RnoINT0098892 @ rn6
Intron Retention
Gene
ENSRNOG00000048036 | Ncan
Description
neurocan [Source:RGD Symbol;Acc:619941]
Coordinates
chr16:21067616-21069271:+
Coord C1 exon
chr16:21067616-21067732
Coord A exon
chr16:21067733-21069157
Coord C2 exon
chr16:21069158-21069271
Length
1425 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GCCCATTGCCTGCTCCCCAGACA
3' ss Score
6.09
Exon sequences
Seq C1 exon
ACCCCACGGATCCCTGCGAGAACAACCCTTGTCTGCACGGGGGCACCTGCCGCACAAATGGCACCATGTACGGCTGTAGTTGTGATCAGGGCTATGCTGGGGAGAATTGTGAAATTG
Seq A exon
GTAAGTGTCCCAACCCAGAGCACTGCTCTGTCCCTTGTGAGTCCAGGTGAAACACCTGAAATTACCTGGGTTTAAACTAGATAGCTGGGCTGCTCTGTCCTAGAGGATTAGCTCAGGACAGCTACTCCCCACCATTAGGATTAGGGGTTAGGAAGGGACAAGAAAAGGGTCAGATGCTCCCCATCCAGCAAAGGCCTGTGGGAGACTACCCTCATCCAGGTACACAGGATTACACTGTGTACCTGGATGAGGGTAGTCTCCCACTCACCTTTGTACCACTCACATTGCTAAAGATGAGATTACATTAAATATAAATGGTGTAAAATAGAAATAAATACATCTAATTTGGGTCCAGCTAATTCCAGTTGCGTGAGATCCAACACCTTCTTCTGGCCTCTGTAGGCAATGCACACAAACGGTACCATGGACACATAGGCAAAGCAAAACATAGCCAACTATGTCTGTGCTAGGAATTGAACCTGGATTCTCTGGACCTTAACCTCTGAGCCATTTCTCTAGCCCTTGTGGTGTAATTTCTTGATCACTGTGCATCCGTTGCTTGACTTCACAACCCCACTAGGAGTTACAGAGTCATAACTGACAATAAAACTGAGGATGAGGCATGGGAGCACAGCCCCAAACCCCAGTACTCAGGAGGCAGAGGCTTGTGGATCTCTATGAGTTTAAGGCCAGCCTGGTCTACATAGCATGTTCCAGGACAGCCAGGGCTACAGATAAAGAGATCCTTTCTCCAAAACAAAGCAAACTCACACAAAATAAATAAATGTCTTTTTTAAATATTTTAAAAATCCAAATGAGTTTAAGTAACAGATGCACCATGTGCACACACACACACTCACACACACATGCACACATACACACATGCACACACCTGTACACACACACTCACATGCACACACATGCACACACACGTACATACGCACAGGCACACACACTCACACATACATGCACACACATACATGCACACATACTCTCATACACACTCATGCACACACATACATACTCTCACACACATTCATGCACACACACTCTCATACACACTCATACACATGCTCACACATATACTCATGCACACTCATACACGCACACTTACACACACACACAGGGGGTTGGAAATTGTTTTGGGGGACAAAGCATCTGGGTTTGTTTACAAATACTGCCAGTGGGGCCCTTGCAAGTAATGACTTTTGGGCTGTGGTACCCCGAGTGCCTGAGTCCCATTCTTCTACCCCCCACGGCACCTGCTGTCATTCATGTTCACCAGTGTCATAGCCGAAGGGCAATCCCTATGGGCAGGCGTCCAGGGGACGGGATGGTTAGAAGAACCTTGACCCATCTTCTACCTGTGGGTTGGGATCTGAGTAGAGACTGACCTCTGACCTCTGCCCATTGCCTGCTCCCCAG
Seq C2 exon
ACATTGATGACTGCTTGTGCAGCCCTTGTGAGAATGGGGGTACCTGCATTGATGAGGTGAATGGTTTCATCTGCCTCTGTCTCCCCAGCTATGGGGGCAACCTGTGCGAGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048036:ENSRNOT00000064308:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.069 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
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCACGGATCCCTGCGAG
R:
GCACAGGTTGCCCCCATAG
Band lengths:
222-1647
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]