DreINT0110071 @ danRer10
Intron Retention
Gene
ENSDARG00000042186 | paplnb
Description
papilin b, proteoglycan-like sulfated glycoprotein [Source:ZFIN;Acc:ZDB-GENE-030131-6023]
Coordinates
chr20:33608314-33608566:-
Coord C1 exon
chr20:33608457-33608566
Coord A exon
chr20:33608375-33608456
Coord C2 exon
chr20:33608314-33608374
Length
82 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTCTGTGTTTTGATATTAAGGAC
3' ss Score
6.49
Exon sequences
Seq C1 exon
TTGAGGCCACCATCTGATGATTATTATGGTGAATATGGCCCTTATGGACCCTGCAGCCGTACATGTGGTGGAGGAGTCGCTGTGAGAACAAGGATCTGCAACACGATGAG
Seq A exon
GTGAGTTGAGTACATCTGAAACTTTTTATTTTTTCTTTGTAGTCTATTTCATTTAAGTCATCTTCTGTGTTTTGATATTAAG
Seq C2 exon
GACGGATGGTGGACACAATTGCGTGGGACCATCAAAGTCCTACAAGCTCTGTAACACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042186:ENSDART00000061836:3
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:
PF0009014=TSP_1=PU(54.0=73.0)
A:
NA
C2:
PF0009014=TSP_1=FE(40.0=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:
TGAGGCCACCATCTGATGATT
R:
TGTGTGTTACAGAGCTTGTAGGAC
Band lengths:
169-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]