HsaINT0042177 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34088970-34090243:-
Coord C1 exon
chr1:34090119-34090243
Coord A exon
chr1:34089067-34090118
Coord C2 exon
chr1:34088970-34089066
Length
1052 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCACTCTTCTCCCTTCCCAGATC
3' ss Score
11.58
Exon sequences
Seq C1 exon
TGCCGTGTGGAGGCAACCTCACAGAGCGCAGGGGCACCATCCTGTCCCCTGGCTTCCCAGAGCCGTACCTCAACAGCCTCAACTGTGTGTGGAAGATCGTGGTCCCCGAAGGCGCTGGCATCCAG
Seq A exon
GTAGGGGCAAGGGGGCGCCTCGGTCGGGCAGGTGGCCGTCTGCTCCCAGGTAACAGCTCACAGGTGACAACCACAGGTGCTGGCTGGTGCCAAGGCCTGAGTCAGGGTGAGCCAGGAAGAGACATATCAGCCCTGTACCTGCCCCTGCGGCTAAGGAGGCTCAGTCCAAGTGTGGAGATGTGGCTCCCATGCAGAAAACACAGCAGGTTCCAGGCCCCAAGAGCTTCAGGGACATGCGGTGGGAGTCGGGTAACCCAGGAAGGAGGAGAGGTGGGCATTGATTGGCCATGGCCAGGAGGGGAGGCTAAAAGAAGAAATGGGCCTGGAGCTGGAATCTGAAGTGTGGGAAGGATTCATAGAAGTTGTTCCTCAAATGGCTAAAGATTTTCTTAAGATTGTGAGGGTTAGAAGGGGAGGCAGTGCTAATGAGAAGAAAGAGCAAAGCACCCAGCACAGCTGAAGCACAGAGAACCCCCAGGCACACACCTAGGGAACCACGCACAGCATGAGCTGTAGAAGCTGAACTGGGGGCATAACTGGTACCCAGGGGTAAGAGCCAGGCAGAGGGAGGCCCCAGCATTGGCGTCAAGGCAGGGAAGAGGGTCAGGAGCCTGCAAGGCCAACAGAGAGGCAGCAAACTGGGAGTCCAGCAGACAGATCTGGGCAGGAGTGGGTTACGGGCTCATTGCTGCAGGACGTCTGATGAAATCAAGGCAGGAAAGTGGGGAAACCCAAGGAACATTCCAGAGATGAGGAGACAGTCAGTGAGACTGTCTTTCCACTTCCTGGAACTTCTTTTCCCCATTCTCTGCCTTGCAAAATATCCACTGTCTTCTAATCATTTTTTTCCACATCTGTCTTCCCCACTGGACAACGAGCTCCTTGGAGTCGGTTCTGCATCTTACTTTTATTGAAAGGGACTAGCACAGTGTTAGGCCCAGAGTAGATTCTCAACAAATTGAATTAACTACGGGAAGGGCAGAAAGGGAAAGCAGAGAAGGAGGGAGGGACGCAGGCTGCCTAACCAACAATTCACTCTTCTCCCTTCCCAG
Seq C2 exon
ATCCAAGTTGTCAGTTTTGTGACAGAGCAGAACTGGGACTCGCTGGAAGTATTTGATGGTGCAGATAACACTGTAACCATGCTGGGGAGTTTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:35
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:
PF0043115=CUB=PU(36.8=92.9)
A:
NA
C2:
PF0043115=CUB=PU(15.0=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACCTCACAGAGCGCAGG
R:
CTGAGAAACTCCCCAGCATGG
Band lengths:
209-1261
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)