DreINT0089815 @ danRer10
Intron Retention
Gene
ENSDARG00000006639 | lnpb
Description
limb and neural patterns b [Source:ZFIN;Acc:ZDB-GENE-030131-9455]
Coordinates
chr6:10623268-10623704:-
Coord C1 exon
chr6:10623517-10623704
Coord A exon
chr6:10623327-10623516
Coord C2 exon
chr6:10623268-10623326
Length
190 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
TTTTCTCCCTCTATTTATAGAGT
3' ss Score
10.15
Exon sequences
Seq C1 exon
GACATAAAGGATCTGGAGGAGTTTCGTGCAAAGAACCAGCGTTTGCTGAAGTTATGGGTCGGCCGGCTTCTCTTCTACTCATCTGCTCTGTACCTGCTGACATGTCTGTGTGTTTATTACCTGTACTTCCCCCAGCAGTGGGGCGCTCGGCTCATCACTGCCCTGCCTCTGCTGGCCTTTCCTGCACT
Seq A exon
GTGAGTCACAAGCACACTAGTACTGGATTAGGACTTTGTAGTAAGCATGCTTTTTGTATTTATGCTGTTAGTGCAGTTATGTTTTACAGTAGCTGTTACTTACACATTGTACAGATATACACACCCTGGCTTAGCGGAGTTGATGTTCATAATTATTAATCGGAGTAATGTTTTCTCCCTCTATTTATAG
Seq C2 exon
AGTTTTACTACTACGAAAAGTGCTCATTTTCCTGTTCTCCAAACGCACAGAGAGAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006639:ENSDART00000133893:4
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:
PF083957=7tm_7=FE(44.3=100),PF110263=DUF2721=FE(50.0=100),PF060117=TRP=FE(56.9=100),PF074317=DUF1512=PU(20.0=22.2)
A:
NA
C2:
PF083957=7tm_7=FE(14.3=100),PF110263=DUF2721=FE(16.1=100),PF060117=TRP=FE(18.3=100),PF074317=DUF1512=FE(28.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGGATCTGGAGGAGTTTCGTG
R:
TGTTTCTCTCTGTGCGTTTGGA
Band lengths:
242-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]