RnoINT0098888 @ rn6
Intron Retention
Gene
ENSRNOG00000048036 | Ncan
Description
neurocan [Source:RGD Symbol;Acc:619941]
Coordinates
chr16:21059042-21059766:+
Coord C1 exon
chr16:21059042-21059169
Coord A exon
chr16:21059170-21059472
Coord C2 exon
chr16:21059473-21059766
Length
303 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
CCGCTCTCTCCCTCTCCCAGGTG
3' ss Score
11.81
Exon sequences
Seq C1 exon
GTACCCGATCACTCAGTCGCGTCCCGGTTGCTATGGTGATCGCAGCAGCCTGCCAGGTGTCCGGAGCTACGGGAGACGCGACCCGCAGGAACTCTACGATGTCTACTGCTTTGCCCGCGAGCTAGGGG
Seq A exon
GTAAGGCAAGGCGCGGCTGGGAGCCTGTCGCCACCTATCCTTGAGTGCTATCCCACGCCCCGTATTTCCTTAAGTCCACACGAATCTCTCCGAATGCTCAGTGTCCTCCAAAGCTGCACGTGGGACCTGGTCACCTCTCCCTGAGTGTCAGGTGTTATTCCAGCCCCCAGTCCTGCTAAGGTCCCCTCAAATCTCTCCAAAGTTGGAGCCACGACTTGGGCCACCCATCTCCGGAGCTCCCTATCCAAAGGTCCACGCGTCCCTCCTCCTCCCACCCTTCTGACCGCTCTCTCCCTCTCCCAG
Seq C2 exon
GTGAAGTCTTTTACGTGGGCCCCGCCCGCCGACTGACCCTGGCGGGGGCGCGGGCACTGTGTCAGCGTCAGGGTGCAGCGCTGGCCTCCGTGGGACAGTTGCACCTGGCCTGGCACGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCAGACGGCAGCGTGCGCTACCCGATCCAGACTCCACGGCGGCGTTGCGGGGGCTCCGCTCCAGGTGTGCGCACAGTGTACCGCTTCGCCAACCGCACTGGCTTTCCTGCGCCAGGAGCCCGCTTCGACGCCTACTGCTTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048036:ENSRNOT00000064308:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=98.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCGGTTGCTATGGTGATC
R:
CGAAGCGGTACACTGTGCG
Band lengths:
345-648
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]