DreINT0099176 @ danRer10
Intron Retention
Gene
ENSDARG00000104248 | muc5a
Description
mucin 5a [Source:ZFIN;Acc:ZDB-GENE-110914-165]
Coordinates
chr25:8097494-8097823:+
Coord C1 exon
chr25:8097494-8097611
Coord A exon
chr25:8097612-8097684
Coord C2 exon
chr25:8097685-8097823
Length
73 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CTGCTTACTTTCCTTACCAGTAC
3' ss Score
7.43
Exon sequences
Seq C1 exon
GTATGGTCGAGGATGACATCGGTCAGAGTGGATGTGTTCCAGTGAACAAATGCCCATGTGTACACAATAACAAAACCTACTTCTCAGGAGACTCGTACACACAGGCTTGTAAAACATG
Seq A exon
GTGAGTTAAGCACAGAAAAACGAACCTTTAAACAGAATTTCACCAAACTAACGCTGCTTACTTTCCTTACCAG
Seq C2 exon
TACATGTGATGCTGGACACTGGACCTGCTCATACCTGGACTGTCCTGGAATCTGCTCTGTTGTTGGAGGGTCTCACGTCACCACTTATGATGGAAAAACCTTCACCTTCAGTGGGAACTGCGACTACATCCTCACTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104248:ENSDART00000162129:8
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:
PF0182612=TIL=PD(29.8=42.5),PF0009313=VWC=PU(35.7=50.0)
A:
NA
C2:
PF0009313=VWC=PD(62.5=74.5),PF0009420=VWD=PU(18.3=59.6)
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:
CGGTCAGAGTGGATGTGTTCC
R:
GACCCTCCAACAACAGAGCAG
Band lengths:
171-244
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]