HsaINT0098616 @ hg19
Intron Retention
Gene
ENSG00000177943 | MAMDC4
Description
MAM domain containing 4 [Source:HGNC Symbol;Acc:24083]
Coordinates
chr9:139750184-139750601:+
Coord C1 exon
chr9:139750184-139750300
Coord A exon
chr9:139750301-139750469
Coord C2 exon
chr9:139750470-139750601
Length
169 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
GCACCATGCTCTTCCCCTAGGGC
3' ss Score
10.36
Exon sequences
Seq C1 exon
GCACCACAGACTTTGAGTCCCCCGAGGCTGGGGGCTGGGAGGACGCCAGCGTGGGGCGGCTGCAGTGGCGGCGTGTCTCAGCCCAGGAGAGCCAGGGGTCCAGTGCAGCTGCTGCTG
Seq A exon
GTGAGGCCCAAGGCCCAAGGCTCAAGCCCCCGCCCGGGTGTGAGCAGCGTCCTCAGAGGGGTCTCTGCTCTGCCTCTGCACTACAGAGGGTCTCTGGACTGGGGATCCCTGAGGGACAGAGTGGGGCCCTGGAAGGGATGAGGCTCTGAGCACCATGCTCTTCCCCTAG
Seq C2 exon
GGCACTTCCTGTCTCTGCAGCGGGCCTGGGGGCAGCTAGGCGCTGAGGCCCGGGTCCTCACACCCCTCCTTGGCCCTTCTGGCCCCAGCTGTGAACTCCACCTGGCTTATTATTTACAGAGCCAGCCCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177943-MAMDC4:NM_206920:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.473 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062918=MAM=PU(44.6=92.5)
A:
NA
C2:
PF0062918=MAM=FE(53.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGAGTCCCCCGAGGCT
R:
TCGGGGCTGGCTCTGTAAATA
Band lengths:
238-407
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)