RnoINT0024988 @ rn6
Intron Retention
Gene
ENSRNOG00000018798 | Bcan
Description
brevican [Source:RGD Symbol;Acc:2194]
Coordinates
chr2:187369281-187370127:-
Coord C1 exon
chr2:187370019-187370127
Coord A exon
chr2:187369653-187370018
Coord C2 exon
chr2:187369281-187369652
Length
366 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GCGTTGACCCCTGTCTACAGAGG
3' ss Score
6.41
Exon sequences
Seq C1 exon
TTCTTCCAAGTTTGCAGCATGATCCCATTGCTTCTGTCCCTGCTGGCAGCTCTGGTCCTGACCCAAGCCCCTGCAGCCCTCGCTGATGACCTGAAAGAAGACAGCTCAG
Seq A exon
GTGAGTAACCCTCCAGAGGGCCATTGCCTCTGCTACATCTCTCCCAGGGCAGAGGGCTGTTCAGCTCCAGTCACCTGCTTCCAGCCTAGGCACACGGACGGAGACAGATAGGGAAGCCCTGTGAGCAAGGGCTGGAACCGATTGCAAAATAGGAATGAATTGGGGACCCTAGCAGGGTTGCAAAGGGACACAAGATAGGATCTTAAGGGTGAAGGTTCAAATTCAGGACCCTGGGCAGGGCTCAGCACCCTGAGCCCGGCGTTGCACCCCAGGCGTGTTGGTCTTGGGGGGCGGGGCTTGAAGCCACGCGCACAGGCGCACTGCGTCCTGCGTCGGGCTGCAGCCAGCGTTGACCCCTGTCTACAG
Seq C2 exon
AGGATCGAGCCTTTCGGGTGCGCATCGGTGCCGCGCAGCTGCGGGGTGTGCTGGGCGGTGCCCTGGCCATCCCATGCCACGTCCACCACCTGAGGCCGCCGCCCAGCCGCCGGGCCGCGCCGGGCTTTCCCCGAGTCAAATGGACCTTCCTGTCCGGGGACCGGGAGGTGGAGGTGCTGGTGGCGCGCGGGCTGCGCGTCAAGGTAAACGAAGCCTATCGGTTCCGCGTGGCGCTGCCTGCCTACCCCGCATCGCTCACAGATGTGTCTTTAGTATTGAGCGAACTGCGGCCCAATGATTCCGGGGTCTATCGCTGCGAGGTCCAGCACGGTATCGACGACAGCAGTGATGCTGTGGAAGTCAAGGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018798:ENSRNOT00000025496:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(12.1=54.8)
A:
NA
C2:
PF0768612=V-set=PD(87.2=98.4),PF073547=Sp38=PU(56.0=33.6),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCGCTGATGACCTGAAAG
R:
AGCGATAGACCCCGGAATCAT
Band lengths:
348-714
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]