GgaINT1024372 @ galGal4
Intron Retention
Gene
ENSGALG00000012438 | SBF1
Description
SET binding factor 1 [Source:HGNC Symbol;Acc:HGNC:10542]
Coordinates
chr1:551155-551998:-
Coord C1 exon
chr1:551900-551998
Coord A exon
chr1:551360-551899
Coord C2 exon
chr1:551155-551359
Length
540 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
AACTGTCTTTGCTGTGCCAGGAG
3' ss Score
6.37
Exon sequences
Seq C1 exon
CTTGTTGCTTATGAAGTGAAGCGCATGCGTGCAGAAGAGGGGAACAAGCAGAAAATATTGCGGCACATCAAGGAGCTGGCAGAGAAACTTTACAAAAAT
Seq A exon
GTGAGTGCAGGAGGGGAACCTGCTCTTATGGGAGGGCTGGGAGAACCTGGCTGAGAGCCCACGTCCGTCTGTCCTTCCTCCGCTCACGTTACTGTAACTGGTGCTGGAAACACCATTATGGAAGCTACTGCTGGACCCCAAGGTGTCTGCCTGGCCTCAGCCTCTCCCTCGCTTCCTGAGTGGAGGTATTCCTGTTTTTGGTGGTCTGGGCATCAGGCACTTCCTTCCCCTTGTTCTGGAGCAGCTGCTGCTTGTGCTGCCTGGCCCAGGGTGCCCGTGGCCATCCCAGCCCTGAGCTCCTGAGGGCTTTTTGCTCTTTGCTGTGTGCTCAGCGTGCTGTCCCTGCAGCTCCTGAGAGCACAGTCTGATGGTGCTGTGAGCCAACAGCCTGCCCTCAGCACTGTGAGGTTCTGGGGGCTGCAAAGTGCTGCTGGGAGAGGAGAGGAGAGAAGCACAGGCTGCTGAGAGATGCCCCTGTGAGCCTGTGGGACAATGCACGACTTCCTCGTGGCTGAAAAGAAACTGTCTTTGCTGTGCCAG
Seq C2 exon
GAGAACCCGTACCCCGCCGTGACCATGCACAAGGTGCAGAAGCCCACTGAAGGCTGTCATCTGCGCCTGCACCAGAAGCCCTTCCCCCGTTTGGATGAGGGCACAGTGCAGTGGATCATCGACCAGGCCACAGCCAAGCTGCAGACAGCCCCTCCAGCTGTGAAAGCAGAGAAGAAGTGCATGGTGCCCTCGGGCCCCCCCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012438:ENSGALT00000020337:13
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=0.145
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF123353=SBF2=PU(2.7=8.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGTTGCTTATGAAGTGAAGCGC
R:
GCACCATGCACTTCTTCTCTG
Band lengths:
286-826
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]