DreINT0024956 @ danRer10
Intron Retention
Gene
ENSDARG00000045799 | acanb
Description
aggrecan b [Source:ZFIN;Acc:ZDB-GENE-100422-16]
Coordinates
chr25:19121203-19121637:-
Coord C1 exon
chr25:19121463-19121637
Coord A exon
chr25:19121331-19121462
Coord C2 exon
chr25:19121203-19121330
Length
132 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
ATTGCATGCATTCTGCTTAGATA
3' ss Score
5.22
Exon sequences
Seq C1 exon
GCATTGTATTTCACTACCGAGCAATTTCTACCCGATACACATTAACCTTTGAAATGGCAAAAGCAGCCTGCATTCAGAACAGTGCTGTTATCGCAACTCCAGCACAGTTGCAAGCTGCCTATGATGATGGATTCCATCAGTGTGATGCTGGCTGGCTTTCAGACCAAACCGTGAG
Seq A exon
GTAATGACAATTGTGTTTAACTGCTTGATATGCACAAAAATATAGTATTTAAGTAAAATAATCAACATCCCCTTCAACTTTTCTAAAGAAACAAACTCATAACTATAATAACATTGCATGCATTCTGCTTAG
Seq C2 exon
ATATCCTATCCATGAACCAAGGGAGCCTTGTTATGGAGACAAAGATAATTTCCCAGGTGTTCGAACATATGGAGTCCGAGACGTCAATGAAACCTATGATGTGTACTGTTTTGCAGAGAAAATGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045799:ENSDART00000149917:4
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:
PF0768612=V-set=PD(4.7=3.4),PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),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:
ACCGAGCAATTTCTACCCGAT
R:
TCATTGACGTCTCGGACTCCA
Band lengths:
250-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]