATGTGTCTGTGTGTATATGTGCATGTCAGATCTGTGTGGACGTGGAGGCTAGCTGCCTCGTGGTGGTGGAAATCAAACTCAGATTCTCTGGAAGAGCAGTCCCTGTTCTTCACTCCAGCCATGTTTTAGTTTGCTTCATGAAGTCTATTTTAGACACAACGCGCATTTTTGATGTATTTCCTTTCTAAACTTCTTGTGTTGGAGTTTGATATCGGTTGATTGGTAAAGCCGATTTCACCCTAAATCTTTTCCATCCAGCATGAAAGAGAGCTTGCCTATAGAGCATTTCTTAGTTGTCTTTAGCAGAGTAACCACAGAGATACAGAAAGGAATCAACTATCTGACTTTAAACTGAGCTGCTAATGGATCTCTTTAGGTGTTGTCCTTTTAAAGCGCTCAGAGTGCTTCCCTTTCTTATGCCATAGATTTGAAATTAATGCTCTTCTTTCCTTTCAG
Seq C2 exon
GCTTTAAATGAAGAGATTATTAATAGAAAGAAGAATGTAGATCAAGCAATAAAAAATGGTCAGGCTCTTCTAAAACAAACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028649:ENSMUST00000082108:56
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.105 A=NA C2=0.088
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(5.6=11.1),PF0043516=Spectrin=PU(41.1=81.5)
A:
NA
C2:
PF0043516=Spectrin=FE(26.2=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAAAAACAGCTGGAAGATATCTTGG
R:
AGTTTGTTTTAGAAGAGCCTGACCA
Band lengths:
241-1991
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