HsaINT0042207 @ hg38
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr1:33533050-33533907:-
Coord C1 exon
chr1:33533796-33533907
Coord A exon
chr1:33533230-33533795
Coord C2 exon
chr1:33533050-33533229
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:ENST00000241312:62
Average complexity
IR
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
Mouse
(mm9)
No conservation detected
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