HsaINT0042207 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:33998650-33999507:-
Coord C1 exon
chr1:33999396-33999507
Coord A exon
chr1:33998830-33999395
Coord C2 exon
chr1:33998650-33998829
Length
566 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
GGGTCTTTCCTCTCATCCAGCCC
3' ss Score
7.53
Exon sequences
Seq C1 exon
GTTGGAAGCACAGTCCTCTTCCGTTGTCAAAAAGGCTACCTGCTTCAGGGCTCCACCACCAGGACCTGCCTCCCAAACCTGACCTGGAGTGGAACCCCACCTGACTGTGTCC
Seq A exon
GTGAGTGCAGACTTCACCCACATCCCAAGAAAATTCCTCTTGCCCCAGCTGGGCATCTGGGTCATGTTTGAATGCTCTGAATGACAGGGAGTTCACAACTCCCCATGCGAACCGACATCGGTCTCTTTGTAGTCCTTACACTTTGGGGCCTCACAGAAGACTTCCACACAAAAGCCTTTCTGATATTGGAAGGCAATCCCTATGCCTTAGCAAAGAAAAAACTATCCAGTGGCAGCAGCAAAAACTAACAACTGCAAGGCCAGGCCTCAGGATGGAGATATCAAGCTTTTGACCCAGTTACTCCTTTACCCCTCAGGAAGTGCTGCAGGCTTAAGTTCCCCCAACTCAGAGTCAACCAAGCCGATATCCACATGATCTCCATCTTGGCCATTCCTCTAGACACAGAGCTTGGGTTAGGGTGGAGGATTAGGGAGGGGGATGCTTGGCATGAAAGGGACTGGAAGGGAAAGGAAGAGGATATTCTATCTAGGAACAGGGGAATGGTCGAAAGGGCCCCTGAAGCCCCTAATCTCCTCCAGTCCAACAGGGTCTTTCCTCTCATCCAG
Seq C2 exon
CCCACCACTGCAGGCAGCCAGAGACGCCAACGCATGCCAACGTCGGGGCCCTGGATTTGCCCTCCATGGGCTACACGCTCATCTACTCCTGCCAGGAGGGCTTCTCCCTCAAGGGTGGCTCCGAGCACCGCACCTGCAAGGCGGATGGCAGCTGGACAGGCAAGCCGCCCATCTGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:62
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.246
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PD(63.6=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGAAGCACAGTCCTCTTC
R:
GGCTTGCCTGTCCAGCTG
Band lengths:
278-844
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)