HsaINT0180007 @ hg19
Intron Retention
Gene
ENSG00000038427 | VCAN
Description
versican [Source:HGNC Symbol;Acc:2464]
Coordinates
chr5:82875799-82878122:+
Coord C1 exon
chr5:82875799-82875981
Coord A exon
chr5:82875982-82876125
Coord C2 exon
chr5:82876126-82878122
Length
144 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
CTTTCTTTCCTTCCATGTAGCAT
3' ss Score
10.68
Exon sequences
Seq C1 exon
TCGCTTGCGGCCAGCCCCCTGTTGTAGAAAATGCCAAGACCTTTGGAAAGATGAAACCTCGTTATGAAATCAACTCCCTGATTAGATACCACTGCAAAGATGGTTTCATTCAACGTCACCTTCCAACTATCCGGTGCTTAGGAAATGGAAGATGGGCTATACCTAAAATTACCTGCATGAACC
Seq A exon
GTAAGTGGTCCTTTAGAAAGAATGGACTACCGTGCTATAACAACTACTAGACACCTTCATTTTACGGCTGTGGTATCGGCAGTTTAGGGTATGGAGCAAGTAATATTGTGTGTTTTCTTTTTTTCTTTCTTTCCTTCCATGTAG
Seq C2 exon
CATCTGCATACCAAAGGACTTATTCTATGAAATACTTTAAAAATTCCTCATCAGCAAAGGACAATTCAATAAATACATCCAAACATGATCATCGTTGGAGCCGGAGGTGGCAGGAGTCGAGGCGCTGATCCCTAAAATGGCGAACATGTGTTTTCATCATTTCAGCCAAAGTCCTAACTTCCTGTGCCTTTCCTATCACCTCGAGAAGTAATTATCAGTTGGTTTGGATTTTTGGACCACCGTTCAGTCATTTTGGGTTGCCGTGCTCCCAAAACATTTTAAATGAAAGTATTGGCATTCAAAAAGACAGCAGACAAAATGAAAGAAAATGAGAGCAGAAAGTAAGCATTTCCAGCCTATCTAATTTCTTTAGTTTTCTATTTGCCTCCAGTGCAGTCCATTTCCTAATGTATACCAGCCTACTGTACTATTTAAAATGCTCAATTTCAGCACCGATGGCCATGTAAATAAGATGATTTAATGTTGATTTTAATCCTGTATATAAAATAAAAAGTCACAATGAGTTTGGGCATATTTAATGATGATTATGGAGCCTTAGAGGTCTTTAATCATTGGTTCGGCTGCTTTTATGTAGTTTAGGCTGGAAATGGTTTCACTTGCTCTTTGACTGTCAGCAAGACTGAAGATGGCTTTTCCTGGACAGCTAGAAAACACAAAATCTTGTAGGTCATTGCACCTATCTCAGCCATAGGTGCAGTTTGCTTCTACATGATGCTAAAGGCTGCGAATGGGATCCTGATGGAACTAAGGACTCCAATGTCGAACTCTTCTTTGCTGCATTCCTTTTTCTTCACTTACAAGAAAGGCCTGAATGGAGGACTTTTCTGTAACCAGGAACATTTTTTAGGGGTCAAAGTGCTAATAATTAACTCAACCAGGTCTACTTTTTAATGGCTTTCATAACACTAACTCATAAGGTTACCGATCAATGCATTTCATACGGATATAGACCTAGGGCTCTGGAGGGTGGGGGATTGTTAAAACACATGCAAAAAAAAAAAAAAAAAAAAAAAAAGAAATTTTGTATATATAACCATTTTAATCTTTTATAAAGTTTTGAATGTTCATGTATGAATGCTGCAGCTGTGAAGCATACATAAATAAATGAAGTAAGCCATACTGATTTAATTTATTGGATGTTATTTTCCCTAAGACCTGAAAATGAACATAGTATGCTAGTTATTTTTCAGTGTTAGCCTTTTACTTTCCTCACACAATTTGGAATCATATAATATAGGTACTTTGTCCCTGATTAAATAATGTGACGGATAGAATGCATCAAGTGTTTATTATGAAAAGAGTGGAAAAGTATATAGCTTTTAGCAAAAGGTGTTTGCCCATTCTAAGAAATGAGCGAATATATAGAAATAGTGTGGGCATTTCTTCCTGTTAGGTGGAGTGTATGTGTTGACATTTCTCCCCATCTCTTCCCACTCTGTTTTCTCCCCATTATTTGAATAAAGTGACTGCTGAAGATGACTTTGAATCCTTATCCACTTAATTTAATGTTTAAAGAAAAACCTGTAATGGAAAGTAAGACTCCTTCCCTAATTTCAGTTTAGAGCAACTTGAAGAAGAGTAGACAAAAAATAAAATGCACATAGAAAAAGAGAAAAAGGGCACAAAGGGATTGGCCCAATATTGATTCTTTTTTTATAAAACCTCCTTTGGCTTAGAAGGAATGACTCTAGCTACAATAATACACAGTATGTTTAAGCAGGTTCCCTTGGTTGTTGCATTAAATGTAATCCACCTTTAGGTATTTTAGAGCACAGAACAACACTGTGTTGATCTAGTAGGTTTCTATTTTTCCTTTCTCTTTACAATGCACATAATACTTTCCTGTATTTATATCATAACGTGTATAGTGTAAAATGTGAATGACTTTTTTTGTGAATGAAAATCTAAAATCTTTGTAACTTTTTATATCTGCTTTTGTTTCACCAAAGAAACCTAAAATCCTTCTTTTACTACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000038427-VCAN:NM_001164098:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.524
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.9)
A:
NA
C2:
NO
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:
CACCTTCCAACTATCCGGTGC
R:
AAGGCACAGGAAGTTAGGACT
Band lengths:
257-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)