HsaINT0042210 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:33988907-33990643:-
Coord C1 exon
chr1:33990482-33990643
Coord A exon
chr1:33989020-33990481
Coord C2 exon
chr1:33988907-33989019
Length
1462 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
ACCTGAACTTTATTTCCCAGGAA
3' ss Score
8.55
Exon sequences
Seq C1 exon
TTCCTGGGGATGTTTTTGCCAAGAATTCCCTGTGGAAAGGGGCCTATGAATACCAGGGGAAGAAGCAGCCAGCCATGCTCAGAGTGACTGGCTTCCAAGTTGCCAACAGCAAGGTCAATGCCACCATGATCGACCACAGTGGCGTGGAGCTGCACTTGGCTG
Seq A exon
GTAAGGAGCAGGCCCCTCTATGAAAGCCGGGAGGATGGATGGGCACACACCCTTGGCAAGGATGAGCCTAATGGCATTGCATCATACTGTCATGCAAGGCTCAGACTTGTCTGGTGGTCAGGGAAGAGGAAGTGTCTATTCATCTTTACATGATAAAGCACTGTGGACTAAAGGGAAATGTTTAAATGGCAAATATTAATAACCTGAATACATAAAGAACTCTTATGAACAAAGAGAAAAGACTGATATCCCTAAACTGAACCAAAAATAGGGGCAGAGACTTCCCAGGATCCCAAGTACAATCAGTCAACAAACAAAAGAAAAAATATTTTTCAGCAATCATCAAAAAAAAAGTAAACTCAAAATGTCATTTTCCACTTACACCATCAACTCAGAGTGTTTTTAAACAATAACACTTAGTGCAGGTCGGGTTCAGCCATGAACGCCAAATTCTAAAATGGTACCATTCTGGGAAAACAATTTGGCGATTTGTGTCAAGATCCTTGAAAATGATTGGACCCATTAATTACATTTCTAACAATTTTTATCATAAGAAGATACGGAGGGAGTCAAACATTTATGAATAAAGGCTGTTCCCATTACAAGGCCATTTGTAGTATATAAAAACTGGAACTAGAAAATTTCCCTAAAATAGAGAAATGGATATTTTAATGATAGTATATCTACTAGATGAAATATTATGCCAGTGTTGAGGGAAATGCATTCATTATAATGTATTTAAAATATGACTCCAGTGTTTTAAAGGAAAATATTACATTCATAAGAAAGAAAACAGGAATAATTTACAGTAACGTGGTTATTTCTTAGTAAGATCAGGAGAGATCATTTTTTCTTCATGCATCTCAGCATTTTCTAAAATTTTCCCAATTTTCAATCTTTCTATAATCAGAAAAAGTAAGTACCTTAGAAAATAAGTGTTTGTTGAATAGATGGATAGATAAGCAAATGTGTGAGTGAATGAACATATTAATGCACAACCCCACATAAAATCCTATCTACGCATTCATACGTGCACACACCTACGCAACTGCAGGATGACATTTGCTCATTTCACACATGATAATAGACATGTTCACATGCTCCCATGCCCAGGACCTCATGAACTATTGCACCCATTGAACTATCTATGCATTAGTGGACAGATTAAAAGACAAAATCATATTCTCACACATGCCTGTGTCAATAGCATCACAACCTCAACCCGGTAATCCAATTATTAACATACATATGCATATATTAATAATTCTTGCATATAACCACGTTCAGCCTACACAAACCCACACTCAACACTACACTTACGACTTAAAGGGATGTGGAGAATGTTTATATCAACATCTACACATGAAATTCCATCCAGAAACTTACACCCACAAACCCACAAATTTGAGTTTTGAAATTTTCCCATATCTTTCATGTGTAACACCTGAACTTTATTTCCCAG
Seq C2 exon
GAACTTACAAGAAAGAAGATTTTCATCTCCTACTCCAGGTGTACCAGATTACAGGGCCTGTGGAGATCTTTATGAATAAGTTCAAAGATGATCACTGGGCTTTAGATGGCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:65
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGGGGATGTTTTTGCCAA
R:
GGCCATCTAAAGCCCAGTGAT
Band lengths:
272-1734
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)