HsaINT0042267 @ hg19
Intron Retention
Gene
ENSG00000164796 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:19291]
Coordinates
chr8:113301594-113303924:-
Coord C1 exon
chr8:113303739-113303924
Coord A exon
chr8:113301768-113303738
Coord C2 exon
chr8:113301594-113301767
Length
1971 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TTAATAATTATGTATTGTAGTGA
3' ss Score
4.87
Exon sequences
Seq C1 exon
TGGTCAACTGTTCTGATCCTGGAATTCCAGCCAATTCTAAAAGAGAAAGTAAAATAGAACATGGAAATTTTACTTACGGCACTGTGGTATTCTATGACTGCAATCCTGGATATTTTTTATTTGGATCTTCAGTTTTGATATGTCAACCAAATGGACAATGGGACAAACCTTTACCAGAATGTATCA
Seq A exon
GTAAGTAGATAATGTGAATTGTTTCTTGAGAACATGTCATGGAAACCATAGGAATGTTTATCATCTTTATAAAATGACCTAAAGATATATATCACAGAGAAGCATATTGATTTTATTGTTTTACTGTTTTGAAATTATACTTTTCTATATTTTGCAAATTCAATGTCCAAATGTAATTTTCTTAAAATTAATGTGATAAATATTTATCTATCATTCTTTGATTTTGCACTTTGGAGCATATAAAATATGAAAAGTAGTCATATTTCCTACTTTACAATATTATCGTCTGTAAGAGGCAACTACACTTTTATTCTGTACTAATATTTAATATTTCATTTAAGGCAAAATTAGTCTTAAACATCCATCATGGATTCAGAATACATGAAGATTTACACAAAGGTGTGACTTAAAACTTATTGACCTTAAATATTTGTCATATAGAGACACATATACTTGTTAATGCAATAAATGTTAATATACATCATCTTTCTAGTCAGTGAATATCTAATAAGTGCATTTTGTTATATGTTATGATAGGAGTTGTAGAATGTACATAAAATAGATTACAGCCAAGATGCTTAAAGTAACACACGTAGTGAGAAAAATAATTTAGCAGTTATAAATCAAACTTCTGTGAAGGCATAGAGGAGTGAACATAAATTCTAGCAATTCAGTCAATTGATAGGCCTCAAATTGAACTAGATCTCAAACAGTTGGTGAGTCTTGGACTTGACAGGGAAGAGAAGAACAATTTCATAGACTGAATGAATAGCGTGTGAAGAAATCGTTCATTTTTGGCAAATAATTTTTGGTTTTATTAAATTGCTAAATAAAATTATTTTATGATTATGCTTCATTTAGAGGATTTTTTTATGTTCATGAGGTGTACTTTTATGAACATTTTGTGACAACATTCATGTACTAATGAAGAAACAACACTTTTTGCTGTGTCTGTAAAATTTGATTCTATGCATATAGTTCAGTAATTTGGCCTGCTGATTAAAATTCATTTGACTTATTTGTGTTGACTGGTCTAATTATTTGAATAATTTACTTACTTATTCTTATGTAGCTACCACATTAAAGTTAAAAATCTCTTCATAGGACTTGTAAACCTGAAGTTCTTCAGGTGTTCTGAGCTCTCATATGTTTTTTGACTTATCATTTCCTATAGCTCTCCCTGGTAGAGTATTATATACTGAAAGGTTTTATTAAGTTTTTGTGTCCTCATGTGCTGTATGATACTCTAGAGATATGTGACACTCAGTATTTCTCTGAGTACAACTAACAGGGGACACATGTTAAATTCTGAAACTACCTATCACTCATAAAGAATATTCTACAATGTATTGACTTTTGATTCTGCTATGAGTAGCAGTTTTAGTTTATAAGCCACTGAGTATTGTCTTTTTACAGCATAATTTATTCATTACTGACTTGAAATGTAATGATTCTAGACTATATATTAAATTGTGAATCACAGATCAATCTTCATTGAATCTCTTGAACCCTCAAGTTCTTTTCATGTAATTTCTGTATTGCTTCACTTTAAATCCACATGGTGTCCTATGTCCTTACTTAGCAAATCCACATTAATCTTCTCCTTAACTTTCACAGATTTTACCAGGAACAGATACAGTTCGAACTCATACACATATATATGTGGACACACACTCATCACTCTCACACGTACAGATTTATCATAATCACTTAATTATTTTTAATGCTTACTTAGCTTACAATGTTGCTGTTAAACTCATCCTCGGAATGAGTAAGTTAACAGAACAGCTGCTATAGCTGCAAACTCCACTTTGTTTTTAAAAAGACACCTTCAACATAGATGTTTGATTTCTGGAGGCTTTAGATGTTTCAGCAGAACATTTACTTCTGGTATGTTCTATAAACATGCTGGTATAGGTTGTTCGATAGGAGATATAAAAAAATTTTATATTTAATAATTATGTATTGTAG
Seq C2 exon
TGATTGACTGTGGACACCCTGGCGTTCCTCCTAATGCAGTCCTGTCTGGCGAGAAGTATACTTTTGGGTCTACTGTTCACTATTCCTGCACAGGAAAGCGTTCCCTTTTAGGCCAGTCATCAAGAACCTGCCAATTGAATGGCCATTGGAGTGGATCACAACCTCATTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164796-CSMD3:NM_052900:54
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
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:
TGGTCAACTGTTCTGATCCTGG
R:
TTGTGATCCACTCCAATGGCC
Band lengths:
347-2318
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)