RnoINT0024989 @ rn6
Intron Retention
Gene
ENSRNOG00000018798 | Bcan
Description
brevican [Source:RGD Symbol;Acc:2194]
Coordinates
chr2:187368827-187369652:-
Coord C1 exon
chr2:187369281-187369652
Coord A exon
chr2:187369002-187369280
Coord C2 exon
chr2:187368827-187369001
Length
279 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GAGTTCTCTCTGCTCCTCAGGGG
3' ss Score
7.01
Exon sequences
Seq C1 exon
AGGATCGAGCCTTTCGGGTGCGCATCGGTGCCGCGCAGCTGCGGGGTGTGCTGGGCGGTGCCCTGGCCATCCCATGCCACGTCCACCACCTGAGGCCGCCGCCCAGCCGCCGGGCCGCGCCGGGCTTTCCCCGAGTCAAATGGACCTTCCTGTCCGGGGACCGGGAGGTGGAGGTGCTGGTGGCGCGCGGGCTGCGCGTCAAGGTAAACGAAGCCTATCGGTTCCGCGTGGCGCTGCCTGCCTACCCCGCATCGCTCACAGATGTGTCTTTAGTATTGAGCGAACTGCGGCCCAATGATTCCGGGGTCTATCGCTGCGAGGTCCAGCACGGTATCGACGACAGCAGTGATGCTGTGGAAGTCAAGGTCAAAG
Seq A exon
GTGAGAGGACAAAGTAGAGATCCCTAAAGAGAGGGAGGAAAGGACTCCAGTACCCCTCCCACTCGTCCCCCACTGAGCTGAGTGTGAGGCTTCTTAGCAAACCCTGCAGTGGGAGGCACAGGCTGAACAGGGGGTCGGGGATGGGGGTTGTGGGGAGATAGCTCCACAAGCTGTAGAGTGAACACGGTTTTGCCTTTTGTGAACAGGAAGTGACAGAGAGGGGAGGAGAGGTCAGTGTGCAGCTGACCACCAAGTTCAGGAGTTCTCTCTGCTCCTCAG
Seq C2 exon
GGGTCGTCTTCCTCTACCGAGAGGGCTCTGCCCGCTATGCTTTCTCCTTCGCTGGAGCCCAGGAAGCCTGTGCTCGCATCGGAGCCCGAATTGCCACCCCTGAGCAGCTGTATGCTGCCTACCTCGGCGGCTATGAACAGTGTGATGCTGGCTGGCTGTCCGACCAAACCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018798:ENSRNOT00000025496:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.008 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(87.2=98.4),PF073547=Sp38=PU(56.0=33.6),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF073547=Sp38=PD(42.7=54.2),PF0019312=Xlink=PU(60.4=98.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTTCCCCGAGTCAAATGGA
R:
CGAAGGAGAAAGCATAGCGGG
Band lengths:
300-579
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]