BtaINT0088742 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106331163-106331489:-
Coord C1 exon
chr11:106331405-106331489
Coord A exon
chr11:106331289-106331404
Coord C2 exon
chr11:106331163-106331288
Length
116 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGG
5' ss Score
5.74
3' ss Seq
TGGGTTAACCCTGCCCCCAGCCC
3' ss Score
5.71
Exon sequences
Seq C1 exon
GTGACCTTCTCTGCCACGAGAAATGCCACCCACAGGGGCACTGTGGCCTTGGACGACGTGGCCTTCTGGCGCTGCGGGCTGCCCA
Seq A exon
GTAAGGTCCCCCGGCCGTGGGCCCACTCCTGGAGCGGGGAGGGGGTCAGCAGGAGGCCCTGGTCAGTGGCCCCGCCTGGGGACTTGGGGCAGGTGATGGGTTAACCCTGCCCCCAG
Seq C2 exon
CCCCCCAGGCACACTGCCCCCGGGGGCACCACCGTTGCCAGAACGAGGCCTGCGTGGAGCCCGCCCAGCTGTGCGACGGGGAGGACAACTGTGGGGACCATTCGGATGAGGATGCGGCCCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:6
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=0.070
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(16.6=89.7)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=90.7)
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:
TGACCTTCTCTGCCACGAGAA
R:
GCCGCATCCTCATCCGAATG
Band lengths:
202-318
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development