MmuINT0094691 @ mm10
Intron Retention
Gene
ENSMUSG00000026941 | Mamdc4
Description
MAM domain containing 4 [Source:MGI Symbol;Acc:MGI:2685841]
Coordinates
chr2:25565711-25566156:-
Coord C1 exon
chr2:25566020-25566156
Coord A exon
chr2:25565931-25566019
Coord C2 exon
chr2:25565711-25565930
Length
89 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTACCACTCTCCACCCTCAGTTG
3' ss Score
8.88
Exon sequences
Seq C1 exon
GGACACTGTGCCTGGCCATGAGGAGGGAGCGGGAGGAAGACATACTACTGTGGTCCCGGTCGGGCACCCATGGCAACCGCTGGCACCAGGCTTGGGTCACTCTTCATCACCAGCCAGAGGCCAGCACCAAGTACCAG
Seq A exon
GTGAGGGCAAGCTTAGCACTTGGTAACAGTGTAGGGTCGCCCCACCACCACCACTACCCCCCCTGCCAATTACCACTCTCCACCCTCAG
Seq C2 exon
TTGCTGTTTGAAGGCCTCCGGAATGGGTACCATGGCACAATGGCCCTGGATGACATAGCTGTGCGGCCTGGCCCCTGCTGGGCCCCCAAGAGCTGTTCCTTTGAAGACTCTGACTGTGGCTTCTCCCCAGGGGGCTGGGGTCTGTGGACGCACCAGAGTAATGCCTCAGGCCTTGCTTCTTGGGGTCCTTGGATAGACCATACCACAGGGACAGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026941:ENSMUST00000114223:19
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=0.000
Domain overlap (PFAM):
C1:
PF0062918=MAM=FE(29.0=100)
A:
NA
C2:
PF0062918=MAM=PD(17.4=36.5),PF0062918=MAM=PU(26.8=56.8)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GGAGCGGGAGGAAGACATACT
R:
AGCTATGTCATCCAGGGCCAT
Band lengths:
172-261
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