HsaINT0110814 @ hg19
Intron Retention
Gene
ENSG00000130287 | NCAN
Description
neurocan [Source:HGNC Symbol;Acc:2465]
Coordinates
chr19:19344598-19345905:+
Coord C1 exon
chr19:19344598-19344714
Coord A exon
chr19:19344715-19345791
Coord C2 exon
chr19:19345792-19345905
Length
1077 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TCTCTTCCCCTCTCTGCCAGACA
3' ss Score
8.98
Exon sequences
Seq C1 exon
TGCACTCAGATCCCTGTGAGAACAACCCTTGTCTTCATGGAGGGACATGTAATGCCAATGGCACCATGTATGGCTGTAGCTGTGATCAGGGCTTCGCCGGGGAGAACTGTGAGATTG
Seq A exon
GTGAGTACCCCAGACTCAGGATCTGAATCTGAATTTGTTTGACTCCAGAGCCTTGGGTTGTACTCCAGCAGCCATGCCCTCAGAATTCAGAGATCACAAAAAGCTGGTTTCAGATGCTCCATTCCCAAACCCCACTCCTTGCATTCAGCTAAATCAGCCCAGTTAGTGGAACCAGAATCAAACAGCTGAGCTTTCATCTCTGGTGTGCTGTCTCCCATTACTACCAGTCAGAGGTGGGAAGGAAAAGACAAAGGAATTATATGTCTGAGACTCCTCCCTGCAAAGGCCCTTTGGAGATCCTGCCCTTTCCTGGGTCGGTGGGAGGTATAAGCACTGCCACCAGAACTGTTGGGTGCTAGCTTCAAAGCCCAACACAAGAAATACTACCAATTATGAAATTACAACAACAAATATAAATGACATAATTTTTTGAGCTCTATGTGTCATCTTGACTTCACAACCTTCACAACCACATGACTGATTACAGAATTATAACAATAAATATAAATGATATAATTTCTTGAGCTCTTCTATTGCTTCCCTACTCACAATCATCCTTGAGTAGGAGCCCATTATTATTACCATTTTCAAAAAAAGTAAGCTGAGTTTCAAGGAGGGGAAGTGACTTGCCCAGTGCCATACGTGCCTCAAGCACTGTCTACACATGGACCAGTAGAAGAGGAGCTCAATGAATATCTAGCTTTACCCACAAACAGCTTTGTGACTCTGTGCAAGTCTTTGCAAATGCCTAAAAGAGACTCCAGCTTCAGCATTCTATGAGCCTGTTTTTGAGAGTATAACCTTCACTTCTCTAGAGTCAGGTAGAACAGTCTGCACATCCTGGCTCTCAGCTGCCCCAGTGGCATCTGCTCTCATTAATGCTAATTTATGTTAATTGTATGAGGTTCCACCCCCTTGCCTGCAGAGTCATTGGGCCATCTGTGCAAACTGTGACTGCTGCACTTAGGTCCAGGATGGATGGTAGGACCATGACCCCATCTTCTGCTTAGTTTCCTGTGGGGGCTCAGAGCCAAGGGGAAGCTGACCTCTAACTCAGTCTCTTCCCCTCTCTGCCAG
Seq C2 exon
ACATTGATGACTGCCTCTGCAGCCCCTGTGAGAATGGAGGCACCTGTATTGATGAGGTCAATGGCTTTGTCTGCCTTTGCCTCCCCAGCTATGGGGGCAGCTTTTGTGAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130287-NCAN:NM_004386:9
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:
PF0000822=EGF=WD(100=77.5),PF0000822=EGF=PU(7.9=7.5)
A:
NA
C2:
PF0000822=EGF=PD(89.5=87.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCACTCAGATCCCTGTGAGA
R:
TTTCTCACAAAAGCTGCCCCC
Band lengths:
230-1307
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)