HsaINT0017009 @ hg19
Intron Retention
Gene
ENSG00000132692 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:23059]
Coordinates
chr1:156617300-156617902:+
Coord C1 exon
chr1:156617300-156617474
Coord A exon
chr1:156617475-156617774
Coord C2 exon
chr1:156617775-156617902
Length
300 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
ATTCTGTCCTTCCTCCCTAGGTA
3' ss Score
12.39
Exon sequences
Seq C1 exon
GGGTCGTCTTTCTCTACCGAGAGGGCTCTGCCCGCTATGCTTTCTCCTTTTCTGGGGCCCAGGAGGCCTGTGCCCGCATTGGAGCCCACATCGCCACCCCGGAGCAGCTCTATGCCGCCTACCTTGGGGGCTATGAGCAATGTGATGCTGGCTGGCTGTCGGATCAGACCGTGAG
Seq A exon
GTGGGCAGGGGCTGTGGATTGGGGCTTCTATTGGCCCCTGAGGTGGCCATGGCCCCCCTTCTGCTGGGTGCTGCCTGCTGTGTCAGGCTGGACATGCAGGGCTTTTTGCCTCTGGGGGATGAGGCTGGTCTGAGGAGGGGAGGTGAGGACCCTGAGCATGTGCATCCCTGCAGTGCTAGAAGGACAGCCAGCTGTCAGCAAGTGTCTGCACTGTGGTGGCAGTGGGGTTCAATAGAATCAATATGGGCTGGCTCCCTGGTGAAAGCATCTGTACTAAGTGATTCTGTCCTTCCTCCCTAG
Seq C2 exon
GTATCCCATCCAGACCCCACGAGAGGCCTGTTACGGAGACATGGATGGCTTCCCCGGGGTCCGGAACTATGGTGTGGTGGACCCGGATGACCTCTATGATGTGTACTGTTATGCTGAAGACCTAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132692-BCAN:NM_198427:4
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=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(0.1=0.0),PF073547=Sp38=PD(44.2=57.6),PF0019312=Xlink=WD(100=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
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:
GGGTCGTCTTTCTCTACCGAGA
R:
CATTTAGGTCTTCAGCATAACAGT
Band lengths:
303-603
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)