DreINT0130926 @ danRer10
Intron Retention
Gene
ENSDARG00000062968 | sbf1
Description
SET binding factor 1 [Source:ZFIN;Acc:ZDB-GENE-040718-139]
Coordinates
chr4:9963142-9963969:+
Coord C1 exon
chr4:9963142-9963367
Coord A exon
chr4:9963368-9963856
Coord C2 exon
chr4:9963857-9963969
Length
489 bp
Sequences
Splice sites
5' ss Seq
ACAGTGCAC
5' ss Score
-7.86
3' ss Seq
AATCTTTTTTTTTTTTCTAGTTG
3' ss Score
9
Exon sequences
Seq C1 exon
GAGAACCCGTACCCTGCAGTGACCATGCACAGAGTCCAAAGGACAGCTGAAAGCGCACATCCTCGGCTGCCACAGACCTCTTTTCCCCTGCTGGATGAGGTGGCCGTGCAGCTCTTCATAGACCACGCTACAGCTAAGCTCAAAACTGCCCCGCCGGTGGTCAAAGCCGAACTCAAGAGCATGGTTCCAACCGGACCGCCGCTCGGTGAGACAAAGTTCACTTACA
Seq A exon
GTGCACGCTTTCCACATTCAGATCAACTAAGAGGAGTTGATATATGTTATGGCTTGACATTATGGGTGTAAGTTTTTATGATGTATCAAGAGTCACGATGTCCAGGGCAATGTCAGCATAAGAGGGATTAATCACTCGCGCACCACTCTCTACAAAACAAATGCATTTATACATATCATTTTGTTAAGACTTGTGTGAGTGAAACCTGCAGTGTGTAAAAATACAGCTCCTATCTAAATGTTTGGGTTTGCTGTTATATGTTTTGTTGATTTAACATGTTTGTTCCATTTAGACTCATTTATTAAAGTGAAACTAAAGCTTTGTGCGCATGTGCTGTATTGATGGTAATTGCATTGCACAGGTCACTCTTCAGATTGTGAAAAATCTATACAGTAGTCCCAAAAATATAGTAGACTGCTTTGTGCTAATCTTCGTTCAAGCTTTGAAATAATAGTTGTCCCTTATTTGTAATCTTTTTTTTTTTTCTAG
Seq C2 exon
TTGACTTTGTGGACCGTAACGGGAATGTTCTGGCGAACAGCGCCAGGAGGTTAGAAGTGGTCCGGAACTGCATCACATACATTTTTGACAATAAAATGCTGGAGGCCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062968:ENSDART00000109452:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.220 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF123353=SBF2=PU(3.2=9.2)
A:
NA
C2:
PF123353=SBF2=FE(17.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAACCCGTACCCTGCAGT
R:
CTTCTTGGCCTCCAGCATTTT
Band lengths:
339-828
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]