BtaINT0088725 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106328679-106329494:-
Coord C1 exon
chr11:106329363-106329494
Coord A exon
chr11:106328796-106329362
Coord C2 exon
chr11:106328679-106328795
Length
567 bp
Sequences
Splice sites
5' ss Seq
GAGGTACCA
5' ss Score
6.43
3' ss Seq
CCACCTCTGCCCGCCCCCAGAGG
3' ss Score
9.24
Exon sequences
Seq C1 exon
GGCACTTCCTGGCTGTGCAGAGGGCCTGGGGGCAGCTGGCCGAGGAGGCCCGGGCGCTCACACCCACCCTTGGCCCCTCGGGCCCCCGCTGCGAGCTCCGCCTGGTTTACTATCTGCAGAGTCACCCCCGAG
Seq A exon
GTACCACCATCCCTTTGCGCCCTCTGCCCCGTCCTGGGGTGGGGGGTCAGAGCCCCCGGGCGAAGGACAGGGGCAGGACGGGCGCCCACAGTGATCCCTTGCCAGGCTTCCTGGAGCTGCTCGTGGTGGAGGGCAGCCGCCGCGAGCTGGTGTGGCAGGCCCTGGGCACCACCGCTGGGGGCTGGAAGGTGGACAGGGTCCTTCTCGGGGCTCGCCGCCGGCCGTTTCGGGTGAGGAGAGCGGCCTGGGGCAGAGAGGGGCCCCCGCGGGGCCTGCCCTGGCTGACGGCCTCCTCCCTCATGCCCCACGAAGCTGGAGTTGGTTGGGCTGGTGGATTTGGACGGCCCCGGGCAGCAGGGCGCAGGGGTGGACGACGTGACCCTGACGGGCTGCAGCCCCACAGCAGCCGCTGAGGAAGACTCAGGTGCTTCCCCCGGGTGCCCGGCCCCCCACCCAGGCCTCCTCGAGGGGCCCCCAGGAGCCCCCTCTCCAGGAGCCAGTCTCCCCGACCCTCTCGGCACTCAGGAGGGGTGTCGGGGGTGCTGACCCACCTCTGCCCGCCCCCAG
Seq C2 exon
AGGTCTCCTGTAACTTTGAGCGGGGGGCCTGCGGCTGGCACACCGGCCACCTAACAGATGCCCACTGGCACCGGGTCGAGAGCCGTGGCCCGAGGTACGACCACACCACGGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.233 A=NA C2=0.275
Domain overlap (PFAM):
C1:
PF0062918=MAM=FE(51.2=100)
A:
NA
C2:
PF0062918=MAM=PD(1.2=2.5),PF0062918=MAM=PU(23.2=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CACTTCCTGGCTGTGCAGAG
R:
TTGGCCCGTGGTGTGGTC
Band lengths:
246-813
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development