DreINT0099174 @ danRer10
Intron Retention
Gene
ENSDARG00000104248 | muc5a
Description
mucin 5a [Source:ZFIN;Acc:ZDB-GENE-110914-165]
Coordinates
chr25:8095168-8096907:+
Coord C1 exon
chr25:8095168-8095378
Coord A exon
chr25:8095379-8096781
Coord C2 exon
chr25:8096782-8096907
Length
1403 bp
Sequences
Splice sites
5' ss Seq
GCCGTGAGT
5' ss Score
8.56
3' ss Seq
TTTTTTTTTTTTTTGAGCAGCAA
3' ss Score
6.36
Exon sequences
Seq C1 exon
ACAAGCCTTTGCCAGCAGTACCTCAGCAGTCCAGGGTTTAGTGGCTGTTATGATGTGATGGACATGAGTTCATTTGAAAAAGCCTGTGAGAGCGACCTGTGTCAATGTTACGGCAACCACGACTGTCTGTGCAACACCCTAACAGAGATTTCACAGCAATGCACACATGCTGGAGGACAACCAGGAACATGGAGGACAAAACAGCTCTGCC
Seq A exon
GTGAGTATCATAAAATAAAAAGAATAAACAATTCATACTCTGAGTGTGTTTACATGCATGTTCTTTAGCTGATTTGTATGCGGTTGTGTAAATGAGTGAGTATTTTTCCTCAGAAAAGGATCAGAAATGACACAAGCATATCGGCTAAGTTATTTTTTCCATTATATTTATTTTGCCTGGCATGTAAACATCCTTACAGGCACATGTGTGACTAGGCTATATAGCCATAAGTCAGTTTAAAATGATAATTTTACTAGCGTCTATTTTCGTCTTAATGTAAACAATTAAGTGGCACAGTTGGTAGCAATGTCGCCTCACTGCAAGAAGGTTGCTGGTTCGAGCCTCTGCTGGGTCAGTTGGTATTTCTGTGTGGAGTTTGCGTGTTCTCCCCATGTTGATTTCCTCCGGGTGCTCCAGTATACCCCAAAAGTCCAAAGACATTTGGTACAGGTGAATTGGGTTAGCTAAAATTGTCCGTAGTGAATGAGAGTGTATGGATGTTTCCCAGTACTGGGTTGCAGCTGGAAGGGCATCTGTTGCGTAAAACATATGCTGGATAAGTTGGCGGTTCATTCTGCTGGTTCATTAAGCTAAAAAGAAAATAAATGAATAAATAAACTATTAATCCATTCAAGTTAATTGACGAGGCACCTTACAACAAGAAGGTCACAAGTTCCAGGCCGGGCCAGTTGGCATTTCTGTGTGGAGTTTGCATGTTCTCCCTGTGTTCGTGTGGGTTTCTTCCAGGTGCTCCGGTTTCCCCCACAATCCAAAGACATGTGCTATAGGTGAATTGGATGGACTAAATTGGCCGTAGTGTATGAGCGTGTGTGAATGTGAGTGTGTATGGGTGTTTCCCAGTACTGGTTTGCAGCTAGAAGGGCATCCGCAGCGTAAAACATGCTGGAATAGTTGGTGGTTCATTCAGCAGTGGCGACCCCTGATAAATAAGGGACTAAGCCGAAGGAAAATAAATGAAAACAAAAATTTGTAAATAAAATAAATGAAAATTATAAAAGCATACCAACATTCATAAATATATAGAACAATATATAACTATAACTGTACATAAATATAAAGAGCAAAATAAAAAAATAATATAAAACGAGTATATTTCTTTCATATTTATTCCATAATTGTCTGTAAGTTTAGCATTAGCATTCTTTAATACTATGAGATTATAATTCTTTATACTGTACAACATTATAATTCACTTAACAAGTAGAAACAGCCACACAAATGATAACATTTTAACTTGCTGAGAAAAAGCTAATTAAATAATAAAGACTTGTACTTTTAGTTTGTGGATAACCAAGTAAAAACAATTTATGTTTATGTGCAAAGTGAATGTATATATTCGTGAAGTAACGTAATAATTGCTTTTTTTTTTTTTTTTTGAGCAG
Seq C2 exon
CAAAGACGTGTCCTCTAAACCTGCTGTACCTGGAGTGTGGTGGTCCATGCAAGAGCACCTGCTCAGCCCCAACTGCAGATCTGATGTGTACCGATCACTGTGTGGACGGCTGCTTCTGCCCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104248:ENSDART00000162129:6
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:
PF087426=C8=FE(93.3=100)
A:
NA
C2:
PF087426=C8=PD(0.1=0.0),PF0182612=TIL=PU(66.7=90.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAGCCTTTGCCAGCAGTAC
R:
CTTCAGGGCAGAAGCAGC
Band lengths:
337-1740
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]