HsaINT0042118 @ hg19
Intron Retention
Gene
ENSG00000183117 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:14026]
Coordinates
chr8:2965240-2966270:-
Coord C1 exon
chr8:2966125-2966270
Coord A exon
chr8:2965321-2966124
Coord C2 exon
chr8:2965240-2965320
Length
804 bp
Sequences
Splice sites
5' ss Seq
ACGGTCAGT
5' ss Score
8.02
3' ss Seq
TCTTTCCATTAATCATTTAGCAT
3' ss Score
5.22
Exon sequences
Seq C1 exon
GGACGGTCCCGATCAGAACTCACCCCAGCTGGGAGTTTTCAGTGGCAACACAGCCCTCGAAACGGCGTATAGCTCCACCAACCAAGTCCTGCTCAAGTTCCACAGCGACTTTTCAAATGGAGGCTTCTTTGTCCTCAATTTCCACG
Seq A exon
GTCAGTTGATTTTCACTCCGTTAGTTAAGACTGAGAATTCCATGTGGTGTTTCCTGCAGTGTTGTCCCACGCCTTGTTTCCAGCTGAAGTTTCTTGATTCAGCCGAGGGCGTGTATGATTCTTTTGCACTGGAGGCCAGCGTTTCCTGTGGTCCTTTTTTTGTTTAATGATGTCTTTATTATTTCACATCGTATCCAGCTTGGATTTATTCCAAGATACATGTATCCTAAGTGAAACTCTAAGATGAAGACCATTGAAAGAGATTTGGTACCTTTTATAGATTTACTCATCCCTGTCTCAAGATAAGGTGTTATAGCAAATGTCATGTAACTATAAATGGTGTGAAAGCAAACCTCCAATAATCCTGGGAATGCACTCTAAACGATATGTAGAACATCTGTCAATCAATCGCTTATCTCTCACGAACACTGCCACCTACAGAATTCCTCAGGACACGGGACAGGGCAGACGTTATCAAATCTGCACATGGACAGGGAGCCAGGTTGTGACTGTTGAGTCATTCTTGCAGAATTCCAAACATCTGTAAAGTGTGTTTATTTAAATGGTATACTTTAAAAAATAATTGTACACTTTTTTCCTTGGGCTTTAACTGTTTTTTGGCACTAAATAATAATATGAACATTTGAAGCTTGGGAATTTTATAAAGCTATGATTCAGGAATAGAGACATTTCAGTCCGTGTACTTAAGCATTATAACAACTGCAAGATGAATGTTTTGTAATAGTTGTGTTTATTCAGCAAGTGTAATTGCAATTATTATTATTCTTTCCATTAATCATTTAG
Seq C2 exon
CATTTCAGCTCAAGAAATGTCAACCTCCCCCAGCGGTTCCACAGGCAGAAATGCTTACTGAGGATGATGATTTCGAAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183117-CSMD1:NM_033225:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(44.8=95.9)
A:
NA
C2:
PF0008415=Sushi=PU(34.5=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACGGTCCCGATCAGAACTCA
R:
TTCGAAATCATCATCCTCAGTAAGCA
Band lengths:
222-1026
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)