HsaINT0145143 @ hg19
Intron Retention
Gene
ENSG00000100241 | SBF1
Description
SET binding factor 1 [Source:HGNC Symbol;Acc:10542]
Coordinates
chr22:50899588-50900147:-
Coord C1 exon
chr22:50899952-50900147
Coord A exon
chr22:50899716-50899951
Coord C2 exon
chr22:50899588-50899715
Length
236 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TCTGCCTGGCCTGTCCTAAGTTG
3' ss Score
4.75
Exon sequences
Seq C1 exon
CCCAAGCTGCTGCGGCCGCGCCTGCTGCCGGGTGAGGAGTGTGTGCTGGACGGCCTGCGCGTCTACCTGCTGCCGGATGGGCGTGAGGAGGGCGCGGGGGGCAGTGCTGGGGGACCAGCATTGCTCCCAGCTGAGGGCGCCGTCTTCCTCACCACGTACCGGGTCATCTTCACGGGGATGCCCACGGACCCCCTGG
Seq A exon
GTGAGCCTGCAGACTCTCTGGCCCTGTCGCCCCCTCTCCCCCAGGTCTTTGGGATGGATGGGCTTTCCCTGCCTCCCTCTCCCTTTTCTCGGGGGTTCTGGGTGCCCGTGGGAAACGGGCCTTTGTCTGCTCCTTCCCCACCCACTTGGGATTCCCCATAACTGTGGTACCCTGAGATTCTGGGACCCCCCCCCCCTTACCTTCCTTGCTTCTGACTCTGCCTGGCCTGTCCTAAG
Seq C2 exon
TTGGGGAGCAGGTGGTGGTCCGCTCCTTCCCGGTGGCTGCGCTGACCAAGGAGAAGCGCATCAGCGTCCAGACCCCTGTGGACCAGCTCCTGCAGGACGGGCTCCAGCTGCGCTCCTGCACATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100241-SBF1:NM_002972:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.091 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0289315=GRAM=PU(74.7=98.5)
A:
NA
C2:
PF0289315=GRAM=PD(24.1=48.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAGGAGTGTGTGCTGGAC
R:
CTGGAATGTGCAGGAGCG
Band lengths:
293-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)