DreINT0180317 @ danRer10
Intron Retention
Gene
ENSDARG00000016538 | zgc:55888
Description
zgc:55888 [Source:ZFIN;Acc:ZDB-GENE-040426-834]
Coordinates
chr4:9470110-9471130:+
Coord C1 exon
chr4:9470110-9470249
Coord A exon
chr4:9470250-9470976
Coord C2 exon
chr4:9470977-9471130
Length
727 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TGCTTGGGATGTCTCTTCAGGGT
3' ss Score
7.27
Exon sequences
Seq C1 exon
ATGGTCCTCAAGCCTCCAGACTTCAGGAGGTCAATGTAACGGTCTATGAGCCACAAAAGTGTAACAGATTTTACAGAGGGAAGGTGTTGAAGTCTATGATATGCGCTGGAGCGAATGAAGGTGGAATGGATGCATGTCAG
Seq A exon
GTAAGTAAATGTTTGCATCTGTATTTGGTATAGCATCACATTCATGGCATAATATTATTTTTAAACTAGATTTTTCTTTCTTTATACTCTTAAGGGTCATTTTCACTAAGCACAATTATGATAAAGAAAGATAAGAAACAACAGCAGAATCCAAACCACAACTATTGCAAAAAAGATGTGGGGAATAAATGATAAAACACTGACAACCATTCAGAACCCATTGAAATGCAAACCTAAAGCTACAAATGACATTGTGCTGGAGCTCTGCTTGATATTAAGCCCTGTTTTCAAAGATTTTTACAATTATTGTGGAATTGATTGGTTCTAATTTGGGAAATGTTGAATTAAATAAATACATTGACATTTTGCAAGCCAGGCTGTCAAATTGAAGTACAAAAGTAAAATAACCTCCACTATCCAGTGCTAGTTTCAGCATCTTTGTATTGCCGCCTTTGAAAATGCTGGAGAAAATGATTAGGTTTAATTCCACTACACTGACCTTGACAGCTAAATTCACTGTTTGATTAGATTGATTACATGAGCTGGATTCAATGGTCAGATGTGCTAACAACAAGGGGGTATACTGCCAAATGAAAGGTGTAAAATAAACAAAAATTAACAGATCATTATCATTCGTCATTATGCACAAATGTATTGTTATATTTATAGTTATTAAGCTTGATGTGAGTTGCATGTTGTCCCGTGTGTGCTTGGGATGTCTCTTCAG
Seq C2 exon
GGTGACTCTGGCGGTCCCCTCTCGTGTTTCGATGGTGAGAGGTACAAGCTTGCTGGAGTGGTCAGTTGGGGGGTCGGATGTGGTCGAGCTCAAAAACCAGGGGTCTACACCACCCTATACCACTACAGACAGTGGATGGTGTCGTCCATGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016538:ENSDART00000012659:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.4=100)
A:
NA
C2:
PF0008921=Trypsin=PD(19.9=86.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGTCCTCAAGCCTCCAGAC
R:
CACGCATGGACGACACCATC
Band lengths:
294-1021
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]