DreINT0037006 @ danRer10
Intron Retention
Gene
ENSDARG00000099412 | bcan
Description
brevican [Source:ZFIN;Acc:ZDB-GENE-030131-6045]
Coordinates
chr16:29388185-29390395:-
Coord C1 exon
chr16:29390102-29390395
Coord A exon
chr16:29389316-29390101
Coord C2 exon
chr16:29388185-29389315
Length
786 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
TCTTGTTTTTTCCCCTGCAGCTA
3' ss Score
11.74
Exon sequences
Seq C1 exon
GGGAGGTTTTTCATGGCTCAACCCCGCAGCGCTTCAGCTTGTCAGAGGCAAAGGCGTACTGTGAGCAGCAGGACGCTCAGCTCGCTACCACAGGTCAGCTGTACGCTGCCTGGAATGATGGTCTGAACCACTGCAGTCCTGGCTGGCTCGCTGACGGAAGCGTTCGCTACCCCATCGTGACCCCCCGTGAACGCTGTGGGGGCTCTGAACCTGGCGTCAAGACCGTCTATCGGTTTAGCAATCAAACAGGATTCCCTGAACCAAACACTCGCCATGATGCTTACTGCTTCAAAG
Seq A exon
GTATTTACAGATTTGAGTTTTATCTGCAAATGTATAAACTGTATAACACAGGATTCAAACTGTGGGGTTCAAAGGGTGTGGTGCTAGGTCTACAATAAATTAAAATAAAGCTGTATTTTATACATAAAAAGCATATTAAATGCAAGTAAAGCACCGACATTAATACTTCAAATTATGCTTCATCATTCATATACAGTATAATTATTCTTAACTGTATCATACTATCATAATCGTACTACATTTTATAATATTTTAAATAATAGTAAAAATCCTCATGAGAAATTGGTAAAAGTGGCAAAGTATAAATATAAAAAAAAATTTAAAATTCTAATGAAAATAAAACAGGTCATTATACATTAGAATTGTTTAATTTTTGATCATTTTAAAATATATACAATAAAACCTAATAAAAAACACATTTTTTCATATGTTTTCTCCGACACAAAAAAATATTTCCCCCATTTTTTCTTACTATGGAAATCACCATCAAATGCATGGTTAACAGCATTTTTCTTTTCTATGTTGTGTTGTGTAATCCATTTTGTGTTATCTTAACAAAACTTATAGAAACTTATAGAAGGTCAATGCATCATATTAAATTATAATACATACTAAGTTTTTCAGAACTATTGTCACTTTTTAGGATCACATTTAACATTTCCCTCTCATGGTATAATTGCATATTTCTACATGATAACATGGTACTGCATTTATATTTTAAGAAAGCAGTCCTGTTTTTTTAATGTAACACTTTGGTATATTTGTTTCTTGTTTTTTCCCCTGCAG
Seq C2 exon
CTAACAGCAACTCTCAAACAGCCCCACCTGCAGATTATATGGCAACATCGCCAGAGGAAACAGAGCAGCATATCGTAACTTTAGCAGAACCCCAAGAGGAATACAGTGTGCATCAGGTCACTCAGCGATCTGAAAATGAAGCTCAGGGAGCTGTTGAGTCCTTTTCAATTTACAGCACTCAAACTGCTTCAGAAACTGAGGAACACAACCATACCTCAAGCCCTCAAGAAGACATCATTATTGGCTCCAGAAAAGACCTCACTACTCCAACCAGCACAGAGGGAAATACTGAGACCATTGAGGTCACCTGGCAAAATGTTGAGTCCATTCCTGAAATTTACATAGATCCAAAACGCAATAATTTCATGCTAGAGGGAGAACCTGAAATAAAAGCTTCAGCTGTCGATGGTGTGAAAAGCAGCAATCATAGACACTACCAACCAATGCCAGATACTAATCTAGAGCCAGGGGAGCCTATCGACTTCATCCCACCTACAGTGGCTCATCATGGAACAACAGAGGAACCGTCCTCTCCACCAAAGGAAATCAATGGGTCCAAACACTACCAACCCATGCCTGACACCAACCTGGATGATGAAGATCATATGACAACTCAGAGCACTACACTGCAATATGACTCAAGCAATAACACAACTCAAGATGCTTCAGTCCAGTCGACGTATCACCCTGATGGTGCAACATTAGAGACAAATGCAGGAAATATCACTGAGGCTCCAGAGTCAGATGACAACCAGGGTCTTTTTACACACACAACTCAGCCCACCTCAACGAGCACATCCAGCAGGGAAGGTTGGTTGGAGAGTTCTGGTGAAGATTCAACCACAGAAAAAGCAATATATCTGGATTTGACCACAAAAGAAGCAGTAAATCTGGATTCGACCACAGAAGAACCAATACACCTGGATTCAACCACAGAAGAAGCAATACACCTGGATTCAACCACAGAAGAAGCAATACACCTGGATTCAACCACAGAAGAAGCAATACACCTGGATTCAACCACAGAAGAAGCAATGTTTAGCACACATAATTCAGAAATATATAGAGCATCTACAGCTGAGACTTTGACAGAAAGCTACTCATCAACACATCTGAACAATATTAGCCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099412:ENSDART00000162835:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.293 A=NA C2=0.989
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=98.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCGCCATGATGCTTACTGC
R:
TTTGCCAGGTGACCTCAATGG
Band lengths:
343-1129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]