HsaINT0042216 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34285314-34286157:-
Coord C1 exon
chr1:34286070-34286157
Coord A exon
chr1:34285439-34286069
Coord C2 exon
chr1:34285314-34285438
Length
631 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
AGACACACTTTGTCTCCCAGGTT
3' ss Score
5.79
Exon sequences
Seq C1 exon
TAACTCAGGTTGGTGTGTCCCAAGGACATAATATGTGTCCAGACCCTGGCATACCCGAAAGGGGCAAAAGACTAGGCTCGGATTTCAG
Seq A exon
GTAAGATCTATTTGGGAATTTTCTGATTGCAAGAAGGGTGGGGTGGCCTGGCTGGGAGGAAGACAGGGGCTGGCCTTCCTGCAGGTGGAAATGGAGAGGATGGCATGGATATAGGAACAGACACTTCCTGGAGAAGAGCTATGGCTTTGACATTCTCTCCTGGTTCAGTCCTTGGCATAGTGCCCATGCTTTAGTGGGGGGAGAGAACTGTAGACTGCCAGTGTTATCCAGAAAACCTATGTACCCAGGGTACAAAGGGCTGCCATCTCAGTAATGACACGCCAGAAGGCAACTCGCGCCTGCAATAATCTAGGAGACCATTTTCCTTAAAGTTTATGGGTATCATCCACCCACGCTTAGCTGCCCTAACTGGTGCTTATCTCAGAGGATCGCTGTTTTGCTCACAAAGTCACCTTTTAACTCAATCCTAAAACCATTAAACAGTCCGAAAAAAGAAGATGAAGAGCAGATGTTCCTTCCAATGGAGATTTTTAGTGATAAAACAGTGGAGCAGAGATTAAGGGCCAGAAGGAAAAATAACATGTGCGGCTTCTTTGTGGAACCAGGAAGGACTTGGGGCGGGGCTTGGCAGGCCCAGGGATGGAGCTCACAGACACACTTTGTCTCCCAG
Seq C2 exon
GTTAGGATCCAGCGTCCAGTTCACCTGCAACGAGGGCTATGACCTGCAAGGGTCCAAGCGGATCACCTGTATGAAAGTGAGCGACATGTTTGCGGCCTGGAGCGACCACAGGCCAGTCTGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.420 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(29.3=56.7)
A:
NA
C2:
PF0008415=Sushi=PD(69.0=93.0)
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:
CTCAGGTTGGTGTGTCCCAAG
R:
GCAGACTGGCCTGTGGTC
Band lengths:
206-837
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)