HsaINT0042142 @ hg19
Intron Retention
Gene
ENSG00000183117 | CSMD1
Description
CUB and Sushi multiple domains 1 [Source:HGNC Symbol;Acc:14026]
Coordinates
chr8:2807753-2808797:-
Coord C1 exon
chr8:2808636-2808797
Coord A exon
chr8:2807866-2808635
Coord C2 exon
chr8:2807753-2807865
Length
770 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
AACTGCTGATCTTTTCACAGGCA
3' ss Score
7.79
Exon sequences
Seq C1 exon
TTCCTTCAGATGTCTTTTTCGTCAATTCACTGTGGAAGGGGTATTATGAATATTTAGGGAAAAGACAACCCGCCACTCTAACTGTTGACTGGTTCAATGCAACAAGCAGTAAGGTGAATGCCACCTTCAGCGAAGCCTCGCCAGTGGAGCTGAAGTTGACAG
Seq A exon
GTAGGTCCCGAAGAATTCACTAAACGCATGGTGTGAGCAGAAATAGACCTGTTATCTTTTCACAGAGAGGTGATCTAGTAAGTATTAAGTACTTATTACTGTTCTGTTGGCTTTGTATATACTGTAACTCATTGGAGCCTCTCCCTAGCCGTGAGAGGTTGGTATTATTTTCTTATTTTAGAGATTACAAAACGAGTACAGAAAAGTGAACTGATTTGCTCAAAATTATGCACATATTAAGTCAAGAATCTGAGATTCGTATACAGATACTGCATGTCTCCAAACTTTATTTCTTAATACTTTTTCTTAACTCATGTGCTCTTCATGAGATTTTTAAAATCATCACACAATTAATAAAATAAAACAGCCTCGATTTATATGGCAAACACTATTTTAAGCACTGTATGTGTATTATCATTTTCATTCTTACATTAATTCTGTGATGTATTTTTACTGTATACTTTTTTAGAGAGAGATTTTTTAATTAGCAAAATCAAATATGTTATTTTTTATTCTTTCTGTGGAATAAGGATATTGAACTTAGTGGAGTGGATTATACCTATTCAAGATAGACAAGGATTTAAGAAGTGATTTTCAGGGGAAAATGGAAGCTCCTAAGCTAAAATTCACAAATAAAAATACAATTTCTGTTTGAGTTTTCTATTATCGATGATATTATCATCTCCGTACCACATTCCACATCAAATGGATTAAAGGGCTGAATTACTAACTTTCTCCAAGGTAAGCCTAAACTGCTGATCTTTTCACAG
Seq C2 exon
GCATTTACAAGAAGGAGGAGGCCCACTTACTCCTGAAAGCTTTTCAAATTAAAGGCCAGGCAGATATTTTTGTAAGCAAGTTCGAAAATGACAACTGGGGACTAGATGGTTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183117-CSMD1:NM_033225:66
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TCCTTCAGATGTCTTTTTCGTCA
R:
ACCATCTAGTCCCCAGTTGTCA
Band lengths:
271-1041
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)