DreINT0130939 @ danRer10
Intron Retention
Gene
ENSDARG00000062968 | sbf1
Description
SET binding factor 1 [Source:ZFIN;Acc:ZDB-GENE-040718-139]
Coordinates
chr4:9982319-9983136:+
Coord C1 exon
chr4:9982319-9982526
Coord A exon
chr4:9982527-9982939
Coord C2 exon
chr4:9982940-9983136
Length
413 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTTTTTGTGTTTGGTTCAGTTA
3' ss Score
8.14
Exon sequences
Seq C1 exon
TTTCTGAAGAGCCCGAGCCCAGTTCATTGACGCTCTCGTCCACCATCCGCTCATCTGACCGTCAAACCATGAGTAATGTGGTGGAGCGGGCCTGCTGTCGGGACTACCAACGGTTGGGACTGGGCACGCTCAGTAACAGCCTGACCCGCTCCAAAAACGAGCCCTTCCGCATCTCCACCGTCAACCGGATGTACACTGTATGCCGAAG
Seq A exon
GTGAGCCCCATTAAAGCGACAGTTCACCCAGAAATAAAGATTTACTCCATCTCGCATGGTTGCAGCCTTATGACTACTATGACTATTTTCTGTCAAGCACAAAAGATGTTTTGAAAAATGCTGGAAACCACTAACCATTGACTTTCATAGGAAGAGAAAATGCTTATGCAAGTCAGTGGTTACCGATTTCCAACATTCTTGCAAACCTTTATGTGTTTTATTTTTTTGTTGAGCACAAAAGAAGATATTTTGAAGAATGTTTGAAACTGGTAACTATTGACTTATATTGTAAGAATAAAATGCTTTGGAAGCCAATAGCTGTCAACTTTATTCAAAATAAAAGTCACTAAAAATGCTGTGGAAAAAAAAGCATTGAAATGTTATTTACAGCTGTGTTTTTGTGTTTGGTTCAG
Seq C2 exon
TTATCCAGGGTTACTGATTGTCCCTCAGAGCATCCCTGATTCCACCATCCAGCGTATTTGCCGCTGTTACCGGCAGAACCGTTTCCCTGTTGTTTGCTGGAGAAACTCGCGCACTAAAGCTGTGCTGCTGCGATCAGCCGGTCTGCATGCTAAAGGAGTCGTGGGCTTCTTCAAATCACCCAATGCACCCACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062968:ENSDART00000109452:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.268 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF066029=Myotub-related=PU(14.5=88.6)
A:
NA
C2:
PF066029=Myotub-related=FE(15.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAGTTCATTGACGCTCTCG
R:
CTCCTTTAGCATGCAGACCGG
Band lengths:
349-762
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]