HsaINT0042244 @ hg19
Intron Retention
Gene
ENSG00000164796 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:19291]
Coordinates
chr8:113418753-113420642:-
Coord C1 exon
chr8:113420547-113420642
Coord A exon
chr8:113418957-113420546
Coord C2 exon
chr8:113418753-113418956
Length
1590 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
AATATAATATTTCTACACAGCTG
3' ss Score
6.35
Exon sequences
Seq C1 exon
GAGAATCACTTCCACTGAGTTCAGGTAATCAGATCACAATTCGATTTACTTCAGTTGGACCAATAACAGCTAAGGGATTTCACTTTGTTTACCAAG
Seq A exon
GTAAGTGACCCTGTAGTCTAGAAACACACTAAGGAATGATATAATTTTCCCATGATGTATTCAGAGTTTTTGAATGATGAAATCCTCTAGATAAAAGTGTTTTTAAGCAGTTTTATTTTGTCCCCTCCACCATCACTAGATCACTGTCACCTTGACCAAAGTAAACAAAATCTATTGCTTCCATCATCATTCTCAGTTTAAATGTCTGATTTTCCTTCCTTCCCACATATTATTTTCAAAACATCTACTTTTTTTTCCTGACAATCCTTTACTATCTACATTTTCTATTTTCTAACAGTCTAGCACTCTAGACTATTTAGTCTAATTTAGTTTAGCACTCGAAATTAAAGATATAAAAATTTTGGTGCTGATGTACTTAAACATGCCAAGGAAATCAGTGTTCCATTCTAAAATTATAGTTTCTCATTCTCTCAGGAGAATTAAAACTTTCTTCAGTTATTAGGACTTTTGTGCAATTAGAAGTTTGTTTACACATTTTATTTCTTGCCTGTGGTAGACAACCTTCTACGTTATCATTAAACCAAGTTAAGAGCCATTATTTGAAATATTGTCTTTGAAATATATATGGTCATATAGTAGTTAATCTCAAATGTATCTTGCACTTTATTACTAAGAAATGTATAAACATTTGTGATTTGTTATTCCTATTAAACCTTCTTACCCCATTTATCAGTTGACTATAATCCTGTACTCTTTTATGTTAAGTAGTACTTCCCCCTGGAAACAATGTGTGGTATTACGACTGCAAAAAGGCACTATAATGAATGGAATTATATTTACTCAAGTCGCATAAGAAGAATTAATCTATTTAGAATTCATCATATCATTTTTTGGGCTATTGTCAATCTCTTTAATCACATTTGTTATGTGTTTTAAAAAGAAAAAACATCCTGTTATCATTCTATTTTACTAAACCAAAAAAAAGGCACAATTAAAGGGCATACCTATAAAATCTAAAAGCAATTTCAAATCTGATATTGTATGATTATTAAAGTAAAAACTTTTATTGTTGTTAATCTGTCTGACATATATTCTACCTAGTCCAAATGTAGTTATCTTTCTCAATAGCAAATGTGTTTGAAATTAAGTTTGTGAAATTTTATGAAACTAATAAAGTACTGTTTGCCTTTATAAAATCTGTTTTTAATTAAGAACCAAATACTGAAAAAAATGTAAAATTATTTGATATAACCTGACACATATTTTTTGAACTTGGTATTCTAAGTTTAAAAAGAAAAAAAACTTTCAGTTTTCATCCCACAAATTACAAAAATATCTAACTAAAACTATTTTGTAATATTAATGAGTTCGGTAAAACAAAAATCGTTGATGTTTAAAGAATCAAAAGTAAAACTTTTCTAATAAAAAACCTTGATGACAATAACAATATTTATTTTAAATTATATTTTATTCTGTCTGAAATTTAAAACTTTAAGAATGTATTCAAATTGTTAATTCAAGTTCTGATAAAAAGTGATGATTTCTCAAAAATGTGTTTAAACAGTTACATTTTGAAATCTGTATTTGTCTACCATATAAAATTAAAATAAATATAATATTTCTACACAG
Seq C2 exon
CTGTTCCTAGAACAAGTTCTACACAATGCAGTTCTGTGCCTGAACCAAGATTCGGAAGAAGAATTGGCAATGAATTTGCAGTCGGTTCATCGGTTCTTTTTGATTGTAATCCAGGATATATTCTCCATGGATCCATAGCAATTAGGTGTGAAACAGTGCCCAATTCTTTGGCCCAGTGGAATGATTCCTTACCTACTTGTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164796-CSMD3:NM_052900:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.004
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(28.3=90.9)
A:
NA
C2:
PF0043115=CUB=PD(9.5=5.8),PF0008415=Sushi=WD(100=94.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAATCACTTCCACTGAGTTCAGG
R:
TCATTCCACTGGGCCAAAGAA
Band lengths:
279-1869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)