DreINT0037000 @ danRer10
Intron Retention
Gene
ENSDARG00000099412 | bcan
Description
brevican [Source:ZFIN;Acc:ZDB-GENE-030131-6045]
Coordinates
chr16:29379138-29379544:-
Coord C1 exon
chr16:29379400-29379544
Coord A exon
chr16:29379324-29379399
Coord C2 exon
chr16:29379138-29379323
Length
76 bp
Sequences
Splice sites
5' ss Seq
TTTGTGAGT
5' ss Score
5.91
3' ss Seq
CGTGTTTTGTTTGTCTTTAGCAG
3' ss Score
8.2
Exon sequences
Seq C1 exon
CTCTATCAAAACTGGTATCGGGGTCAACCAGACAGCTACTTCCTATCAGGAGAGGACTGTGTTGTTATGGTGTGGTATGACGATGGCCGCTGGAGTGATATCCCCTGTAACTACCAGCTTTCCTACACCTGCAAAAAGGGCATTT
Seq A exon
GTGAGTAAATAACTTTCACCATTGATAATTTTGGCCCAGAAAGAGCAAATGTTCATCGTGTTTTGTTTGTCTTTAG
Seq C2 exon
CAGCATTCTGTGGCCAGCCCCCTCTTGTGCTGCATGCTAAGATGTTTGGACGCCGTCAGTTAAAGTACAGGGCGAATTCACAGGTGCGCTACTACTGTGAGTCAGGCTTCATTCAGAGACAGAACCCTATCATCACCTGTCAGAGCAATGGACTATGGGAGGAACCCAAAATCATGTGTTCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099412:ENSDART00000162835:12
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=PD(42.5=91.8)
A:
NA
C2:
PF0008415=Sushi=WD(100=90.5)
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:
ATGGTGTGGTATGACGATGGC
R:
AGTAGCGCACCTGTGAATTCG
Band lengths:
172-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]