HsaINT0161996 @ hg19
Intron Retention
Gene
ENSG00000148290 | SURF1
Description
surfeit 1 [Source:HGNC Symbol;Acc:11474]
Coordinates
chr9:136219301-136219621:-
Coord C1 exon
chr9:136219549-136219621
Coord A exon
chr9:136219464-136219548
Coord C2 exon
chr9:136219301-136219463
Length
85 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TCACACACCTTCCTTTATAGATT
3' ss Score
8.79
Exon sequences
Seq C1 exon
AGTCACCATCCTGGTAAATAGAGGGTTCGTTCCCAGGAAGAAAGTGAATCCTGAAACCCGGCAGAAAGGCCAG
Seq A exon
GTAAGGGACATGGACTCTTCCTACTTTAGAGAAGGCTCTGGGAGTCCACCAGGCTCCATGCAATCTCACACACCTTCCTTTATAG
Seq C2 exon
ATTGAGGGAGAAGTGGACCTCATTGGGATGGTGAGGCTGACAGAAACCAGGCAGCCTTTTGTCCCTGAGAACAATCCAGAAAGGAACCACTGGCATTATCGAGACCTGGAAGCTATGGCCAGAATCACAGGCGCAGAGCCCATCTTCATTGATGCCAACTTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148290-SURF1:NM_003172:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.511 A=NA C2=0.236
Domain overlap (PFAM):
C1:
PF0210410=SURF1=FE(11.0=100)
A:
NA
C2:
PF0210410=SURF1=FE(24.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCTGAAACCCGGCAGAAAG
R:
TCAATGAAGATGGGCTCTGCG
Band lengths:
178-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)