HsaINT0042197 @ hg19
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:19290]
Coordinates
chr1:34033193-34035147:-
Coord C1 exon
chr1:34034974-34035147
Coord A exon
chr1:34033367-34034973
Coord C2 exon
chr1:34033193-34033366
Length
1607 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TTCCCCATCCCTCACCAAAGCTG
3' ss Score
4.29
Exon sequences
Seq C1 exon
TCATCTCCTGTGGAGAGCTCCCGATTCCCCCCAATGGCCACCGCATCGGAACACTGTCTGTCTACGGGGCAACAGCCATCTTCTCCTGCAATTCCGGATACACACTGGTGGGCTCCAGGGTGCGTGAGTGCATGGCCAATGGGCTCTGGAGTGGCTCTGAAGTCCGCTGCCTTG
Seq A exon
GTAAGTGACCTCTGCAGGCCTATCCTGCCCAGTTTTTCTCCTTGAGATAGATTAGATCTTTCCAAAGCTGAGATCCAGTCTTTAAACAGTATCATTTCACCTATTGACATAAAATGCTTAATCCAAACACCAACTATTGGCCATCAGGCATGACTAAAACCCTGGAACAGCTTCTCCTGGGCCACCCAAAAGAAGGAGAAGAACCTCAGATCTAAAGAGACAAGCTTTTGAGGGGTTCTCATTCTGGTTAGAAAGACAATCCCTTCCTATTGGCCTTTGTATAATGAGTGAAGCCCCAGTCTCCATTTTTGGCAAATTTGCAGACGCATTCCTGTAACACACCTAAAATACCTTTTATATTATCTATTAGCAAATTTTACACACAACATATAGATCTATACATATATACTAAGCAAATTACAGAAACATAAAACAACCTGGCTTCCAAAGGACAAAGTTATCATTTCCTCCATGGCTAATCCACTCCCTGGTTCTATGGTTCTGTCTCCTCTCACACCTTTCTTGGACCCCTGGAGTCTAAAAGAGGGCCCCAGCCACATAAACCTAATAGGATAGATTGAATGGTCTGTCCTGGGGTGAACAGTGCTGTCTTGCCACTGTCTCAGGCCCATTAAGGACACAGTCACAGGTTATTTCCACAGAGAGCCAAAGGAAGCTGGTAGAAATGCCAGGAATATATTCTACCCAAATCCCATATAATAAAAAGAATTCACCTAGGTGCTACTCAAGGAGAAGGAAGGAAAGATGAATTTAGCCAAACCATCTGTTTTTACATAGTTGTTTCAACACAGCCAGGTTTTGACTGCCTTAATGTAGACAATGGTGCCCTCCATGCAGCAGATGCTCGGTGAAAAACAAGATGCCCAGGCTAGGTGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAAGCAAAGGCGGGTGGATCATTTGAGGCCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAATCCATCTCTACTAAAAATACAAAAATTAGCTGGGTATGGTGGTGGATGCCTGTAGTCCCAGCTACTTGGGAGGCTAAGGCAGGAGAATCCCTTGAACCTAGGAGGTGGACATTGCAGTGAGCCAAGATCGTGCCACTGCAGTCCAGCCTGGCAGACAGAGCAAGATCTTGTCTCAAAAAAAAAAAAAAAAGATGCTCCTGAGTTTGAGTTTTTGGGGGCGTTTCTTGTTTGTTTGTTTGTTTTTTTATAGAAGGCTTTTTTGTATCTGGTTGGTAAGAAAAAGTGGGGGATGATCCTGGGGACAGTGAGGTAACTGATCATTTTGCACACATCTGTGTAGAGACACAGAAACTGAAGCTCAGAAGTGAGTGGCCATTTGGGGTACAACCTTGGGATTTGGGGTGCCAAGTCCTCAACACTATTTTTGTCATGCTGAGGGTTCCTGAAGTCACTCCTAGATTGCTACTCTCAGGGAGAGGTGGGAAAAGTAATGAGTTGTGGGATAGTTGGTCCTTTTCCCCACCATCCCTGTCTCTAGCCACTCAGACCAAGCTCCACTCCATTTTCTATAAGCTCCTCTTCGATGTACTCTCTTCCCCATCCCTCACCAAAG
Seq C2 exon
CTGGACACTGTGGGACTCCTGAGCCCATTGTCAACGGACACATCAATGGGGAGAACTACAGCTACCGGGGCAGTGTGGTGTACCAATGCAATGCTGGCTTCCGCCTGATCGGCATGTCTGTGCGCATCTGCCAGCAGGATCATCACTGGTCGGGCAAGACCCCTTTCTGTGTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904-CSMD2:NM_052896:53
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:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAGCTCCCGATTCCCCC
R:
CACACAGAAAGGGGTCTTGCC
Band lengths:
335-1942
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)