DreINT0099082 @ danRer10
Intron Retention
Gene
ENSDARG00000058556 | muc5.2
Description
mucin 5.2 [Source:ZFIN;Acc:ZDB-GENE-121108-1]
Coordinates
chr25:8340546-8340924:+
Coord C1 exon
chr25:8340546-8340713
Coord A exon
chr25:8340714-8340829
Coord C2 exon
chr25:8340830-8340924
Length
116 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAT
5' ss Score
7.88
3' ss Seq
ATCTTTATTATTTTATTCAGAGA
3' ss Score
5.96
Exon sequences
Seq C1 exon
GACTGTGTGGAAACTACAATGATGTCCAATCAGATGACTTTAAAACAGATTTGGGTATCACAGAGGGCACAGCGATATCTTTTGCCAACTTTTGGAAGAAAACCCCATATAGTTGTCCTGATCTTGAAAACACATTTGACAACCCCTGTAGCCTGAGTGTGGACACAG
Seq A exon
GTATATGAAGTATTACAATAAACGGTTTTAAATAGTAATAACTAATTAATGGTATTCGCAAATGCATATGTTGCAAACTTTACAGAACTATGTCGAATCTTTATTATTTTATTCAG
Seq C2 exon
AGAAACTTGCTAAAGACTGGTGTTCCCGTCTGACTAACCAAAGTGGAGCCTTTTCTGCATGTCATTCAGAAATATGCCCAAAGATTTACTATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058556:ENSDART00000153536:15
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:
PF0009420=VWD=PD(12.3=33.3),PF087426=C8=PU(0.1=0.0)
A:
NA
C2:
PF087426=C8=PU(40.8=96.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGGAAACTACAATGATGTCCA
R:
GGGCATATTTCTGAATGACATGCA
Band lengths:
244-360
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]