GgaINT0124309 @ galGal3
Intron Retention
Gene
ENSGALG00000003187 | SURF1_CHICK
Description
NA
Coordinates
chr17:7538437-7538761:-
Coord C1 exon
chr17:7538683-7538761
Coord A exon
chr17:7538565-7538682
Coord C2 exon
chr17:7538437-7538564
Length
118 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCATTGTGGTTCTCTGCAGACG
3' ss Score
9.58
Exon sequences
Seq C1 exon
ATATCACACTGCTTGCTCAGAAGAACATTTTTCGGGTTTCCCCGAACGAAAGCAGGTTCTGCTGTGACCCAGCAGGGAG
Seq A exon
GTGAGCAGAGCTGTGTGGGGTTCTGTCGCCTTCAGCCTCACACTGAGGTGCCGTTTCCTCAGGGATGTAGCACCTCTCCTCCTGTTCCTGCCCGGTTCCTCATTGTGGTTCTCTGCAG
Seq C2 exon
ACGTTTGCCTGAGGCTCTGCAGCCCACGAAGCTCCACGACAGCCACCAGTGCAGCTGGAGAGGACGCCTGGCTGAAGTGGGGCCTCCTCCTCGTGCCCCTGACTGCATTCTGTCTCGGCACATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003187:ENSGALT00000005056:2
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0210410=SURF1=PU(6.4=32.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACACTGCTTGCTCAGAAGA
R:
GCCATGTGCCGAGACAGAATG
Band lengths:
202-320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]