HsaINT0110811 @ hg19
Intron Retention
Gene
ENSG00000130287 | NCAN
Description
neurocan [Source:HGNC Symbol;Acc:2465]
Coordinates
chr19:19335786-19337882:+
Coord C1 exon
chr19:19335786-19336079
Coord A exon
chr19:19336080-19337294
Coord C2 exon
chr19:19337295-19337882
Length
1215 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGT
5' ss Score
8.42
3' ss Seq
TCTTCTGCTTTCTCCCACAGCTC
3' ss Score
12.4
Exon sequences
Seq C1 exon
GCGAGGTCTTCTACGTGGGCCCGGCCCGCCGCCTGACACTGGCCGGCGCGCGTGCACAGTGCCGCCGCCAGGGTGCCGCGCTGGCCTCGGTGGGACAGCTGCACCTGGCCTGGCATGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCCGACGGCAGCGTGCGCTACCCGATCCAGACGCCGCGCCGGCGCTGCGGGGGCCCAGCCCCGGGCGTGCGCACCGTCTACCGCTTCGCTAACCGGACCGGCTTCCCCTCACCCGCCGAGCGCTTCGACGCCTACTGCTTCCGAG
Seq A exon
GTGCGTGCGTCCCCTGGTGGCCGCGCCCCCAGGGCTTTCACTTTGGCGAAGGCCACGTCCCTGAAAGCCTCGCCAAGCCAAGGGAGAGACACATGGAAGCTCGCTTTGTGATAAGCCACATCCCTGGGTGAGGGCCACGCCCCCGGGTGAAGGCCACACCCGTTACGACAAGTCTTTCCCTAGGAGCCCCGTCCTGGGTAAAGAACAGGGCTCCAGAGGAGGCCACTCTGGTGGGGAGTCACCTTTGCTGGGTGGGCTGTATCTCCTGAGGTCCGGAGGCCCCATAACCTTGAAAGACAAGCCCCTAGGTGGGGCATACTCTACCTAGAGCCACGCCCATACGCAGAAACACCCCCGTGGAAGAGATAATGCCTCAATTGGCCACCTCTGGGCACCACACCGGATGTGGGAGCAGGGATGACACTCGCCCTTGTTGGGGGGCAGTGGGGACAGCTTTGGAAGCTGCAAGCATCAACCCCAAGGAGCCATGTCCTCTAAGTAAGCTGCCCCAGTCCTGGCATGGGCATACCATGCCCACGGGGCACCACCTGTACCAGGGGAGGATCCGTCACCAAGGTTGAGTTGAACCCCTCAACAGGCAGACCCAAGTTCATGAGAGTTGGACACTACCTGAGCTTTGCCCATGAGCCAAATTGTCTTTTTTTCTTTTTTCTTTTGAGACAGAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCAACCTCCACCTCCCTTGTTCAAGCAATTCTCCTGCCTCAGCCTTCGGAGTAGCTGGGACTACAGGAATGTGCCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACGGACGTGAGCCACCGCGCCTGGCCCAAATTCTCTTGAGTCCTCACTGCAGCCAGTTGACTCTGACCCTGACAGTGGCTCAGGTGGTCTCCAGCCTGAACAGTGGAGGTGAAAATTTTGCACTTCCCTCTCCCAGGCTGGGGGAATCTCAGAAACTACTTAGGAGAGACAGAGGTACACAGAAGGCTTATGCTGCAGCATGCTGGAAAGTGGGTAGACTTCAAGCAGAACTTCCCAGGCAACCCCTGGGCCTAACACAACCTCTTCTGCTTTCTCCCACAG
Seq C2 exon
CTCATCACCCCACGTCACAACATGGAGACCTAGAGACCCCATCCTCTGGGGATGAGGGGGAGATTCTGTCAGCAGAGGGGCCCCCAGTTAGAGAACTGGAGCCCACCCTGGAGGAGGAAGAGGTGGTCACCCCTGACTTCCAGGAGCCTCTGGTGTCCAGTGGGGAAGAAGAAACCCTGATTTTGGAGGAGAAGCAGGAGTCTCAACAGACCCTCAGCCCTACCCCTGGGGACCCCATGCTGGCCTCATGGCCCACTGGGGAAGTGTGGCTAAGCACGGTGGCCCCCAGCCCTAGCGACATGGGGGCAGGCACTGCAGCAAGTTCACACACGGAGGTGGCCCCAACTGACCCTATGCCTAGGAGAAGGGGGCGCTTCAAAGGGTTGAATGGGCGCTACTTCCAGCAGCAGGAACCGGAGCCGGGGCTGCAAGGGGGGATGGAGGCCAGCGCCCAGCCCCCCACCTCAGAGGCTGCAGTGAACCAAATGGAGCCTCCGTTGGCCATGGCAGTCACAGAGATGTTGGGCAGTGGCCAGAGCCGGAGCCCCTGGGCTGATCTGACCAATGAGGTGGATATGCCTGGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130287-NCAN:NM_004386:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.121 A=NA C2=0.980
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=98.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCGACGCCTACTGCTTCC
R:
GTGTGTGAACTTGCTGCAGTG
Band lengths:
354-1569
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)