HsaINT0161998 @ hg19
Intron Retention
Gene
ENSG00000148290 | SURF1
Description
surfeit 1 [Source:HGNC Symbol;Acc:11474]
Coordinates
chr9:136218666-136218997:-
Coord C1 exon
chr9:136218916-136218997
Coord A exon
chr9:136218838-136218915
Coord C2 exon
chr9:136218666-136218837
Length
78 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GGCTTGCTTTCAACCCCTAGGTA
3' ss Score
9.15
Exon sequences
Seq C1 exon
AGAGCACAGTCCCTGGAGGACCCATTGGAGGGCAAACCAGAGTTACTCTGAGGAACGAGCATCTGCAGTACATCGTGACCTG
Seq A exon
GTGAGTCCCCAGCGGCCCTCTGGCTTCCTCCCCTTCAGCCTAGCAGCCTGCTAATGCTGGCTTGCTTTCAACCCCTAG
Seq C2 exon
GTATGGACTCTCTGCAGCTACATCCTACCTGTGGTTTAAGAAATTCCTACGTGGGACACCTGGTGTGTGACAGATCAGCTGCTGAAGCCCTGTCCCTGGATAATGCAGTATTTCAAGACTGCCTTTATGCTGGATCATGTGCTACTGGTATAAAGTTCTGGCCTTCTACCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148290-SURF1:NM_003172:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0210410=SURF1=FE(12.3=100)
A:
NA
C2:
PF0210410=SURF1=PD(2.7=25.0)
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:
CTGAGGAACGAGCATCTGCAG
R:
CCAGTAGCACATGATCCAGCA
Band lengths:
183-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)