BtaINT0025243 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015789 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:HGNC:23059]
Coordinates
chr3:14236380-14237554:-
Coord C1 exon
chr3:14237444-14237554
Coord A exon
chr3:14236755-14237443
Coord C2 exon
chr3:14236380-14236754
Length
689 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CCGGCTCCGCCCGTCCACAGAGG
3' ss Score
8.6
Exon sequences
Seq C1 exon
TCCCTCCCTCATCCTGCAGCATGGCCCCACTGTTCCTGCCCCTCCTGGCAACCCTGGTTCTGGCCTGGATCCCTGTGGCCTTGGCTGATGCTCTGGAAGGAGACAGCTCAG
Seq A exon
GTAAGTAACCCCACTCAGGGTCATGGTTTGTCTCCTACATCTCCCCTGTGGTAGGAAGGAGCCTCTTGTCCAGCCCTAAGCAACCTCTGTCAGCCTCCAGGGCCCAGGAATTGGGAGCACTGTGGGGGAGGGCCTATGCAGGGACACTTGAAAATCAGGGATGATTTGTGGGCCCTTGATAGGGTGATGGAATCCGGGGAGTAGGGCTGGGGTGGGGCACTAGGTACAAGGCTGTCGGTCTCTAGGGTGGAGGATGGGGGACCCTCCGGGACTATGAATGGGGCTGCGAGGCTGAACAGGGATGGAACTGGAAGAAATCCAGAAAGGGGCTCTGAAGGAACAGACTAGGGAAATTTTGAGAAGAGGGTTGCAGGACCCAGGGGTGAGGCTTGAGGACCCAGAGTGGGGCCCAGGAATCCTAGGGTGGTATTGGGAGGCTCTGGGGGCAAAACTAGCTGAGAGACTTTGTGGACGGGTCTGTCGACCCTGAGGGGTGGGCGTGAGGGACCTACAGGTGAGTTTGCAGGACTCAGCGGCCAGAGCCCTGAGTTCCTGGTTGGGGGCCGGGGGGCGGGGTTACGAAAACCCGAGGGCGGGGCGTTGGGATCCTGGGGCGGGGCTTAGAAACCCCGGGGTGGGGCGCGGTAGATCTACAACGCGAAGTTCCAGCCGGCTCCGCCCGTCCACAG
Seq C2 exon
AGGACAGGGCCTTCCGCGTGCGCATCGCGGGCGACGCGCCGCTGCAGGGCGTGCTGGGCGGCGCCCTCACCATCCCATGCCACGTTCACTACCTGCGGCCGTCGCCGAGCCGCCGGGCCGCGCAGGGCTCCCCGCGGGTTAAGTGGACCTTCCTGTCCGGCGGCCGGGAGGCCGAGGTGCTAGTGGCGCGGGGCCTACGCGTCAAGGTGAGCGAGGCCTACCGGTTCCGCGTGGCACTGCCTGCTTACCCGGCGTCACTCACCGACGTCTCCCTGGTGCTGAGTGAGCTGCGGCCCAACGACTCAGGCATTTACCGCTGCGAGGTCCAGCACGGCATCGACGACAGCAGCGACGCGGTGGAGGTCAAGGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015789:ENSBTAT00000020965:2
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=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(1.6=6.5)
A:
NA
C2:
PF0768612=V-set=PD(97.6=98.4),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGCTGATGCTCTGGAAGG
R:
TAAATGCCTGAGTCGTTGGGC
Band lengths:
345-1034
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]