BtaINT0088728 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021550 | MAMDC4
Description
Bos taurus MAM domain containing 4 (MAMDC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001143873]
Coordinates
chr11:106327873-106328286:-
Coord C1 exon
chr11:106328150-106328286
Coord A exon
chr11:106328081-106328149
Coord C2 exon
chr11:106327873-106328080
Length
69 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GACCTCTCTCTGCCCCCCAGCTG
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGACCCTACGCCTGGCGATGAGGCGAGAAGGGGAGGCAGAAACGCACTTGTGGTCGCGGTCTGGCACCCACGGCAACTGCTGGCACGAAGCCTGGGCCACCCTCCACCACCAGCCGGACTCGGGCGCCAAGTACCAG
Seq A exon
GTGAGGCCCAGGGCGTGGGTGCGGTGGGTGAGGCGAGGCCCCAGCCGCTGACCTCTCTCTGCCCCCCAG
Seq C2 exon
CTGCTGTTTGAGGGCCTCCGGGATGGGTACCACGGCAGCATGGCACTGGACGATGTGACCCTGCGGCCCGGGCCCTGCTGGGCCCCCAGGCGCTGCTCCTTTGAGGACTCAGCCTGTGGCTTCTCCGTGGGGGGCCGGGGCCTCTGGACACGCCAGGCCAACGCCTCGTGGGGCCCCCACGCTGACCACACCACGGAGACAGCTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021550:ENSBTAT00000032582:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0062918=MAM=FE(29.0=100)
A:
NA
C2:
PF0062918=MAM=PD(17.4=38.6),PF0062918=MAM=PU(24.8=54.3)
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:
GAGAAGGGGAGGCAGAAACG
R:
GTCACATCGTCCAGTGCCATG
Band lengths:
172-241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development