GgaINT0011635 @ galGal3
Intron Retention
Gene
ENSGALG00000020939 | SLC35C2
Description
NA
Coordinates
chr20:10678664-10679201:-
Coord C1 exon
chr20:10679033-10679201
Coord A exon
chr20:10678748-10679032
Coord C2 exon
chr20:10678664-10678747
Length
285 bp
Sequences
Splice sites
5' ss Seq
TGGGTATGT
5' ss Score
7.43
3' ss Seq
TATTGATTCTCTTCTTGCAGGGC
3' ss Score
9.44
Exon sequences
Seq C1 exon
AGGGTGGCATTGGTGCTGGTGGTTGTGCTCATCGCTGGGGGGCTCTTCATGTTCACCTACAAGTCCACGCAGTTCAACACACAGGGGTTCATGCTGGTGCTCTGTGCCTCTTTCCTTGGGGGTGTTCGCTGGACTCTCACACAGATACTTATGCAGAAGGCTGAACTGG
Seq A exon
GTATGTAAAGAGCAGGAACTGGGAGGTGGTGCTGGTGAAGGGTGGGGAATAAGGAGGCTGTGACTTACTGCAGAAACAAAACCTCTTGTGTAAGGGACAGCGTTCGAAGCCTGGGATGGGGATCGTCTGTTGGTGGGTAATAAAGATAGTTTGGCCTCTGCAGCAGCATCAGCCTGGGCATTGCAAAGAAGGCTTACATCTACACGTAGTACTGATAGCTCAAGGGAGGACTTACTACTCCCTGGTTTGTTGTTACTTGATCCATTATTGATTCTCTTCTTGCAG
Seq C2 exon
GGCTCCAGAACCCCATTGATATCATGTTTCACCTGCAGCCACTCATGTTCCTGGTGCTCTTCCCTCTGTTTGCAGTGTTTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020939:ENSGALT00000039096:7
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:
PF0089215=EamA=PD(14.6=33.3),PF0315111=TPT=PU(18.5=49.1)
A:
NA
C2:
PF0315111=TPT=FE(18.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATTGGTGCTGGTGGTTGTGC
R:
TGCAAACAGAGGGAAGAGCAC
Band lengths:
236-521
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]