MmuINT1022699 @ mm10
Intron Retention
Gene
ENSMUSG00000026941 | Mamdc4
Description
MAM domain containing 4 [Source:MGI Symbol;Acc:MGI:2685841]
Coordinates
chr2:25566452-25566823:-
Coord C1 exon
chr2:25566712-25566823
Coord A exon
chr2:25566569-25566711
Coord C2 exon
chr2:25566452-25566568
Length
143 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTCT
5' ss Score
0.28
3' ss Seq
CCTACCCCCCCCCCCCCCAGAGC
3' ss Score
10.39
Exon sequences
Seq C1 exon
CTGGAGTTTGTCAGTCTGGTGGACTTGGATGGCCCTGGCCAGCAGGGGGCTGGGGTGGACAATGTGACTCTGAGAGACTGCAACCCCATGGTGACCACTGAAAGTGACCAAG
Seq A exon
GTTTCTCTGGCCCATCTCCCATCCCTACCCAGGAGCTACTTACTACCTAGCCCACCTCTAATCCTGTCTTAGGACAGCTGGGAAGGGGGCAGACAGCAGTGCTGACCTCACCCCCCTCAACCCCCTACCCCCCCCCCCCCCAG
Seq C2 exon
AGCTCTCCTGTAACTTTGAACGGGACTCCTGCAGCTGGCATACAGGCCACCTCACAGATGCCCACTGGCACCGTATAAAAAGCCACGGCTCTCAGCTTGACCACACAACTGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026941:ENSMUST00000114223:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=NA C2=0.050
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(17.9=73.7)
A:
NA
C2:
PF0062918=MAM=PD(3.4=7.5),PF0062918=MAM=PU(22.6=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGAGTTTGTCAGTCTGGTGG
R:
GGCCAGTTGTGTGGTCAAGC
Band lengths:
226-369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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