DreINT0098269 @ danRer10
Intron Retention
Gene
ENSDARG00000103308 | mst1
Description
macrophage stimulating 1 [Source:ZFIN;Acc:ZDB-GENE-020806-3]
Coordinates
chr6:53420391-53420857:-
Coord C1 exon
chr6:53420743-53420857
Coord A exon
chr6:53420528-53420742
Coord C2 exon
chr6:53420391-53420527
Length
215 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
GTGACCTCTGTTGGGAATAGATG
3' ss Score
4.57
Exon sequences
Seq C1 exon
TATATGTAAGGAAATGCATTGTGGGTAAAGGAGAAGACTATCGAGGGAAAGTGTCGACAACTACAAGTGGACGAACATGTCAACAGTGGTGGTCAAAATTCCCTCATGACCACAG
Seq A exon
GTATGCGATCAATGTAATGTATGTGTATGAATGTAATTTCATGTATTTGTCTGTGAAACATGTTCCAAATATTTAATGTGTAAATATTTAAACAGCAGTCTAATATCTTACATTTTGATTTGTTTAATGCACCTTTGTATACAGTATTATACTCTAAGATACTGACTCATTGTGCGGCTGCGATGTTAGAATGATGTGACCTCTGTTGGGAATAG
Seq C2 exon
ATGGACTCCGTCTGCGACTAATGGCCTGGAACTGAACTACTGCCGAAATCCAGACGGCGACCGCATCGGCCCCTGGTGTTACACCACTGACCCCGAACGCAGATACGAGAGCTGCAATATCCCTCAGTGCAAAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103308:ENSDART00000162791:4
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:
PF0002421=PAN_1=PD(0.1=0.0),PF0005113=Kringle=PU(42.9=84.6)
A:
NA
C2:
PF0005113=Kringle=PD(55.8=91.5)
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:
TATATGTAAGGAAATGCATTGTGGGT
R:
CGTCTTTGCACTGAGGGATAT
Band lengths:
252-467
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]