RnoINT0098889 @ rn6
Intron Retention
Gene
ENSRNOG00000048036 | Ncan
Description
neurocan [Source:RGD Symbol;Acc:619941]
Coordinates
chr16:21059473-21061624:+
Coord C1 exon
chr16:21059473-21059766
Coord A exon
chr16:21059767-21061027
Coord C2 exon
chr16:21061028-21061624
Length
1261 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGT
5' ss Score
8.42
3' ss Seq
CTCTTCTGCTTTTTCTATAGCTC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GTGAAGTCTTTTACGTGGGCCCCGCCCGCCGACTGACCCTGGCGGGGGCGCGGGCACTGTGTCAGCGTCAGGGTGCAGCGCTGGCCTCCGTGGGACAGTTGCACCTGGCCTGGCACGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCAGACGGCAGCGTGCGCTACCCGATCCAGACTCCACGGCGGCGTTGCGGGGGCTCCGCTCCAGGTGTGCGCACAGTGTACCGCTTCGCCAACCGCACTGGCTTTCCTGCGCCAGGAGCCCGCTTCGACGCCTACTGCTTCCGAG
Seq A exon
GTGCGTTAGGACGTGCCCCTGCAGGTCATGCCCTAGAGCCATCGTCTTGGGCCACTCTTCGTGGGTGTATGTCATCCAAACAGGTTAACAGTTGAGGGTGTCTGATTAAGCCATGCCCCTCAGAGTGGTCCCTGCCTGACCACAGACGGTCCAACCTCTGAAACTACCCGTTGTACCTGTGGGTGTGTTCCCTTGGACCGCAGCCCCATCAGGAAAGCTTAGTTAGGGCTGTGCTTCATATCACAAGGCCCCTGAAGGTGCCTCGTGAAAGCCACGCCTCCATTGGCATTTCTCCTTCCAGACCACACCCCATAATCTGCATTGGGCGGCACAAACCACATCCCACTATTGTGTTTCCTTGAATCAGGAGTTTCTGAAGACCACATGCCCTGCGAGTAGGTCCTCTCCAAATCATGTCCCTCGACAGGATCCTTGTTGGAGACCACATCTCATGCTTTAACCCATAACCCCTAAGAGGACCGTTGATGATGAGTGTGTTCTGTGGGTGTGTCTACTGTGGTCATGCTTCTAGACGGAGGCAAGCGAAGGCCACATTCCTACCAGCATTTATTTATTTATGTTTTGCTTGAGACAGGGTCTCACTATGCAGCCCTGGCTGCCCTGGAACTCATGGGGATGCACCTGCCTCTGCCTCCCAAATGCTGCAGCTTTTGCCCTCAGGCCCAGAAACTTTCTATTTGTTCTCCAGCTATGGCTGCAGTTCACTTGGTAGATCACATACCTAGCAAGACAAAGGCCTGAGTCCCATATCGATCACCAAATAAAGCCAGGTGTGGGGCTGAGCGTCTGGGAGAAGGAGGCAAAAGAATCAGAAGTATTAAAGGTCACTCTTGTACCCAGCACTTGAAAGGCTGAGGTGGGAGAATCTCTGAGGGTTTGAAGCAAACCTGGGCTACATGTTGAATTCCAGGTGAGCTTGGGTAACAGACAGACAGAAGACAGAGCACTAATGGGTGGAGCTCTGCCTCTTCCTCTATGGGCTCCGCCCTGGGTGGGTCTTATCTGTCTACCTGTCCCCACACCACACCACTCCTCACTTTTCCATCTCCGAGTTCTACCGGTGAACCCAGCTGCCTCTGATGCTCACATGACTAGCTGACCTGACCTTGACCTGCACATTCTGGGCAGAGACCACCCAGAAAGACAGATGCCCAGATGTGGCAGGCTAGGATGTGCATAGACAATCATGCAGGAATTTCCCAGCATGCCCGGGCCCACACCTCTTCTGCTTTTTCTATAG
Seq C2 exon
CTCATCACCATACACCACAACGTGGAGACTCCGAGATCCCCTCATCTGGAGATGAGGGGGAGATTGTGTCAGCAGAGGGGCCGCCAGCCCCAGAACTAAAGCCCAGATTGGGGGAGCAGGAGGTGATAACACCTGACTTCCAGGAACCTCTCGTATCCAGTGGAGAAGATGAACCCCTAGATTTGACAAGGACACAAGCATCTCAGGAGACGCTCGCCTCTACCCCAGGGGGTCCCACACTGGCTTCATGGCCCTCTCGGGAAAAGTGGCTGCTTACAGGTGTCACAAGCTCCACGGGTGTCCCCAGCCCCAGCAGCCTGGGAGTAGACATGGAAGAGACAACACCCTCAGGCACACAGGTAGCCCCCACCCCCACAATGAGGAGGGGCCGCTTTAAAGGGTTGAATGGTCGACACTTCCAGCAACAGGGCCCAGAAGACCAGCTTCTGGAGGCAGCAGAGGCCAGTGCCCAGCCTCCCACCCTGGAAGTTACTGCTGACCACATGGGGCCTTCTGCAGCCACAGAGGCCTTGGAGAGTGACCAGAGCCACAGTCCTTGGGCCATTCTGACCAATGAAGTGGATGTGCCAGGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000048036:ENSRNOT00000064308:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.969
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=98.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGTCTTTTACGTGGGCCCC
R:
CTCCAGATGAGGGGATCTCGG
Band lengths:
343-1604
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]