HsaINT0042187 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34066465-34068146:-
Coord C1 exon
chr1:34067969-34068146
Coord A exon
chr1:34066611-34067968
Coord C2 exon
chr1:34066465-34066610
Length
1358 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGC
5' ss Score
6.99
3' ss Seq
ACCTTGTTTCCTGTGTACAGGGA
3' ss Score
8.98
Exon sequences
Seq C1 exon
TCCCTTGTGGCGGGAACATCACTTCTTCCAACGGCACTGTGTACTCCCCGGGGTTCCCTAGCCCGTACTCCAGCTCCCAGGACTGTGTCTGGCTGATCACCGTGCCCATTGGCCATGGCGTCCGCCTCAACCTCAGCCTGCTGCAGACAGAGCCCTCTGGAGATTTCATCACCATCTG
Seq A exon
GTAGGCCAGGTGCCATGTCAACAGCCAATTAGAAAGGAGCATTACTGGGGTTCTACACTGGGTTACCAGTCAGTTACCTATTGGTTTAGAAAAACCAAGAGGTGAATGGTTTTTAAAGGCTGTCAGCCTCCTGGGTTTCAAATAAACATAGTGGAATGGGGCTCAGCTCCAACTGGCCATTATGGCTCCTTAAAGGGAGAGGAATGGGAGGGCAGTGGCTCCCAGCCTGCAACCCTGCCAGGGCCAGGGAAAGTACCAGTGGGTGTGTTAATGGGAGTAGGTGTGGGTACACAGACTTTCCTCGGTATTTCCAGAGTTCAAACCAACATTCTACATGTACCTGGGCTAAGCCACCCAGACTAATGGAAGAGATTTGAGGTGGAATTTTGTGATGTCCCGTTGGTCATCTGGTGCTGAGCCAGCACTTTCCAGCAGAACTTTCTGCAGTGATGGAACTGTTCTATGTCTATGCTGCCCAATATGGTAGCCACTGGCTACAGAGTACTTGGATATGACTGAGGGTCTGATTTTTAAATGTTATTTAATCTTGATAATTTAAATGTAAATAGCCATGTGTGGCTGGCAGTGGCTGAATTGGACAGCTCAGCTCTGAGTTATGTAGTTATATACAACAAGAGTTAATTTTACATTGGGAATACAAATTAGCATTTGATATGTGCAGTTTCCTGGACAGTTTCTTCCCAAACCACTGGATCTTTGGAAGAGCAAATAATTTTAAAATTCCTTTGTTTGGTGGTTACTGCCATTCTGAGAATCATCGGGGTTAGGGGAATTCTCTTCCAAAATTCCCAGGGCTTGGATAACTGTAACCAGACTGCCCTGGGTTAATTTCCAGCATGATTTCCAAGCAATGGCTAGGAACAGACAGGAGGGGTTAGATAAGGTTTCAGGGAAGAAATCTTTTGTCCCAAAAGGCATTGTGGGTATACTCTTTGCTTGGAAGACAAGGCAATGGAGCATGGAGCCGATATGCATAGCAGCAGGTTTTCACACCAGCTCCTCAGCCCTGTCCTAGTGCTGCCCCAGACTGAGAGGACCTGTGGTAAGACCCACACCCCTGCTCCATGGAGCCTAAATTTGCCCAGGAGCCCATTGGGCTGGTGAAGAATCAGGTGGATGAGGAATCAGTGTGAGCTTCACCAATTCTATCAACTATGTTGGGAGACCAAGTTGGGAACGGTTGGGAGAGGTATTTAGGGCATGGTGTGGGGAAGTGTTGGTACAAAAAGAATCATAGCCTCCCACTCCAGGTCTGTCTTAAGGCCACTGATGGCACCAAGTGGAGCAGGCAGCCATGGTGACTAGTGACATGCCAGGACCTTGTTTCCTGTGTACAG
Seq C2 exon
GGATGGGCCACAGCAAACAGCACCACGGCTCGGCGTCTTCACCCGGAGCATGGCCAAGAAAACAGTGCAGAGTTCATCCAACCAGGTCCTGCTCAAGTTCCACCGTGATGCAGCCACAGGGGGGATCTTCGCCATAGCTTTCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(54.3=95.0)
A:
NA
C2:
PF0043115=CUB=PD(44.8=94.0)
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:
GTGGCGGGAACATCACTTCTT
R:
CGGAGAAAGCTATGGCGAAGA
Band lengths:
318-1676
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)