HsaINT0042257 @ hg19
Intron Retention
Gene
ENSG00000164796 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:19291]
Coordinates
chr8:113331066-113332210:-
Coord C1 exon
chr8:113332130-113332210
Coord A exon
chr8:113331180-113332129
Coord C2 exon
chr8:113331066-113331179
Length
950 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAG
5' ss Score
6.93
3' ss Seq
TCCCCTCTTTTGTTTAATAGGTG
3' ss Score
11.22
Exon sequences
Seq C1 exon
CCTATCAACTAAGGGTGTGCCAACCTCCACCACCTGTGCCCAATGCTGAAATTTTGACGGAAGATGATGAATTTGAAATAG
Seq A exon
GTAAAGCTGTTAAATTATTTTCAAGGAAAACATACTGCTGGCAGAACTATTTGCTTAAAAATAAGCCAAAATACAGAATAGTAATAGCCTGTCTTGAGACCCTCATTCCCTGTGTTGATAGAGATTATTTAGAATTTTTAAGAAGGGAGAAGGAGTGAAAAGAGGAAAGGGATTATTAGAGAAGAAAAATTAATTTTGTTTTTCTGGAATGTACAATAAGAAAACGTGTTAAAATTTGAAGCCGTTAACTGTATTCTGATGGTTCTTTCCAAACTATTATTTTGCTGCCTTCTGACACTATAGTTCTAACCTTTGTTCTTTGAATTCAGGCCTATGCCTGACTTGGCAGAATGAATGGTTTGTAGGCCATATTAGAAGACATATTTCATTTCCATATCTTGGAAAATGCTTAGTTGATTCTACTCAATTTAATCATAAAGTTGCTTTAAAACTGAGTTGGAAATTCAACCCAAATAATGCCACACAGTTTGAAAAAAAATTATATACGAAGACATCTTAATGTTGCTGTAATAAACTTTTATTATTCATTATTATTATTATATTGATTTTGGTTGAGACACACAAAGAAACTATCAGTGACCGATGTAACTTCAATAAATAGAAAGCCTTCTAACTACTTGTTGTATTTTTATTGAATATCTCACCTATATCAACTAAATTATTTCCTTATGACTATTGCTTATATCCAGCCAGCATGCACCAGTACAGAGGGAATGGCAGTTCACTTTTGCCTTCAGTCCTGATGGGTCAATGAGTATTATATACTGGTTTTTCAATATTTTGAATATAACTCCTACTTATACCTAATAACATTTTTATACTGATTGAAAATAACTAAAGGAGAAAATATTCTCCTACAATTGAAATATTTGTTTATTTTTATCATCACCTTGTTGCTTATATGAAACCTCCCCTCTTTTGTTTAATAG
Seq C2 exon
GTGATATTATTAGGTATCAGTGTCTTCCAGGATTTACTTTAGTTGGTAATGCAATTCTGACGTGCAGATTAGGAGAACGACTGCAGATGGATGGAGCACCTCCAGTTTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164796-CSMD3:NM_052900:45
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PU(36.2=75.0)
A:
NA
C2:
PF0008415=Sushi=PD(62.1=92.3)
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:
TCAACTAAGGGTGTGCCAACC
R:
CTTGACAAACTGGAGGTGCTC
Band lengths:
191-1141
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)