HsaINT0042161 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34180187-34182101:-
Coord C1 exon
chr1:34181886-34182101
Coord A exon
chr1:34180376-34181885
Coord C2 exon
chr1:34180187-34180375
Length
1510 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
ATCTCCTGCTACCTTTCCAGAGT
3' ss Score
8.83
Exon sequences
Seq C1 exon
GTGTGTTCTTCACTTTCCACACCTTCCACCTGGAAAGTGGCCATGACTACCTCCTCATCACTGAGAACGGCAGCTTCACCCAGCCCCTGAGGCAGCTAACTGGATCTCGGCTGCCAGCTCCCATCAGCGCTGGGCTCTATGGCAACTTCACTGCCCAGGTCCGCTTCATCTCTGATTTCTCCATGTCATATGAAGGATTCAACATCACCTTCTCAG
Seq A exon
GTAAAGAGTATGAGGGTCCCTGAGGGGAAGAGACCATGGTGCTATTTGCTCTCTCCTTCTGCTACCAGTCTCTGGTTTTCCTAGCAGATAGATATTAATCCACTCTCCAGTCCCTGGGAAGTTGACCTTAGTGCTTCAGCAAAAGATGCTTGGGTTAGACCCAAGTAAGAACTTACCTATAATGGTCTTGGAAGGAGTTAGCATAATCACTGAGGATTCTTATTCTATGAAGGTGTTTAGGATTTGCTCTGAACATGGCCCACCTAGCTGGATGAACTAGAGGACTTCACAAAAGTCCCTTCCTACCTTAGTTATTCGAGATTTTTCTTCTGATTCCACTTCCACATTGCCAACCCCAGCAATATGAAAAAAAAAAAAGGTTTGAAATTAACATATTGGAGTGGTTTAGTCTCATTTGGGATCTTTTTCATCAATGCTAATTTTGTAGTAATAGATATTTATCTCTCTGTTTAGGGATTTGGAAAAGAAAGTGCTTTTATTTGGCATTCAGGGAGAAAAGAGGACCCTTGGCTCCTCTCATACCGAGCCCTTCACCATTCTTGTCCCGTAGCACCCCAGAGTACCTCCCTCCACCTTTCTCAGCCACGGCCAGGAGTATCAGATGGATTCCTCCTGGGATGGACAAGAGGTATCCAGCTTCTAGGAACTGGGGTGTGGCCCAGCTTAGTCCCCTGCCAGGCCTCCAATGCAGAAGTCACCTGTCACATCCCTGGATTCACTTGGCCAATGGGACATATCCAGCCAGTGAGACTCAACCCTTATGAGAGAGACCCTCTTTCTCATCACACATCCCTGGAGGACTGCATCCTGAAGGGAGAAGCCCTTGCAGACGAGGGACTAGTCACTTCTATGCTGTCACTAGAGGCCCCAGGCAGGGCTTTGGCCCATAAATGCCCCTGGTCATGCTTGCCGTCTGCCTCAAGTGCCAACGTAGCTGAGACATGGCTTCTCGTCAGGCATTTGGAGTGTCTTCACCAGTGGGAGTTGCCTGAGGCTAAGTCATGTATTCTGACCTTCTAGAACCTGCTGGTTGAATGTATCTAGTTTGTTGCCCAGAGACAAGGAAGCAGGAGAGCCTGTGAGCCCCAAGGCACAGGTTTAAAATGGAGATAAAAGGATAGCACAGAGAAGAGCTGAGTCCTGAGGATCCTCAGAAATCCTCCTGGGAAGCCTGTCTAGGAAAGGCTGTGCCCTTTCACTGCTCACAGGAGTGGGTGCAGACCGCCCGTCCTGGCCTCCCCGTGCTTCTCTCTGCCTCTGCCTCCCCGTGCTTCCCCATGTTTCTCTCTGCCTCTGCTCCCCTCGGGCTCTCACTTCTTCTCTTTTTGGGCCAGTGTCACCTTTTGTGGGCCAGTGTGCGCATGCCCTCTTCTCTGTCTTTCGTTGTCCCTGGCCCTTTCCCCCTGGTGTTTTGCCTGTGCGTTCCCATCTTTTTGCTTTGTGTCTCCCCGCAATGTCTCTGAGCCCGGATCTCCTGCTACCTTTCCAG
Seq C2 exon
AGTACGACTTGGAGCCCTGTGAGGAGCCCGAGGTCCCAGCCTACAGCATCCGGAAGGGCTTGCAGTTTGGCGTGGGCGACACCTTGACCTTCTCCTGCTTCCCCGGGTACCGTCTGGAGGGCACCGCCCGCATCACGTGCCTGGGGGGCAGACGGCGCCTGTGGAGCTCGCCTCTGCCAAGGTGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:20
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=PD(64.8=95.9)
A:
NA
C2:
PF0008415=Sushi=WD(100=87.5)
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:
CATCACTGAGAACGGCAGCTT
R:
CAACACACCTTGGCAGAGGC
Band lengths:
350-1860
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)