BtaINT0088726 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106328429-106328795:-
Coord C1 exon
chr11:106328679-106328795
Coord A exon
chr11:106328564-106328678
Coord C2 exon
chr11:106328429-106328563
Length
115 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AGCGCCTTGCACCCCCACAGGCC
3' ss Score
7.59
Exon sequences
Seq C1 exon
AGGTCTCCTGTAACTTTGAGCGGGGGGCCTGCGGCTGGCACACCGGCCACCTAACAGATGCCCACTGGCACCGGGTCGAGAGCCGTGGCCCGAGGTACGACCACACCACGGGCCAAG
Seq A exon
GTAAGCCAGGGTGCCCAGGGGGCAGCTGCTAGACCCCGCCTGCTGGAGGCAGAGAGGAGCGCGGGGCTGAGCCCTCCAGCCTGGGCCCACAGCCCAGCGCCTTGCACCCCCACAG
Seq C2 exon
GCCACTTCGTGCTCCTGGACCCCGTGGACCCCCCAGCCCGGGGCCCTGCTGCCCACCTGCTCACCCAGCCCAGGGTGCCCTCAGCCCCTCAGGAGTGCCTCTCCTTCTGGTTCCACCTCTTCGGGCCCCAGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.275 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(1.2=2.5),PF0062918=MAM=PU(23.2=90.0)
A:
NA
C2:
PF0062918=MAM=FE(29.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTCTCCTGTAACTTTGAGCG
R:
CCCGAAGAGGTGGAACCAGAA
Band lengths:
242-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development