HsaINT0017003 @ hg19
Intron Retention
Gene
ENSG00000132692 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:23059]
Coordinates
chr1:156627919-156628525:+
Coord C1 exon
chr1:156627919-156628063
Coord A exon
chr1:156628064-156628334
Coord C2 exon
chr1:156628335-156628525
Length
271 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
CTAACTGTCTTCCTTTGCAGTGT
3' ss Score
11.15
Exon sequences
Seq C1 exon
CTCTATGAGAACTGGAACCCTGGGCAGCCTGACAGCTACTTCCTGTCTGGAGAGAACTGCGTGGTCATGGTGTGGCATGATCAGGGACAATGGAGTGACGTGCCCTGCAACTACCACCTGTCCTACACCTGCAAGATGGGGCTGG
Seq A exon
GTGAGGGCAGGCAAAGGAGGGTCCCAGCAAGGAAGTGGAGGGGTGGGCTAGGGGACCAGAGGGACTGATGTTTGTAGACAGAGAGTGCAAAGCAACATAGAGGAGTCAGAACGTGTTCCAGACCATGGGAGAGCTAACAAGTTACGTGGGTCCACTCGGAATCCCTGATCTTTTTTTGTCATGTTGTGGCCCATTTTTCTCTTCCCCATGGAGATTCTGGGAACTGTCACCCACAGAGCCAGGCTCAGTTCCTAACTGTCTTCCTTTGCAG
Seq C2 exon
TGTCCTGTGGGCCGCCACCGGAGCTGCCCCTGGCTCAAGTGTTCGGCCGCCCACGGCTGCGCTATGAGGTGGACACTGTGCTTCGCTACCGGTGCCGGGAAGGACTGGCCCAGCGCAATCTGCCGCTGATCCGATGCCAAGAGAACGGTCGTTGGGAGGCCCCCCAGATCTCCTGTGTGCCCAGAAGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132692-BCAN:NM_021948:12
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=0.016
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PD(42.5=91.8)
A:
NA
C2:
PF0008415=Sushi=WD(100=89.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCTGACAGCTACTTCCTGT
R:
TTCTGGGCACACAGGAGATCT
Band lengths:
306-577
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)