BtaINT0088722 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106329832-106330180:-
Coord C1 exon
chr11:106330096-106330180
Coord A exon
chr11:106330012-106330095
Coord C2 exon
chr11:106329832-106330011
Length
84 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACCCCCGCGCTGGCCCACAGAGC
3' ss Score
7.24
Exon sequences
Seq C1 exon
ATCCTCCTGGCTGGGCAGACAGGCCCGGGGGGCGTCGTGGGCCTGGATGACCTCATCCTGTCCAACCACTGCAAGCCAATCCCAG
Seq A exon
GTGAGCCTGCTGGGCACCCTCACGCCCCACCCTGGGAGAAGCACAGGCCCCGCCAACCCACCTGACCCCCGCGCTGGCCCACAG
Seq C2 exon
AGCTGGCGGGTCCACCTCCAGGGTGCTGGGCCCCAGGCCCCTGGCCCCAGCCACCCAGCCTGCGGCCTCGGAGCTTCTGCGAGCCCGGACACTTCTTCTGTGGGGACCTGTGTGTCCCCCCGGAGCAGCTGTGTGACTTCCAGCAGCAATGCCCGGGGGGTGAGGACGAGCAGGAATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:11
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=0.352
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(16.1=86.2)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=59.0)
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:
CTCATCCTGTCCAACCACTGC
R:
TTGCTGCTGGAAGTCACACAG
Band lengths:
183-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development