HsaINT0098613 @ hg19
Intron Retention
Gene
ENSG00000177943 | MAMDC4
Description
MAM domain containing 4 [Source:HGNC Symbol;Acc:24083]
Coordinates
chr9:139749389-139749790:+
Coord C1 exon
chr9:139749389-139749562
Coord A exon
chr9:139749563-139749705
Coord C2 exon
chr9:139749706-139749790
Length
143 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTGAGCCCCTCTGCCCTCAGATC
3' ss Score
10.58
Exon sequences
Seq C1 exon
CTGGTCTTCTATCAGTACCTGAGTGGGTCTGAGGCTGGCTGCCTCCAGCTGTTCCTGCAGACTCTGGGGCCCGGCGCCCCCCGGGCCCCCGTCCTGCTGCGGAGGCGCCGAGGGGAGCTGGGGACCGCCTGGGTCCGAGACCGTGTTGACATCCAGAGCGCCTACCCCTTCCAG
Seq A exon
GTAGGGAACAGCAAGAGGGTGGGGTCTGGGGAGCCGCACTGTGGGCAGGGGAGGGGAACCCACAAGGTACCCACTGCGGGTGGACAGGGACCAGACCCCAGGGGGAAATAGGCTGGGCACCCCCTGAGCCCCTCTGCCCTCAG
Seq C2 exon
ATCCTCCTGGCCGGGCAGACAGGCCCGGGGGGCGTCGTGGGTCTGGACGACCTCATCCTGTCTGACCACTGCAGACCAGTCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177943-MAMDC4:NM_206920:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.086 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062918=MAM=FE(36.8=100)
A:
NA
C2:
PF0062918=MAM=PD(16.1=86.2)
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:
TCAGTACCTGAGTGGGTCTGA
R:
GACTGGTCTGCAGTGGTCAGA
Band lengths:
244-387
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)