HsaINT0098634 @ hg19
Intron Retention
Gene
ENSG00000177943 | MAMDC4
Description
MAM domain containing 4 [Source:HGNC Symbol;Acc:24083]
Coordinates
chr9:139748444-139748788:+
Coord C1 exon
chr9:139748444-139748528
Coord A exon
chr9:139748529-139748662
Coord C2 exon
chr9:139748663-139748788
Length
134 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGG
5' ss Score
5.74
3' ss Seq
GTTAACCCTGCCCCACCCAGCCC
3' ss Score
3.73
Exon sequences
Seq C1 exon
GTGACCTTCTCTGCCACCCGAAATGCCACCCACAGGGGCGCTGTGGCTCTAGATGACCTAGAGTTCTGGGACTGTGGTCTGCCCA
Seq A exon
GTAAGGCACCGCCTCTTCCTGTTCCACCCCCGGGAGGGCCCCCACCTGCCCACTCCCCTGCTCAGACCCTGTCTGCCCCCGAGTGCTCTCCCACTCCTGGGGCCTCGGTGAAGGGTTAACCCTGCCCCACCCAG
Seq C2 exon
CCCCCCAGGCCAACTGTCCCCCGGGACACCACCACTGCCAGAACAAGGTCTGCGTGGAGCCCCAGCAGCTGTGCGACGGGGAAGACAACTGCGGGGACCTGTCTGATGAGAACCCACTCACCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000177943-MAMDC4:NM_206920:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.140
Domain overlap (PFAM):
C1:
PF0062918=MAM=PD(16.6=89.7)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=90.7)
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:
GTGACCTTCTCTGCCACCCG
R:
ACAGGTGAGTGGGTTCTCATCA
Band lengths:
210-344
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)