RnoINT0088586 @ rn6
Intron Retention
Gene
ENSRNOG00000016584 | Mamdc4
Description
MAM domain containing 4 [Source:RGD Symbol;Acc:708583]
Coordinates
chr3:2788732-2789178:-
Coord C1 exon
chr3:2788959-2789178
Coord A exon
chr3:2788870-2788958
Coord C2 exon
chr3:2788732-2788869
Length
89 bp
Sequences
Splice sites
5' ss Seq
AGGGTACTT
5' ss Score
5.15
3' ss Seq
GCTGGTCTCCCTTCCCCAAGGGC
3' ss Score
6.73
Exon sequences
Seq C1 exon
TTGCTGTTTGAAGGCCTCCGGGATGGGTACCATGGCACAATGGGCCTGGATGACATGGCTGTGCGGCCTGGCCCCTGCTGGGCCGCCAAGAGATGTTCCTTTGAAGACTCTGACTGTGGCTTCTCCCCAGGGGGCTGGGGGCTGTGGACACGCCAGAATAATGCCTCAGGCCTTGGTCCTTGGGGTCCTTGGATAGACCATACCACAGGGACAGCCCAGG
Seq A exon
GTACTTGGTCTGGTGGGGATGGGGGTGTGGTGGGGGTGGGTTTACAGAAGGCTGGTACAGGAAGCTGATGCTGGTCTCCCTTCCCCAAG
Seq C2 exon
GGCACTACATGGTGGTGGACACCAGCCCAAATTTACTGCCCAAAGGTCATGTGGCCTCTCTGACTTCAGAGGAGCACCCGCCCCTGTCCCGGCCTGCCTGCCTGACCTTCTGGTACCACCTGAGCTTCCACAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016584:ENSRNOT00000022390:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.128
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(17.4=36.5),PF0062918=MAM=PU(26.8=56.8)
A:
NA
C2:
PF0062918=MAM=FE(29.3=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:
GGTCCTTGGGGTCCTTGGATA
R:
GGATTGTGGAAGCTCAGGTGG
Band lengths:
182-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]