HsaINT0042216 @ hg38
Intron Retention
Gene
ENSG00000121904 | CSMD2
Description
CUB and Sushi multiple domains 2 [Source:HGNC Symbol;Acc:HGNC:19290]
Coordinates
chr1:33819713-33820556:-
Coord C1 exon
chr1:33820469-33820556
Coord A exon
chr1:33819838-33820468
Coord C2 exon
chr1:33819713-33819837
Length
631 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
AGACACACTTTGTCTCCCAGGTT
3' ss Score
5.79
Exon sequences
Seq C1 exon
TAACTCAGGTTGGTGTGTCCCAAGGACATAATATGTGTCCAGACCCTGGCATACCCGAAAGGGGCAAAAGACTAGGCTCGGATTTCAG
Seq A exon
GTAAGATCTATTTGGGAATTTTCTGATTGCAAGAAGGGTGGGGTGGCCTGGCTGGGAGGAAGACAGGGGCTGGCCTTCCTGCAGGTGGAAATGGAGAGGATGGCATGGATATAGGAACAGACACTTCCTGGAGAAGAGCTATGGCTTTGACATTCTCTCCTGGTTCAGTCCTTGGCATAGTGCCCATGCTTTAGTGGGGGGAGAGAACTGTAGACTGCCAGTGTTATCCAGAAAACCTATGTACCCAGGGTACAAAGGGCTGCCATCTCAGTAATGACACGCCAGAAGGCAACTCGCGCCTGCAATAATCTAGGAGACCATTTTCCTTAAAGTTTATGGGTATCATCCACCCACGCTTAGCTGCCCTAACTGGTGCTTATCTCAGAGGATCGCTGTTTTGCTCACAAAGTCACCTTTTAACTCAATCCTAAAACCATTAAACAGTCCGAAAAAAGAAGATGAAGAGCAGATGTTCCTTCCAATGGAGATTTTTAGTGATAAAACAGTGGAGCAGAGATTAAGGGCCAGAAGGAAAAATAACATGTGCGGCTTCTTTGTGGAACCAGGAAGGACTTGGGGCGGGGCTTGGCAGGCCCAGGGATGGAGCTCACAGACACACTTTGTCTCCCAG
Seq C2 exon
GTTAGGATCCAGCGTCCAGTTCACCTGCAACGAGGGCTATGACCTGCAAGGGTCCAAGCGGATCACCTGTATGAAAGTGAGCGACATGTTTGCGGCCTGGAGCGACCACAGGCCAGTCTGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000121904:ENST00000241312:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(29.3=56.7)
A:
NA
C2:
PF0008415=Sushi=PD(69.0=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGTTGGTGTGTCCCAAG
R:
GCAGACTGGCCTGTGGTC
Band lengths:
206-837
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