HsaINT0098626 @ hg19
Intron Retention
Gene
ENSG00000177943 | MAMDC4
Description
MAM domain containing 4 [Source:HGNC Symbol;Acc:24083]
Coordinates
chr9:139752852-139753305:+
Coord C1 exon
chr9:139752852-139752998
Coord A exon
chr9:139752999-139753170
Coord C2 exon
chr9:139753171-139753305
Length
172 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
CAGCCTCCTCTTGTTCCCAGGCC
3' ss Score
7.94
Exon sequences
Seq C1 exon
GTTCCTGTGATTTTGAGTCTGGCCTGTGTGGCTGGAGCCACCTGGCCTGGCCCGGCCTGGGCGGATACAGCTGGGACTGGGGCGGGGGAGCCACCCCCTCTCGTTACCCCCAGCCCCCTGTGGACCACACCCTGGGCACAGAGGCAG
Seq A exon
GTACGTGCCCACTGGAGCCAGGTGGGGAGGCACACACAGCCACCTGGCCTCCTGCTGCCCACCCACAGAGTACATGCCCCATCCAGAGGAGGCCCTGCTCACCGAGCCTCTGCTCGGGCCCTGAGGGCTGGCTCTGCCCATCAGCTGGGCATCAGCCTCCTCTTGTTCCCAG
Seq C2 exon
GCCACTTTGCCTTCTTTGAAACTGGCGTGCTGGGCCCCGGGGGCCGGGCCGCCTGGCTGCGCAGCGAGCCTCTGCCGGCCACCCCAGCCTCCTGCCTCCGCTTCTGGTACCACATGGGTTTTCCTGAGCACTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177943-MAMDC4:NM_206920:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062918=MAM=PU(28.3=94.0)
A:
NA
C2:
PF0062918=MAM=FE(27.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTGAGTCTGGCCTGTGTGG
R:
CATGTGGTACCAGAAGCGGAG
Band lengths:
253-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)