HsaINT0042274 @ hg19
Intron Retention
Gene
ENSG00000164796 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:19291]
Coordinates
chr8:113266482-113267656:-
Coord C1 exon
chr8:113267483-113267656
Coord A exon
chr8:113266556-113267482
Coord C2 exon
chr8:113266482-113266555
Length
927 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATA
5' ss Score
6.84
3' ss Seq
CTTTTTAATCTTCATTTTAGAGC
3' ss Score
9.29
Exon sequences
Seq C1 exon
CAAAGTTTTGTGGTGACCCTGGTATACCTGCCCAAGGAAAAAGAGAAGGCAAAAGCTTTATATACCAGTCAGAGGTTTCATTCAGCTGCAATTTTCCTTTCATATTAGTGGGATCAAGCACCAGAATATGTCAAGCAGATGGCACTTGGAGTGGTTCATCACCTCACTGCATAG
Seq A exon
GTAATATTAATTAAAGGCTGATTATGCACAGTAACTGTGTAATTAATAGGGGTGACATTTAATGGTTTTCTTTATCCTATAACCTATAGTTGGCTTAATATAAAAACAAGTGTAAAATATAGAAGCAATTAGAAGGCACTGGAAATGAATATTGGTAGAAAATACAACATTAATTTTAGCACTTTAAACTTCCAGAAGAAACACTTGAAAGAATTTTGTTGTATATCAGTAAAATGAAAAATAAAAATACTTTCAGGTAGTGACATTATTAAGTACTAACATTTTACTTAGATTTTTATAGTTAATAAAGAATCTTCATATGAAATTAGATTTGCTCCAAAAATATCTAAAAGTTATATTGATTTCAAAATGATTGTAACTATATTTCTGTAATCCTAAAATTAATGCCATATTTGGTAAACTAACCAAATAATCTGTCATTCAAATAAACCGACACATCTACCTACCATTATTATGCCTGAATATCCTATGGGTGTCAGTAAAATCCAAATTATCAAGTCCTGTTTCTGGGAAAAAACTGTTATTTCTTCAAAGAAATATTACCCTACCCCAAATCATAGTTTAGCAAGGTCTTTGGACAAATGTTATATGCATGTACACTGCTTTCATATCCTTTATCTTTCCTTAATTTTACATCCACAGAGCTAGTTGAATGTCAAGTGCTTTTATATCGGAAGGGTTCAAAGTTCAAGAATTTCATAATTCATATCAAATGGAGTCTACCTGACTTTCTTGCTTCAAGATTAACAGGCTTCTGTCCATGGAGAGATGTTATTACATTTACATTATTTATTATTTCCTAGATCCTTTGTACCAAACCCCAGATTATTTAAAATTGTTTTCTGTGAGAGAACTATATCTATTGTAAATTTTAAAGGACTAATATCTTTTTAATCTTCATTTTAG
Seq C2 exon
AGCCTACCCAAACCTCTTGTGAAAACCCAGGTGTGCCTCGGCATGGATCTCAGAACAATACATTCGGATTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164796-CSMD3:NM_052900:60
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=0.200
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.5)
A:
NA
C2:
PF0008415=Sushi=PU(32.7=72.0)
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:
AAAGTTTTGTGGTGACCCTGGT
R:
TGAAATCCGAATGTATTGTTCTGAGA
Band lengths:
246-1173
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)