DreINT0036998 @ danRer10
Intron Retention
Gene
ENSDARG00000099412 | bcan
Description
brevican [Source:ZFIN;Acc:ZDB-GENE-030131-6045]
Coordinates
chr16:29380165-29381130:-
Coord C1 exon
chr16:29380972-29381130
Coord A exon
chr16:29380248-29380971
Coord C2 exon
chr16:29380165-29380247
Length
724 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TGGCTTTTCTGTTTGCTTAGATA
3' ss Score
6.53
Exon sequences
Seq C1 exon
ATCTAGAGCATTGTGAACCAGGCTGGGAGAAGTTCCAGGGGTTTTGCTACAAGCATTTCGCCAAGCGTCAGAAATGGGAAGTGGCAGAGCAGCACTGTCGCATGTGCGGAGGTCACCTGGTTTCTGTTATGTCACCTGAGGAACAGTTGTTCATCAATG
Seq A exon
GTATGTCTAAGCAGCTGTTTGCATAGATGACCCATTCCTCTTGATCTAATCAGTTTGACTTCTTATCAGGTGATGGCAGAACATTCAGATTGATGGAACTTGATTTGAACTTGAAGTGTGCTAAACGAGGTCATTTTCAGGTTACTGAATTCGAAAAATTGCAGAAATGTCCTGCGGATTGTGTGTTTGTTGCTGGTAGCTATGTGCAAGTTTGTGTTATAATGGATCATAATTAGCTGGTTAAAAAAGATTTCTTTATTTTGAATGTCTCGCTGAATAATTCACTTACCTGTTTTATTTTTAAAAAAAACATAAAATCCATGCTTTTTTCATTGGTAAATAGCAAAAATTAAAAGTAAATGCCTATTTTTTATAAAATGTACATTTGCATATGCAATACTAATTTGATGTTTATTGAACTATTGTATTAAAGCAATGTCTGCTTCAGAAAAGCAAGAATATTGGTTAAACAAAGAATCAAAAAAGCTGGTTTAGCTTACAGTACATACAGGAGTTCTTAAAGAACCAGGGTTGTTGACATAACTTTGAGAGGCCCTGCATGAAGGGCTTTTAACATGTCACCTTTTTCATGTGAGTGAATGAGGGTTGTGTTCAAGGGGCCTCTGCAAATCTGTCACATATAATGCATCAGGGTGTTAAACAGGACGTGTTTTGTGTCTTACTGAAAATGTATGCTGGTTATTTGGCTTTTCTGTTTGCTTAG
Seq C2 exon
ATAAATACAGGGAGTATCAGTGGACGGGCCTCAACGACAAAACAATTGAGGGAGATTTCCGTTGGTCAGATGGAAACCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099412:ENSDART00000162835:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PU(30.2=59.3)
A:
NA
C2:
PF0005916=Lectin_C=FE(25.5=100)
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:
AGAGCATTGTGAACCAGGCTG
R:
CAGAGGGTTTCCATCTGACCA
Band lengths:
238-962
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]