DreINT0099163 @ danRer10
Intron Retention
Gene
ENSDARG00000104248 | muc5a
Description
mucin 5a [Source:ZFIN;Acc:ZDB-GENE-110914-165]
Coordinates
chr25:8098369-8098806:+
Coord C1 exon
chr25:8098369-8098503
Coord A exon
chr25:8098504-8098629
Coord C2 exon
chr25:8098630-8098806
Length
126 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTAAATCTGATTTGCTTCAGGTC
3' ss Score
8.47
Exon sequences
Seq C1 exon
GTCCTGTGAGCATCTTCCAGCCCTCTTCATCGTTCATTATTGCTGATTTACACAGTATTCGTCTGGAAATCCAGCTAGCTCCAATTATGCAGTTGTATATTGTAGCCAGCACTGAAGAGAAAGGGAAAATGACTG
Seq A exon
GTGAGTAAAGAAAGACAGCAAATCCTGCTTTTAATGATTCACTGTAATCCTATTTTAAGAACCATGCATCTCATTAATACAATTGTAATACATTTGTTGTATTTTCTTAAATCTGATTTGCTTCAG
Seq C2 exon
GTCTGTGTGGAAACTATAACGATGTCCAAAAAGACGACTTTAAAACAGAATCGGGCATTATAGAGGGCACATCCACAACCTTTGTCAACTACTGGATAAAAAACAGAGCACAGTACAGCTGTACAGATGTTAAAGACACATTTACAGAAAACCCCTGTAGCCTGCGCATTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104248:ENSDART00000162129:12
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=FE(28.8=100)
A:
NA
C2:
PF0009420=VWD=PD(12.4=32.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGTGAGCATCTTCCAGC
R:
CAGCTGTACTGTGCTCTGTTT
Band lengths:
256-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]